2ICU | pdb_00002icu

Crystal Structure of Hypothetical Protein YedK From Escherichia coli

PDB DOI: https://doi.org/10.2210/pdb2ICU/pdb

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

Deposited: 2006-09-13 Released: 2006-11-07
Deposition Author(s): Chen, L., Liu, Z.J., Li, Y., Zhao, M., Rose, J., Ebihara, A., Yokoyama, S., Wang, B.C., Southeast Collaboratory for Structural Genomics (SECSG), RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free:
0.203 (Depositor), 0.204 (DCC)
R-Value Work:
0.173 (Depositor), 0.172 (DCC)
R-Value Observed:
0.174 (Depositor)

wwPDB Validation 3D Report Full Report

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This is version 1.6 of the entry. See complete history.

Literature

Crystal Structure of Hypothetical Protein YedK From Escherichia coli

Chen, L., Liu, Z.J., Li, Y., Zhao, M., Rose, J., Ebihara, A., Yokoyama, S., Wang, B.C.

To be published.

Macromolecule Content

Total Structure Weight: 51.43 kDa
Atom Count: 4,066
Modeled Residue Count: 423
Deposited Residue Count: 458
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hypothetical protein yedK	A, B	229	Escherichia coli K-12	Mutation(s): 4 Gene Names: yedK EC: 3.4 (UniProt), 4 (UniProt)
UniProt
Find proteins for P76318 (Escherichia coli (strain K12)) Explore P76318 Go to UniProtKB: P76318
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P76318
Sequence Annotations Expand
Reference Sequence

Small Molecules

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: 1.60 Å
R-Value Free: 0.203 (Depositor), 0.204 (DCC)
R-Value Work: 0.173 (Depositor), 0.172 (DCC)
R-Value Observed: 0.174 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.687	α = 90
b = 67.366	β = 98.29
c = 75.125	γ = 90

Software Package:

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

Structure Validation

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Entry History

Deposition Data

Released Date: 2006-11-07

Deposition Author(s):

Southeast Collaboratory for Structural Genomics (SECSG)

RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History (Full details and data files)

Version 1.0: 2006-11-07
Type: Initial release
Version 1.1: 2008-05-01
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Source and taxonomy, Version format compliance
Version 1.3: 2017-09-13
Changes: Refinement description
Version 1.4: 2018-01-24
Changes: Structure summary
Version 1.5: 2024-10-30
Changes: Data collection, Database references, Derived calculations, Structure summary
Version 1.6: 2025-10-22
Changes: Structure summary

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.