3KB2 | pdb_00003kb2

Crystal Structure of YorR protein in complex with phosphorylated GDP from Bacillus subtilis, Northeast Structural Genomics Consortium Target SR256

PDB DOI: https://doi.org/10.2210/pdb3KB2/pdb

Classification: structural genomics, unknown function
Organism(s): Bacillus subtilis
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2009-10-20 Released: 2009-10-27
Deposition Author(s): Forouhar, F., Friedman, D., Seetharaman, J., Janjua, J., Xiao, R., Cunningham, K., Ma, L., Ho, C., Everett, J.K., Nair, R., Acton, T.B., Rost, B., Montelione, G.T., Tong, L., Hunt, J.F., Northeast Structural Genomics Consortium (NESG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free:
0.262 (Depositor), 0.273 (DCC)
R-Value Work:
0.195 (Depositor), 0.207 (DCC)
R-Value Observed:
0.196 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

Literature

Northeast Structural Genomics Consortium Target SR256

Forouhar, F., Friedman, D., Seetharaman, J., Janjua, J., Xiao, R., Cunningham, K., Ma, L., Ho, C., Everett, J.K., Nair, R., Acton, T.B., Rost, B., Montelione, G.T., Tong, L., Hunt, J.F.

To be published.

Macromolecule Content

Total Structure Weight: 41.61 kDa
Atom Count: 3,018
Modeled Residue Count: 338
Deposited Residue Count: 346
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SPBc2 prophage-derived uncharacterized protein yorR	A, B	173	Bacillus subtilis	Mutation(s): 0 Gene Names: BSU20280, yorR
UniProt
Find proteins for O31896 (Bacillus subtilis (strain 168)) Explore O31896 Go to UniProtKB: O31896
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O31896
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
G3D Query on G3D Download:Ideal Coordinates CCD File SDF format, chain E [auth B] SDF format, chain C [auth A] MOL2 format, chain E [auth B] MOL2 format, chain C [auth A] mmCIF format, chain E [auth B] mmCIF format, chain C [auth A]	C [auth A], E [auth B]	GUANOSINE-3'-MONOPHOSPHATE-5'-DIPHOSPHATE C₁₀ H₁₆ N₅ O₁₄ P₃ HEYSFDAMRDTCJM-UUOKFMHZSA-N		Interactions Focus chain C [auth A] Focus chain E [auth B] Interactions & Density Focus chain C [auth A] Focus chain E [auth B]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain F [auth B] SDF format, chain D [auth A] MOL2 format, chain F [auth B] MOL2 format, chain D [auth A] mmCIF format, chain F [auth B] mmCIF format, chain D [auth A]	D [auth A], F [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain F [auth B] Interactions & Density Focus chain D [auth A] Focus chain F [auth B]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.262 (Depositor), 0.273 (DCC)
R-Value Work: 0.195 (Depositor), 0.207 (DCC)
R-Value Observed: 0.196 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.478	α = 90
b = 63.05	β = 91.57
c = 70.456	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
DENZO	data reduction
SCALEPACK	data scaling
SnB	phasing
REFMAC	refinement

Structure Validation

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Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2009-10-27

Deposition Author(s):

Northeast Structural Genomics Consortium (NESG)

Revision History (Full details and data files)

Version 1.0: 2009-10-27
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2017-11-01
Changes: Refinement description
Version 1.3: 2019-07-17
Changes: Data collection, Derived calculations, Refinement description
Version 1.4: 2024-11-27
Changes: Data collection, Database references, Derived calculations, Structure summary