3NO5

Crystal structure of a Pfam DUF849 domain containing protein (Reut_A1631) from Ralstonia eutropha JMP134 at 1.90 A resolution

PDB DOI: https://doi.org/10.2210/pdb3NO5/pdb

Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
Organism(s): Cupriavidus pinatubonensis JMP134
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2010-06-24 Released: 2010-08-25
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.224
R-Value Work: 0.206
R-Value Observed: 0.207

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of a Pfam DUF849 domain containing protein (Reut_A1631) from Ralstonia eutropha JMP134 at 1.90 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Macromolecule Content

Total Structure Weight: 182.01 kDa
Atom Count: 13,719
Modelled Residue Count: 1,638
Deposited Residue Count: 1,650
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, B, C, D, E A, B, C, D, E, F	275	Cupriavidus pinatubonensis JMP134	Mutation(s): 0 Gene Names: Reut_A1631
UniProt
Find proteins for Q471D6 (Cupriavidus pinatubonensis (strain JMP 134 / LMG 1197)) Explore Q471D6 Go to UniProtKB: Q471D6
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q471D6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain J [auth B] SDF format, chain K [auth C] SDF format, chain R [auth D] SDF format, chain W [auth E] SDF format, chain Y [auth F] MOL2 format, chain G [auth A] MOL2 format, chain J [auth B] MOL2 format, chain K [auth C] MOL2 format, chain R [auth D] MOL2 format, chain W [auth E] MOL2 format, chain Y [auth F] mmCIF format, chain G [auth A] mmCIF format, chain J [auth B] mmCIF format, chain K [auth C] mmCIF format, chain R [auth D] mmCIF format, chain W [auth E] mmCIF format, chain Y [auth F]	G [auth A] J [auth B] K [auth C] R [auth D] W [auth E] G [auth A], J [auth B], K [auth C], R [auth D], W [auth E], Y [auth F]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain J [auth B] Focus chain K [auth C] Focus chain R [auth D] Focus chain W [auth E] Focus chain Y [auth F] Interactions & Density Focus chain G [auth A] Focus chain J [auth B] Focus chain K [auth C] Focus chain R [auth D] Focus chain W [auth E] Focus chain Y [auth F]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain L [auth C] SDF format, chain M [auth C] SDF format, chain N [auth C] SDF format, chain O [auth C] SDF format, chain S [auth D] SDF format, chain T [auth D] SDF format, chain U [auth D] SDF format, chain X [auth E] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain L [auth C] MOL2 format, chain M [auth C] MOL2 format, chain N [auth C] MOL2 format, chain O [auth C] MOL2 format, chain S [auth D] MOL2 format, chain T [auth D] MOL2 format, chain U [auth D] MOL2 format, chain X [auth E] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain L [auth C] mmCIF format, chain M [auth C] mmCIF format, chain N [auth C] mmCIF format, chain O [auth C] mmCIF format, chain S [auth D] mmCIF format, chain T [auth D] mmCIF format, chain U [auth D] mmCIF format, chain X [auth E]	H [auth A] I [auth A] L [auth C] M [auth C] N [auth C] H [auth A], I [auth A], L [auth C], M [auth C], N [auth C], O [auth C], S [auth D], T [auth D], U [auth D], X [auth E]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain I [auth A] Focus chain L [auth C] Focus chain M [auth C] Focus chain N [auth C] Focus chain O [auth C] Focus chain S [auth D] Focus chain T [auth D] Focus chain U [auth D] Focus chain X [auth E] Interactions & Density Focus chain H [auth A] Focus chain I [auth A] Focus chain L [auth C] Focus chain M [auth C] Focus chain N [auth C] Focus chain O [auth C] Focus chain S [auth D] Focus chain T [auth D] Focus chain U [auth D] Focus chain X [auth E]
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain P [auth C] SDF format, chain Q [auth C] SDF format, chain V [auth D] MOL2 format, chain P [auth C] MOL2 format, chain Q [auth C] MOL2 format, chain V [auth D] mmCIF format, chain P [auth C] mmCIF format, chain Q [auth C] mmCIF format, chain V [auth D]	P [auth C], Q [auth C], V [auth D]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain P [auth C] Focus chain Q [auth C] Focus chain V [auth D] Interactions & Density Focus chain P [auth C] Focus chain Q [auth C] Focus chain V [auth D]

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	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.224
R-Value Work: 0.206
R-Value Observed: 0.207
Space Group: P 1 2₁ 1
Diffraction Data: https://doi.org/10.18430/M33NO5

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 83.181	α = 90
b = 81.221	β = 103.68
c = 140.429	γ = 90

Software Package:

Software Name	Purpose
MolProbity	model building
PHENIX	refinement
PHASER	phasing
SCALA	data scaling
PDB_EXTRACT	data extraction
MOSFLM	data reduction
BUSTER	refinement

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2010-08-25

Deposition Author(s):

Joint Center for Structural Genomics (JCSG)

Revision History (Full details and data files)

Version 1.0: 2010-08-25
Type: Initial release
Version 1.1: 2011-07-13
Changes: Source and taxonomy, Version format compliance
Version 1.2: 2017-11-08
Changes: Refinement description
Version 1.3: 2023-02-01
Changes: Database references, Derived calculations
Version 1.4: 2023-09-20
Changes: Data collection, Refinement description
Version 1.5: 2023-11-22
Changes: Data collection
Version 1.6: 2024-11-27
Changes: Structure summary