BMRBj - BMREntryMaster

Found 1 Document (1.363 seconds)

BMRB: 5163

1RDG

Solution structure of desulfovibrio gigas zinc rubredoxin, NMR, 20 structures

Authors

Lamosa, P., Brennan, L., Vis, H., Turner, D.L., Santos, H.

Assembly

RUBREDOXIN

Entity

1. RUBREDOXIN (polymer, Thiol state: all other bound), 52 monomers, 5677.262 Da Detail

MDIYVCTVCG YEYDPAKGDP DSGIKPGTKF EDLPDDWACP VCGASKDAFE KQ

2. ZN (non-polymer), 65.409 Da

Total weight

5742.6714 Da

Max. entity weight

5677.262 Da

Entity Connection

metal coordination 4 Detail

ID	Type	Value order	Atom ID 1	Atom ID 2
1	metal coordination	sing	2:ZN1:ZN	1:CYS6:SG
2	metal coordination	sing	2:ZN1:ZN	1:CYS9:SG
3	metal coordination	sing	2:ZN1:ZN	1:CYS39:SG
4	metal coordination	sing	2:ZN1:ZN	1:CYS42:SG

Source organism

Desulfovibrio gigas

Exptl. method

NMR

Refine. method

TORSION ANGLE DYNAMICS WITH SIMULATED ANNEALING

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 98.1 %, Completeness: 84.5 %, Completeness (bb): 93.3 % Detail

Polymer type: polypeptide(L)

	Total	¹H
All	84.5 % (251 of 297)	84.5 % (251 of 297)
Backbone	93.3 % (97 of 104)	93.3 % (97 of 104)
Sidechain	79.8 % (154 of 193)	79.8 % (154 of 193)
Aromatic	100.0 % (28 of 28)	100.0 % (28 of 28)
Methyl	94.4 % (17 of 18)	94.4 % (17 of 18)

1. RUBREDOXIN

MDIYVCTVCG YEYDPAKGDP DSGIKPGTKF EDLPDDWACP VCGASKDAFE KQ

Show sample condition

Sample

Temperature 308 (±0.2) K, pH 7.6 (±0.2)

#	Name	Isotope labeling	Type	Concentration
1	RUBREDOXIN			2.5 mM
2	ZINC (II) ION			2.5 mM

Protein Blocks Logo

Calculated from 20 models in PDB: 1E8J, Strand ID: A Detail

Release date

2002-02-13

Citation

NMR structure of Desulfovibrio gigas rubredoxin: a model for studying protein stabilization by compatible solutes
Lamosa, P., Brennan, L., Vis, H., Turner, D.L., Santos, H.
Extremophiles. (2001), 5, 303-311, PubMed 11699644 , DOI 10.1007/s007920100206 , Abstract

Related entities 1. RUBREDOXIN, : 1 : 3 : 214 entities Detail

Experiments performed 3 experiments Detail

Chemical shift validation 4 contents Detail

Properties

Input source #1: Assigned chemical shifts - Assigned chemical shifts	bmr5163_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)
2:1:ZN:ZN	1:6:CYS:SG	unknown	unknown	n/a
2:1:ZN:ZN	1:9:CYS:SG	unknown	unknown	n/a
2:1:ZN:ZN	1:39:CYS:SG	unknown	unknown	n/a
2:1:ZN:ZN	1:42:CYS:SG	unknown	unknown	n/a

Non-standard residues

None

Content subtype: bmr5163_3.str

#	Content subtype	Saveframe	Status	# of rows	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	chem_shift_set_1	Warning	282		98.1 (chain: 1, length: 52)
1	Chemical shift references	chemical_shift_reference	OK	1		No information

Assigned chemical shifts

Saveframe: chem_shift_set_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: 1, Chain length: 52, Sequence coverage: 98.1%
- Total number of assignments
  - ¹H chemical shifts: 282
- Completeness of assignments
  - Entity_assemble_ID: 1
- Histogram of normalized assigned chemical shifts
- Random coil index and derived parameters (S² and NMR RMSD)
  - Chain_ID: 1

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
13	TYR	HH	8.813
28	THR	HG1	6.373

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	297	246	82.8

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	104	97	93.3

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	193	149	77.2

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	19	17	89.5

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	28	28	100.0

Keywords iron-sulfur-protein, zinc-substitution, thermostability

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Found 1 Document (1.363 seconds)

BMRB: 5163

Sample

Related entities 1. RUBREDOXIN, : 1 : 3 : 214 entities Detail

Experiments performed 3 experiments Detail

Instrument

Sample

Instrument

Sample

Instrument

Sample

Chemical shift validation 4 contents Detail