3K6C | pdb_00003k6c

Crystal structure of protein ne0167 from nitrosomonas europaea

PDB DOI: https://doi.org/10.2210/pdb3K6C/pdb
Entry: 3K6C supersedes: 1ZPY

Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
Organism(s): Nitrosomonas europaea
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2009-10-08 Released: 2009-10-27
Deposition Author(s): Chang, C., Evdokimova, E., Savchenko, A., Edwards, A.M., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free:
0.261 (Depositor), 0.289 (DCC)
R-Value Work:
0.221 (Depositor), 0.260 (DCC)
R-Value Observed:
0.223 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 3K6C

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

Literature

Crystal Structure of Protein Ne0167 from Nitrosomonas Europaea

Chang, C., Evdokimova, E., Savchenko, A., Edwards, A.M., Joachimiak, A.

To be published.

Macromolecule Content

Total Structure Weight: 114.06 kDa
Atom Count: 7,911
Modeled Residue Count: 909
Deposited Residue Count: 950
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uncharacterized protein NE0167	A, B, C, D, E A, B, C, D, E, F, G, H, I, J	95	Nitrosomonas europaea	Mutation(s): 0 Gene Names: NE0167
UniProt
Find proteins for Q82XT5 (Nitrosomonas europaea (strain ATCC 19718 / CIP 103999 / KCTC 2705 / NBRC 14298)) Explore Q82XT5 Go to UniProtKB: Q82XT5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q82XT5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B, C, D, E A, B, C, D, E, F, G, H, I, J	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: 0.261 (Depositor), 0.289 (DCC)
R-Value Work: 0.221 (Depositor), 0.260 (DCC)
R-Value Observed: 0.223 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.417	α = 90
b = 134.551	β = 96.24
c = 78.458	γ = 90

Software Package:

Software Name	Purpose
HKL-3000	phasing
SHELXD	phasing
SHELXE	model building
MLPHARE	phasing
DM	model building
RESOLVE	model building
Coot	model building
ARP/wARP	model building
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
DM	phasing
RESOLVE	phasing

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2009-10-27

Deposition Author(s):

Midwest Center for Structural Genomics (MCSG)

This entry supersedes: 1ZPY

Revision History (Full details and data files)

Version 1.0: 2009-10-27
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Refinement description, Version format compliance
Version 1.2: 2017-11-01
Changes: Refinement description
Version 1.3: 2024-10-09
Changes: Data collection, Database references, Derived calculations, 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.