4NZK | pdb_00004nzk

Crystal structure of a DHHW family protein (EUBSIR_00411) from Eubacterium siraeum DSM 15702 at 1.49 A resolution

PDB DOI: https://doi.org/10.2210/pdb4NZK/pdb

Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
Organism(s): [Eubacterium] siraeum DSM 15702
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2013-12-12 Released: 2014-01-15
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.49 Å
R-Value Free:
0.158 (Depositor), 0.160 (DCC)
R-Value Work:
0.125 (Depositor), 0.130 (DCC)
R-Value Observed:
0.126 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.5 of the entry. See complete history.

Literature

Crystal structure of a hypothetical protein (EUBSIR_00411) from Eubacterium siraeum DSM 15702 at 1.49 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Macromolecule Content

Total Structure Weight: 39.55 kDa
Atom Count: 2,904
Modeled Residue Count: 303
Deposited Residue Count: 353
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uncharacterized protein	A	353	[Eubacterium] siraeum DSM 15702	Mutation(s): 0 Gene Names: EUBSIR_00411
UniProt
Find proteins for B0MKR4 ([Eubacterium] siraeum DSM 15702) Explore B0MKR4 Go to UniProtKB: B0MKR4
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	B0MKR4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain C [auth A] SDF format, chain B [auth A] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] MOL2 format, chain B [auth A] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A] mmCIF format, chain B [auth A]	B [auth A], C [auth A], D [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A]
UNL Query on UNL Download Ideal Coordinates CCD File	E [auth A]	Unknown ligand LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]

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: 1.49 Å
R-Value Free: 0.158 (Depositor), 0.160 (DCC)
R-Value Work: 0.125 (Depositor), 0.130 (DCC)
R-Value Observed: 0.126 (Depositor)

Diffraction Data: https://doi.org/10.18430/M34NZK

Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 102.125	α = 90
b = 102.125	β = 90
c = 123.311	γ = 120

Software Package:

Software Name	Purpose
MolProbity	model building
PDB_EXTRACT	data extraction
SHELX	phasing
SHARP	phasing
SCALA	data scaling
REFMAC	refinement
MOSFLM	data reduction
SHELXD	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2014-01-15

Deposition Author(s):

Joint Center for Structural Genomics (JCSG)

Revision History (Full details and data files)

Version 1.0: 2014-01-15
Type: Initial release
Version 1.1: 2014-12-24
Changes: Structure summary
Version 1.2: 2017-11-22
Changes: Refinement description
Version 1.3: 2018-01-24
Changes: Database references
Version 1.4: 2023-02-01
Changes: Database references, Derived calculations
Version 1.5: 2024-11-27
Changes: Data collection, Structure summary

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.