6ANS | pdb_00006ans

Crystal structure of a putative uncharacterized protein from Burkholderia cenocepacia

PDB DOI: https://doi.org/10.2210/pdb6ANS/pdb

Classification: UNKNOWN FUNCTION
Organism(s): Burkholderia cenocepacia J2315
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2017-08-14 Released: 2017-08-30
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free:
0.188 (Depositor), 0.191 (DCC)
R-Value Work:
0.150 (Depositor), 0.153 (DCC)
R-Value Observed:
0.151 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Crystal structure of a putative uncharacterized protein from Burkholderia cenocepacia

Bowatte, K., Delker, S.L., Abendroth, J., Lorimer, D.D., Edwards, T.E.

To be published.

Macromolecule Content

Total Structure Weight: 176.14 kDa
Atom Count: 12,118
Modeled Residue Count: 1,457
Deposited Residue Count: 1,560
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	390	Burkholderia cenocepacia J2315	Mutation(s): 0 Gene Names: BCAL2258
UniProt
Find proteins for B4EDY7 (Burkholderia cenocepacia (strain ATCC BAA-245 / DSM 16553 / LMG 16656 / NCTC 13227 / J2315 / CF5610)) Explore B4EDY7 Go to UniProtKB: B4EDY7
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	B4EDY7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain S [auth D] SDF format, chain N [auth C] SDF format, chain I [auth B] SDF format, chain E [auth A] MOL2 format, chain S [auth D] MOL2 format, chain N [auth C] MOL2 format, chain I [auth B] MOL2 format, chain E [auth A] mmCIF format, chain S [auth D] mmCIF format, chain N [auth C] mmCIF format, chain I [auth B] mmCIF format, chain E [auth A]	E [auth A], I [auth B], N [auth C], S [auth D]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain E [auth A] Focus chain I [auth B] Focus chain N [auth C] Focus chain S [auth D] Interactions & Density Focus chain E [auth A] Focus chain I [auth B] Focus chain N [auth C] Focus chain S [auth D]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain U [auth D] SDF format, chain P [auth C] SDF format, chain K [auth B] SDF format, chain G [auth A] MOL2 format, chain U [auth D] MOL2 format, chain P [auth C] MOL2 format, chain K [auth B] MOL2 format, chain G [auth A] mmCIF format, chain U [auth D] mmCIF format, chain P [auth C] mmCIF format, chain K [auth B] mmCIF format, chain G [auth A]	G [auth A], K [auth B], P [auth C], U [auth D]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain K [auth B] Focus chain P [auth C] Focus chain U [auth D] Interactions & Density Focus chain G [auth A] Focus chain K [auth B] Focus chain P [auth C] Focus chain U [auth D]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain V [auth D] SDF format, chain Q [auth C] SDF format, chain L [auth B] SDF format, chain H [auth A] MOL2 format, chain V [auth D] MOL2 format, chain Q [auth C] MOL2 format, chain L [auth B] MOL2 format, chain H [auth A] mmCIF format, chain V [auth D] mmCIF format, chain Q [auth C] mmCIF format, chain L [auth B] mmCIF format, chain H [auth A]	H [auth A], L [auth B], Q [auth C], V [auth D]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain L [auth B] Focus chain Q [auth C] Focus chain V [auth D] Interactions & Density Focus chain H [auth A] Focus chain L [auth B] Focus chain Q [auth C] Focus chain V [auth D]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain J [auth B] SDF format, chain T [auth D] SDF format, chain R [auth D] SDF format, chain O [auth C] SDF format, chain M [auth C] SDF format, chain F [auth A] MOL2 format, chain J [auth B] MOL2 format, chain T [auth D] MOL2 format, chain R [auth D] MOL2 format, chain O [auth C] MOL2 format, chain M [auth C] MOL2 format, chain F [auth A] mmCIF format, chain J [auth B] mmCIF format, chain T [auth D] mmCIF format, chain R [auth D] mmCIF format, chain O [auth C] mmCIF format, chain M [auth C] mmCIF format, chain F [auth A]	F [auth A] J [auth B] M [auth C] O [auth C] R [auth D] F [auth A], J [auth B], M [auth C], O [auth C], R [auth D], T [auth D]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain J [auth B] Focus chain M [auth C] Focus chain O [auth C] Focus chain R [auth D] Focus chain T [auth D] Interactions & Density Focus chain F [auth A] Focus chain J [auth B] Focus chain M [auth C] Focus chain O [auth C] Focus chain R [auth D] Focus chain T [auth D]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B, C, D	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: 0.188 (Depositor), 0.191 (DCC)
R-Value Work: 0.150 (Depositor), 0.153 (DCC)
R-Value Observed: 0.151 (Depositor)

Diffraction Data: https://doi.org/10.18430/M36ANS

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.1	α = 90
b = 134.47	β = 90.43
c = 98.08	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
XSCALE	data scaling
PHASER	phasing
PARROT	phasing
ARP	model building
Coot	model building
PHENIX	refinement
PDB_EXTRACT	data extraction

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2017-08-30

Deposition Author(s):

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History (Full details and data files)

Version 1.0: 2017-08-30
Type: Initial release
Version 1.1: 2024-10-30
Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary