BMRBj - BMREntryMaster

Found 1 Document (1.316 seconds)

BMRB: 6223

8I3P

Sequential resonance assignment of yeast cytosine deaminase in complex with a transition state analogue

Authors

Yao, L., Liu, A., Li, Y., Felczak, K., Li, G., Yan, H.

Assembly

YCD dimer

Entity

1. Yeast cytosine deaminase (polymer, Thiol state: free and other bound), 158 monomers, 17506.81 × 2 Da Detail

MVTGGMASKW DQKGMDIAYE EAALGYKEGG VPIGGCLINN KDGSVLGRGH NMRFQKGSAT LHGEISTLEN CGRLEGKVYK DTTLYTTLSP CDMCTGAIIM YGIPRCVVGE NVNFKSKGEK YLQTRGHEVV VVDDERCKKI MKQFIDERPQ DWFEDIGE

2. 5-fluorine, 2-hydroxypyrimidine (non-polymer), 1 monomers, na Da
3. ZN (non-polymer), 65.409 Da

Total weight

35079.03 Da

Max. entity weight

17506.81 Da

Entity Connection

na 4 Detail

ID	Type	Value order	Atom ID 1	Atom ID 2
1	na	sing	1:CYS91:SG	3:ZN1:ZN
2	na	sing	1:CYS94:SG	3:ZN1:ZN
3	na	sing	1:CYS91:SG	3:ZN1:ZN
4	na	sing	1:CYS94:SG	3:ZN1:ZN

Source organism

Saccharomyces cerevisiae

Exptl. method

NMR

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 94.9 %, Completeness: 53.4 %, Completeness (bb): 93.0 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	53.4 % (962 of 1800)	39.2 % (368 of 939)	64.7 % (449 of 694)	86.8 % (145 of 167)
Backbone	93.0 % (874 of 940)	92.5 % (308 of 333)	93.2 % (422 of 453)	93.5 % (144 of 154)
Sidechain	21.4 % (213 of 997)	9.6 % (58 of 606)	40.7 % (154 of 378)	7.7 % (1 of 13)
Aromatic	0.0 % (0 of 124)	0.0 % (0 of 62)	0.0 % (0 of 60)	0.0 % (0 of 2)
Methyl	21.3 % (32 of 150)	18.7 % (14 of 75)	24.0 % (18 of 75)

1. Yeast cytosine deaminase

MVTGGMASKW DQKGMDIAYE EAALGYKEGG VPIGGCLINN KDGSVLGRGH NMRFQKGSAT LHGEISTLEN CGRLEGKVYK DTTLYTTLSP CDMCTGAIIM YGIPRCVVGE NVNFKSKGEK YLQTRGHEVV VVDDERCKKI MKQFIDERPQ DWFEDIGE

Show sample condition

Sample

Temperature 298 (±0.5) K, pH 7.0 (±0.1)

#	Name	Isotope labeling	Type	Concentration
1	Yeast cytosine deaminase	[U-70% 2H, U-100% 13C, U-100% 15N]		1.8 mM

LACS Plot; CA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	null	indirect	0.1013291
¹³C	DSS	methyl protons	null	indirect	0.2514495

Referencing offset: 0.1 ppm, Outliers: 2 Detail

LACS Plot; CB

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	null	indirect	0.1013291
¹³C	DSS	methyl protons	null	indirect	0.2514495

Referencing offset: 0.1 ppm, Outliers: 2 Detail

LACS Plot; HA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	null	indirect	0.1013291
¹³C	DSS	methyl protons	null	indirect	0.2514495

Referencing offset: -0.07 ppm, Outliers: 2 Detail

LACS Plot; CO

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	null	indirect	0.1013291
¹³C	DSS	methyl protons	null	indirect	0.2514495

Referencing offset: -0.3 ppm, Outliers: 3 Detail

Release date

2007-03-21

Citation

Simultaneous NMR assignment of backbone and side chain amides in large proteins with IS-TROSY
Liu, A., Li, Y., Yao, L., Yan, H.
J. Biomol. NMR (2006), 36, 205-214, PubMed 17091334 , DOI 10.1007/s10858-006-9072-3 , Abstract

Related entities 1. Yeast cytosine deaminase, : 1 : 7 : 1 : 17 entities Detail

Interaction partners 1. Yeast cytosine deaminase, : 14 interactors Detail

More details for 14 interactors identified by 5 citations

Experiments performed 1 experiments Detail

Chemical shift validation 5 contents Detail

Properties

Input source #1: Assigned chemical shifts - Assigned chemical shifts	bmr6223_3.str
Diamagnetism of the molecular assembly	True (excluding Oxygen atoms)
Whether the assembly has a disulfide bond	None
Whether the assembly has a other bond	True (see coodinates for details)
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)

Ptnr_site_1	Ptnr_site_2	Redox_state_prediction_1	Redox_state_prediction_2	Distance (Å)
1:91:CYS:SG	4:1:ZN:ZN	reduced, CA 58.4, CB 28.1 ppm	unknown	n/a
1:94:CYS:SG	4:1:ZN:ZN	reduced, CA 64.4, CB 31.2 ppm	unknown	n/a
2:91:CYS:SG	4:1:ZN:ZN	unknown	unknown	n/a
2:94:CYS:SG	4:1:ZN:ZN	unknown	unknown	n/a

Non-standard residues

None

Content subtype: bmr6223_3.str

#	Content subtype	Saveframe	Status	# of rows	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	shift_set_1	Warning	877		94.9 (chain: 1, length: 158)
1	Chemical shift references	chemical_shift_reference	OK	3		No information

Assigned chemical shifts

Saveframe: shift_set_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: 1, Chain length: 158, Sequence coverage: 94.9%
- Total number of assignments
  - ¹³C chemical shifts: 424
  - ¹⁵N chemical shifts: 145
  - ¹H chemical shifts: 308
- Completeness of assignments
  - Entity_assemble_ID: 1
- Redox state of CYS
- Peptide bond of PRO
- Histogram of normalized assigned chemical shifts
- Random coil index and derived parameters (S² and NMR RMSD)
  - Chain_ID: 1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	82	5	6.1
¹H chemical shifts	82	0	0.0

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Found 1 Document (1.316 seconds)

BMRB: 6223

Sample

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. Yeast cytosine deaminase, : 1 : 7 : 1 : 17 entities Detail

Interaction partners 1. Yeast cytosine deaminase, : 14 interactors Detail

Experiments performed 1 experiments Detail

Instrument

Sample

Chemical shift validation 5 contents Detail

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	694	424	61.1
¹⁵N chemical shifts	174	145	83.3
¹H chemical shifts	939	308	32.8

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	316	294	93.0
¹⁵N chemical shifts	154	145	94.2
¹H chemical shifts	333	308	92.5

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	378	130	34.4
¹⁵N chemical shifts	20	0	0.0
¹H chemical shifts	606	0	0.0