2PW6 | pdb_00002pw6

Crystal structure of uncharacterized protein JW3007 from Escherichia coli K12

• PDB DOI: https://doi.org/10.2210/pdb2PW6/pdb

• Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
• Organism(s): Escherichia coli K-12
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2007-05-10 Released: 2007-06-12 
• Deposition Author(s): Newton, M.G., Takagi, Y., Ebihara, A., Shinkai, A., Kuramitsu, S., Yokayama, S., Li, Y., Chen, L., Zhu, J., Ruble, J., Liu, Z.J., Rose, J.P., Wang, B.-C., Southeast Collaboratory for Structural Genomics (SECSG), RIKEN Structural Genomics/Proteomics Initiative (RSGI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.27 Å
• R-Value Free: 
  0.267 (Depositor), 0.263 (DCC) 
• R-Value Work: 
  0.235 (Depositor), 0.232 (DCC) 
• R-Value Observed: 
  0.236 (Depositor) 

Literature

Crystal structure of uncharacterized protein JW3007 from Escherichia coli K12.

Newton, M.G., Takagi, Y., Ebihara, A., Shinkai, A., Kuramitsu, S., Yokayama, S., Li, Y., Chen, L., Zhu, J., Ruble, J., Liu, Z.J., Rose, J.P., Wang, B.-C.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA,PQS (software)

Macromolecule Content 

• Total Structure Weight: 30.69 kDa 
• Atom Count: 1,923 
• Modeled Residue Count: 244 
• Deposited Residue Count: 271 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uncharacterized protein ygiD	A	271	Escherichia coli K-12	Mutation(s): 12  Gene Names: ygiD, b3039, JW3007 EC: 1.13.11.29
UniProt
Find proteins for P24197 (Escherichia coli (strain K12)) Explore P24197  Go to UniProtKB:  P24197

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	B [auth A], C [auth A], D [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.27 Å
• R-Value Free:  0.267 (Depositor), 0.263 (DCC) 
• R-Value Work:  0.235 (Depositor), 0.232 (DCC) 
• R-Value Observed: 0.236 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 83.94	α = 90
b = 83.94	β = 90
c = 85.509	γ = 120

Software Package:

Software Name	Purpose
SCA2STRUCTURE	model building
REFMAC	refinement
SERGUI	data collection
HKL-2000	data reduction
SCALEPACK	data scaling
SCA2STRUCTURE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-06-12 
Deposition Author(s): Newton, M.G., Takagi, Y., Ebihara, A., Shinkai, A., Kuramitsu, S., Yokayama, S., Li, Y., Chen, L., Zhu, J., Ruble, J., Liu, Z.J., Rose, J.P., Wang, B.-C., Southeast Collaboratory for Structural Genomics (SECSG), RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History  

• Version 1.0: 2007-06-12
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Source and taxonomy, Version format compliance
• Version 1.3: 2017-09-13
  Changes: Refinement description
• Version 1.4: 2018-01-24
  Changes: Database references, Structure summary
• Version 1.5: 2024-10-30
  Changes: Data collection, Database references, Derived calculations, Structure summary