5KAK

Crystal structure of an uncharacterized NIPSNAP-like domain protein from Burkholderia xenovorans

PDB DOI: https://doi.org/10.2210/pdb5KAK/pdb

Classification: UNKNOWN FUNCTION
Organism(s): Paraburkholderia xenovorans LB400
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2016-06-01 Released: 2016-06-15
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.65 Å
R-Value Free: 0.251
R-Value Work: 0.206
R-Value Observed: 0.207

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Crystal Structure of Putative uncharacterized protein from Burkholderia xenovorans LB400

Seattle Structural Genomics Center for Infectious Disease (SSGCID), Delker, S.L., Mayclin, S.J., Lorimer, D., Edwards, T.E.

To be published.

Macromolecule Content

Total Structure Weight: 121.5 kDa
Atom Count: 9,050
Modelled Residue Count: 945
Deposited Residue Count: 1,008
Unique protein chains: 1

Macromolecules

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(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, G, H	126	Paraburkholderia xenovorans LB400	Mutation(s): 0 Gene Names: Bxe_B2134
UniProt
Find proteins for Q13PY7 (Paraburkholderia xenovorans (strain LB400)) Explore Q13PY7 Go to UniProtKB: Q13PY7
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q13PY7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain J [auth C] SDF format, chain K [auth C] SDF format, chain L [auth D] SDF format, chain M [auth F] SDF format, chain N [auth H] MOL2 format, chain I [auth A] MOL2 format, chain J [auth C] MOL2 format, chain K [auth C] MOL2 format, chain L [auth D] MOL2 format, chain M [auth F] MOL2 format, chain N [auth H]	I [auth A] J [auth C] K [auth C] L [auth D] M [auth F] I [auth A], J [auth C], K [auth C], L [auth D], M [auth F], N [auth H]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain J [auth C] Focus chain K [auth C] Focus chain L [auth D] Focus chain M [auth F] Focus chain N [auth H] Interactions & Density Focus chain I [auth A] Focus chain J [auth C] Focus chain K [auth C] Focus chain L [auth D] Focus chain M [auth F] Focus chain N [auth H]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.65 Å
R-Value Free: 0.251
R-Value Work: 0.206
R-Value Observed: 0.207
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.63	α = 90
b = 70.83	β = 98.62
c = 109.02	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
MOLREP	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2016-06-15

Deposition Author(s):

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History (Full details and data files)

Version 1.0: 2016-06-15
Type: Initial release
Version 1.1: 2016-07-06
Changes: Data collection
Version 1.2: 2023-09-27
Changes: Data collection, Database references, Derived calculations, Refinement description

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Deposit Data

Help and Resources

5KAK

Crystal structure of an uncharacterized NIPSNAP-like domain protein from Burkholderia xenovorans

Crystal Structure of Putative uncharacterized protein from Burkholderia xenovorans LB400

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Expand

Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)