1K4N | pdb_00001k4n

Structural Genomics, Protein EC4020

PDB DOI: https://doi.org/10.2210/pdb1K4N/pdb

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

Deposited: 2001-10-08 Released: 2002-08-14
Deposition Author(s): Zhang, R.G., Joachimiak, A., Edwards, A., Savchenko, A., Skarina, T., Midwest Center for Structural Genomics (MCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free:
0.217 (Depositor)
R-Value Work:
0.199 (Depositor)
R-Value Observed:
0.210 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 1K4N

This is version 1.3 of the entry. See complete history.

Literature

Conserved protein YecM from Escherichia coli shows structural homology to metal-binding isomerases and oxygenases.

Zhang, R.G., Duke, N., Laskowski, R., Evdokimova, E., Skarina, T., Edwards, A., Joachimiak, A., Savchenko, A.

(2003) Proteins 51: 311-314

PubMed: 12660999 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1002/prot.10307
Primary Citation Related Structures:
1K4N

Organizational Affiliation

Biosciences Division and Structural Biology Center, Argonne National Laboratory, Argonne, Illinois 60439, USA.

Macromolecule Content

Total Structure Weight: 21.81 kDa
Atom Count: 1,713
Modeled Residue Count: 183
Deposited Residue Count: 192
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein EC4020	A	192	Escherichia coli	Mutation(s): 2
UniProt
Find proteins for P52007 (Escherichia coli (strain K12)) Explore P52007 Go to UniProtKB: P52007
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P52007
Sequence Annotations Expand
Reference Sequence

Small Molecules

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A	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: 0.217 (Depositor)
R-Value Work: 0.199 (Depositor)
R-Value Observed: 0.210 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 38.661	α = 90
b = 41.783	β = 90
c = 105.748	γ = 90

Software Package:

Software Name	Purpose
d*TREK	data scaling
HKL-2000	data reduction
CNS	refinement
d*TREK	data reduction
HKL-2000	data scaling
CNS	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2002-08-14

Deposition Author(s):

Midwest Center for Structural Genomics (MCSG)

Revision History (Full details and data files)

Version 1.0: 2002-08-14
Type: Initial release
Version 1.1: 2008-04-27
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2024-11-20
Changes: Data collection, Database references, Derived calculations, Refinement description, 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.