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Found 1 Document (1.338 seconds)

BMRB: 16404

2KLY

Solution structure of human ubiquitin conjugating enzyme Ube2g2

Authors

Ju, T., Bocik, W., Majumdar, A., Tolman, J.R.

Assembly

Human ubiquitin-conjugating enzyme E2G2 isoform 1

Entity

1. Human ubiquitin-conjugating enzyme E2G2 isoform 1 (polymer, Thiol state: all free), 165 monomers, 18566.11 Da Detail

MAGTALKRLM AEYKQLTLNP PEGIVAGPMN EENFFEWEAL IMGPEDTCFE FGVFPAILSF PLDYPLSPPK MRFTCEMFHP NIYPDGRVCI SILHAPGDDP MGYESSAERW SPVQSVEKIL LSVVSMLAEP NDESGANVDA SKMWRDDREQ FYKIAKQIVQ KSLGL

Formula weight

18566.11 Da

Source organism

Homo sapiens

Exptl. method

solution NMR

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 99.4 %, Completeness: 93.2 %, Completeness (bb): 98.2 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	93.2 % (1811 of 1943)	91.2 % (926 of 1015)	94.6 % (723 of 764)	98.8 % (162 of 164)
Backbone	98.2 % (943 of 960)	97.8 % (318 of 325)	98.1 % (476 of 485)	99.3 % (149 of 150)
Sidechain	89.7 % (1021 of 1138)	88.1 % (608 of 690)	92.2 % (400 of 434)	92.9 % (13 of 14)
Aromatic	70.1 % (122 of 174)	70.1 % (61 of 87)	69.0 % (58 of 84)	100.0 % (3 of 3)
Methyl	98.1 % (157 of 160)	97.5 % (78 of 80)	98.8 % (79 of 80)

1. Human ubiquitin-conjugating enzyme E2G2 isoform 1

MAGTALKRLM AEYKQLTLNP PEGIVAGPMN EENFFEWEAL IMGPEDTCFE FGVFPAILSF PLDYPLSPPK MRFTCEMFHP NIYPDGRVCI SILHAPGDDP MGYESSAERW SPVQSVEKIL LSVVSMLAEP NDESGANVDA SKMWRDDREQ FYKIAKQIVQ KSLGL

Show sample condition

Sample #1

Solvent system 90% H2O, 10% D2O, Pressure 1 atm, Temperature 295 K, pH 7.0, Details 20mM phosphate buffer, 50mM NaCl, 0.5mM EDTA, 1mM TCEP; 90% H2O, 10% D2O

#	Name	Isotope labeling	Concentration
1	Human ubiquitin-conjugating enzyme E2G2 isoform 1	[U-99% 13C; U-99% 15N]	1.0 mM
2	phosphate buffer	natural abundance	20 mM
3	NaCl	natural abundance	50 mM
4	EDTA	natural abundance	0.5 mM
5	TCEP	natural abundance	1 mM
6	H2O	natural abundance	90 %
7	D2O	natural abundance	10 %

Sample #2

Solvent system 90% H2O, 10% D2O; 8 mg/ml bacteriophage Pf1, Pressure 1 atm, Temperature 295 K, pH 7.0, Details 20mM phosphate buffer, 50mM NaCl, 0.5mM EDTA, 1mM TCEP; 90% H2O, 10% D2O; 8 mg/ml bacteriophage Pf1

#	Name	Isotope labeling	Concentration
8	Human ubiquitin-conjugating enzyme E2G2 isoform 1	[U-99% 15N]	0.7 mM
9	phosphate buffer	natural abundance	20 mM
10	NaCl	natural abundance	50 mM
11	EDTA	natural abundance	0.5 mM
12	TCEP	natural abundance	1 mM
13	H2O	natural abundance	90 %
14	D2O	natural abundance	10 %
15	bacteriophage Pf1	natural abundance	8 mg/mL

Sample #3

Solvent system 90% H2O, 10% D2O; 4.5% stretched polyacrylamide gel, Pressure 1 atm, Temperature 295 K, pH 7.0, Details 20mM phosphate buffer, 50mM NaCl, 0.5mM EDTA, 1mM TCEP; 90% H2O, 10% D2O; 4.5% stretched polyacrylamide gel

#	Name	Isotope labeling	Concentration
16	Human ubiquitin-conjugating enzyme E2G2 isoform 1	[U-99% 13C; U-99% 15N]	1.0 mM
17	phosphate buffer	natural abundance	20 mM
18	NaCl	natural abundance	50 mM
19	EDTA	natural abundance	0.5 mM
20	TCEP	natural abundance	1 mM
21	H2O	natural abundance	90 %
22	D2O	natural abundance	10 %
23	polyacrylamide gel	natural abundance	4.5 %

LACS Plot; CA

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹³C	water	protons	4.8 ppm	internal	indirect	0.2514495
¹H	water	protons	4.8 ppm	internal	direct	1.0
¹⁵N	water	protons	4.8 ppm	internal	indirect	0.1013291

Referencing offset: 0.03 ppm, Outliers: 1 Detail

LACS Plot; CB

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹³C	water	protons	4.8 ppm	internal	indirect	0.2514495
¹H	water	protons	4.8 ppm	internal	direct	1.0
¹⁵N	water	protons	4.8 ppm	internal	indirect	0.1013291

Referencing offset: 0.03 ppm, Outliers: 1 Detail

LACS Plot; HA

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹³C	water	protons	4.8 ppm	internal	indirect	0.2514495
¹H	water	protons	4.8 ppm	internal	direct	1.0
¹⁵N	water	protons	4.8 ppm	internal	indirect	0.1013291

Referencing offset: -0.02 ppm, Outliers: 4 Detail

LACS Plot; CO

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹³C	water	protons	4.8 ppm	internal	indirect	0.2514495
¹H	water	protons	4.8 ppm	internal	direct	1.0
¹⁵N	water	protons	4.8 ppm	internal	indirect	0.1013291

Referencing offset: 0.04 ppm, Outliers: 2 Detail

Protein Blocks Logo

Calculated from 10 models in PDB: 2KLY, Strand ID: A Detail

Release date

2009-12-17

Citation

Solution structure and dynamics of human ubiquitin conjugating enzyme Ube2g2
Ju, T., Bocik, W., Majumdar, A., Tolman, J.R.
Proteins (2010), 78, 1291-1301, PubMed 20014027 , DOI 10.1002/prot.22648 , Abstract

Related entities 1. Human ubiquitin-conjugating enzyme E2G2 isoform 1, : 1 : 8 : 1 : 2 : 284 entities Detail

Interaction partners 1. Human ubiquitin-conjugating enzyme E2G2 isoform 1, : 33 interactors Detail

More details for 33 interactors identified by 8 citations

Experiments performed 6 experiments Detail

1 3D_15N-separated_NOESY

Instrument

Varian Inova - 800 MHz

Sample

State isotropic, Solvent system 90% H2O, 10% D2O, Pressure 1 atm, Temperature 295 K, pH 7.0, Details 20mM phosphate buffer, 50mM NaCl, 0.5mM EDTA, 1mM TCEP; 90% H2O, 10% D2O

#	Name	Isotope labeling	Concentration
1	Human ubiquitin-conjugating enzyme E2G2 isoform 1	[U-99% 13C; U-99% 15N]	1.0 mM
2	phosphate buffer	natural abundance	20 mM
3	NaCl	natural abundance	50 mM
4	EDTA	natural abundance	0.5 mM
5	TCEP	natural abundance	1 mM
6	H2O	natural abundance	90 %
7	D2O	natural abundance	10 %

2 3D_13C-separated_NOESY

Instrument

Varian Inova - 800 MHz

Sample

State isotropic, Solvent system 90% H2O, 10% D2O, Pressure 1 atm, Temperature 295 K, pH 7.0, Details 20mM phosphate buffer, 50mM NaCl, 0.5mM EDTA, 1mM TCEP; 90% H2O, 10% D2O

#	Name	Isotope labeling	Concentration
1	Human ubiquitin-conjugating enzyme E2G2 isoform 1	[U-99% 13C; U-99% 15N]	1.0 mM
2	phosphate buffer	natural abundance	20 mM
3	NaCl	natural abundance	50 mM
4	EDTA	natural abundance	0.5 mM
5	TCEP	natural abundance	1 mM
6	H2O	natural abundance	90 %
7	D2O	natural abundance	10 %

3 2D_NOESY

Instrument

Varian Inova - 800 MHz

Sample

State isotropic, Solvent system 90% H2O, 10% D2O, Pressure 1 atm, Temperature 295 K, pH 7.0, Details 20mM phosphate buffer, 50mM NaCl, 0.5mM EDTA, 1mM TCEP; 90% H2O, 10% D2O

#	Name	Isotope labeling	Concentration
1	Human ubiquitin-conjugating enzyme E2G2 isoform 1	[U-99% 13C; U-99% 15N]	1.0 mM
2	phosphate buffer	natural abundance	20 mM
3	NaCl	natural abundance	50 mM
4	EDTA	natural abundance	0.5 mM
5	TCEP	natural abundance	1 mM
6	H2O	natural abundance	90 %
7	D2O	natural abundance	10 %

4 3D HNHA

Instrument

Varian Inova - 800 MHz

Sample

State isotropic, Solvent system 90% H2O, 10% D2O, Pressure 1 atm, Temperature 295 K, pH 7.0, Details 20mM phosphate buffer, 50mM NaCl, 0.5mM EDTA, 1mM TCEP; 90% H2O, 10% D2O

#	Name	Isotope labeling	Concentration
1	Human ubiquitin-conjugating enzyme E2G2 isoform 1	[U-99% 13C; U-99% 15N]	1.0 mM
2	phosphate buffer	natural abundance	20 mM
3	NaCl	natural abundance	50 mM
4	EDTA	natural abundance	0.5 mM
5	TCEP	natural abundance	1 mM
6	H2O	natural abundance	90 %
7	D2O	natural abundance	10 %

5 IPAP-HSQC

Instrument

Varian Inova - 800 MHz

Sample

State anisotropic, Solvent system 90% H2O, 10% D2O; 8 mg/ml bacteriophage Pf1, Pressure 1 atm, Temperature 295 K, pH 7.0, Details 20mM phosphate buffer, 50mM NaCl, 0.5mM EDTA, 1mM TCEP; 90% H2O, 10% D2O; 8 mg/ml bacteriophage Pf1

#	Name	Isotope labeling	Concentration
8	Human ubiquitin-conjugating enzyme E2G2 isoform 1	[U-99% 15N]	0.7 mM
9	phosphate buffer	natural abundance	20 mM
10	NaCl	natural abundance	50 mM
11	EDTA	natural abundance	0.5 mM
12	TCEP	natural abundance	1 mM
13	H2O	natural abundance	90 %
14	D2O	natural abundance	10 %
15	bacteriophage Pf1	natural abundance	8 mg/mL

6 IPAP-HSQC

Instrument

Varian Inova - 800 MHz

Sample

State anisotropic, Solvent system 90% H2O, 10% D2O; 4.5% stretched polyacrylamide gel, Pressure 1 atm, Temperature 295 K, pH 7.0, Details 20mM phosphate buffer, 50mM NaCl, 0.5mM EDTA, 1mM TCEP; 90% H2O, 10% D2O; 4.5% stretched polyacrylamide gel

#	Name	Isotope labeling	Concentration
16	Human ubiquitin-conjugating enzyme E2G2 isoform 1	[U-99% 13C; U-99% 15N]	1.0 mM
17	phosphate buffer	natural abundance	20 mM
18	NaCl	natural abundance	50 mM
19	EDTA	natural abundance	0.5 mM
20	TCEP	natural abundance	1 mM
21	H2O	natural abundance	90 %
22	D2O	natural abundance	10 %
23	polyacrylamide gel	natural abundance	4.5 %

NMR combined restraints 4 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, RDC restraints	combined_16404_2kly.nef
Input source #2: Coordindates	2kly.cif
Diamagnetism of the molecular assembly	True (excluding Oxygen atoms)
Whether the assembly has a disulfide bond	None
Whether the assembly has a other bond	None
Whether the assembly contains a cyclic polymer	None
Overall data processing status	Warning

Disulfide bonds

None

Other bonds (neither disulfide, covalent nor hydrogen bonds, e.g. Zinc–sulphur bond)

None

Non-standard residues

None

Sequence alignments

Entity_assembly_ID (NMR): A vs Auth_asym_ID (model): A

-0--------10--------20--------30--------40--------50--------60--------70--------80--------90-------1
GHMAGTALKRLMAEYKQLTLNPPEGIVAGPMNEENFFEWEALIMGPEDTCFEFGVFPAILSFPLDYPLSPPKMRFTCEMFHPNIYPDGRVCISILHAPGD
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
GHMAGTALKRLMAEYKQLTLNPPEGIVAGPMNEENFFEWEALIMGPEDTCFEFGVFPAILSFPLDYPLSPPKMRFTCEMFHPNIYPDGRVCISILHAPGD
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100

00-------110-------120-------130-------140-------150-------160-----
DPMGYESSAERWSPVQSVEKILLSVVSMLAEPNDESGANVDASKMWRDDREQFYKIAKQIVQKSLGL
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
DPMGYESSAERWSPVQSVEKILLSVVSMLAEPNDESGANVDASKMWRDDREQFYKIAKQIVQKSLGL
-------110-------120-------130-------140-------150-------160-------

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	167	0	0	100.0

Content subtype: combined_16404_2kly.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	1790		97.0 (chain: A, length: 167)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	Warning	2958 (1)	noe	97.6 (chain: A, length: 167)
1	RDC restraints	CNS/XPLOR_dipolar_coupling_3	OK	191 (191)	.	64.1 (chain: A, length: 167)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 167, Sequence coverage: 97.0%
- Total number of assignments
  - ¹H chemical shifts: 910
  - ¹³C chemical shifts: 715
  - ¹⁵N chemical shifts: 165
- Completeness of assignments
  - Entity_assemble_ID: A
- Redox state of CYS
- Peptide bond of PRO
- Tautomeric state of HIS
- Rotameric state of ILE , LEU, and VAL
- Histogram of normalized assigned chemical shifts
- Random coil index and derived parameters (S² and NMR RMSD)
  - Chain_ID: A

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
79	HIS	ND1	255.0
79	HIS	NE2	165.0
94	HIS	ND1	205.1
94	HIS	NE2	188.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	1024	910	88.9
¹³C chemical shifts	771	715	92.7
¹⁵N chemical shifts	172	161	93.6

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	330	319	96.7
¹³C chemical shifts	334	319	95.5
¹⁵N chemical shifts	152	148	97.4

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	694	591	85.2
¹³C chemical shifts	437	396	90.6
¹⁵N chemical shifts	20	13	65.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	89	88	98.9
¹³C chemical shifts	89	88	98.9

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	89	59	66.3
¹³C chemical shifts	86	56	65.1
¹⁵N chemical shifts	3	3	100.0

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 167, Sequence coverage: 97.6%
- Total number of restraints: 2951
- Weight of restraints: 1.0 (2951)
- Potential type of restraints: square-well-parabolic (2951)
- Range of distance target values: 2.25, 5.0 (Å)
- Histogram of distance target values
- Histogram of discrepancy in distance target values
- Distance restraints per residue
  - Chain_ID: A
- Distance restraints on contact map

RDC restraints

Saveframe: CNS/XPLOR_dipolar_coupling_3

Status: OK
Experiment type: .

Sequence coverage of experimental data

Entity_assembly_ID: A, Chain length: 167, Sequence coverage: 64.1%

-0--------10--------20--------30--------40--------50--------60--------70--------80--------90-------1
GHMAGTALKRLMAEYKQLTLNPPEGIVAGPMNEENFFEWEALIMGPEDTCFEFGVFPAILSFPLDYPLSPPKMRFTCEMFHPNIYPDGRVCISILHAPGD
    ||||| ||||||| |||  |||||| || || | ||||| | |||| ||||| ||||| ||| ||   |||||| || ||| |||||||  ||   
....GTALK.LMAEYKQ.TLN..EGIVAG.MN.EN.F.WEALI.G.EDTC.EFGVF.AILSF.LDY.LS...MRFTCE.FH.NIY.DGRVCIS..HA...

00-------110-------120-------130-------140-------150-------160-----
DPMGYESSAERWSPVQSVEKILLSVVSMLAEPNDESGANVDASKMWRDDREQFYKIAKQIVQKSLGL
           || | |||    || || || || ||| || | |||| ||| | | | || || ||
...........WS.V.SVE....SV.SM.AE.ND.SGA.VD.S.MWRD.REQ.Y.I.K.IV.KS.GL

Total number of restraints: 191
Potential type of restraints: undefined (191)
Range of observed RDC values: 100.0, -100.0 (Hz)
RDC restraints per residue
- Chain_ID: A
  None

Keywords alpha beta fold

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Found 1 Document (1.338 seconds)

BMRB: 16404

Sample #1

Sample #2

Sample #3

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. Human ubiquitin-conjugating enzyme E2G2 isoform 1, : 1 : 8 : 1 : 2 : 284 entities Detail

Interaction partners 1. Human ubiquitin-conjugating enzyme E2G2 isoform 1, : 33 interactors Detail

Experiments performed 6 experiments Detail

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

NMR combined restraints 4 contents Detail