5W15 | pdb_00005w15

Crystal structure of an alpha/beta hydrolase fold protein from Burkholderia ambifaria.

PDB DOI: https://doi.org/10.2210/pdb5W15/pdb

Classification: HYDROLASE
Organism(s): Burkholderia ambifaria MC40-6
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2017-06-01 Released: 2017-06-14
Deposition Author(s): SSGCID, Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.75 Å
R-Value Free:
0.188 (Depositor), 0.190 (DCC)
R-Value Work:
0.166 (Depositor), 0.169 (DCC)
R-Value Observed:
0.166 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of an alpha/beta hydrolase fold protein from Burkholderia ambifaria.

Irwin, R.M., Mayclin, S.J., Lorimer, D., Edwards, T.E.

To be published.

Macromolecule Content

Total Structure Weight: 123.63 kDa
Atom Count: 10,072
Modeled Residue Count: 1,080
Deposited Residue Count: 1,100
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Alpha/beta hydrolase fold protein	A, B, C, D	275	Burkholderia ambifaria MC40-6	Mutation(s): 0 Gene Names: BamMC406_3075
UniProt
Find proteins for B1YPY7 (Burkholderia ambifaria (strain MC40-6)) Explore B1YPY7 Go to UniProtKB: B1YPY7
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	B1YPY7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A]	E [auth A], F [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Interactions & Density Focus chain E [auth A] Focus chain F [auth A]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain P [auth D] SDF format, chain N [auth C] SDF format, chain M [auth C] SDF format, chain K [auth B] SDF format, chain J [auth B] SDF format, chain I [auth A] SDF format, chain H [auth A] SDF format, chain G [auth A] MOL2 format, chain P [auth D] MOL2 format, chain N [auth C] MOL2 format, chain M [auth C] MOL2 format, chain K [auth B] MOL2 format, chain J [auth B] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] mmCIF format, chain P [auth D] mmCIF format, chain N [auth C] mmCIF format, chain M [auth C] mmCIF format, chain K [auth B] mmCIF format, chain J [auth B] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A]	G [auth A] H [auth A] I [auth A] J [auth B] K [auth B] G [auth A], H [auth A], I [auth A], J [auth B], K [auth B], M [auth C], N [auth C], P [auth D]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain M [auth C] Focus chain N [auth C] Focus chain P [auth D] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain M [auth C] Focus chain N [auth C] Focus chain P [auth D]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain O [auth D] SDF format, chain L [auth C] MOL2 format, chain O [auth D] MOL2 format, chain L [auth C] mmCIF format, chain O [auth D] mmCIF format, chain L [auth C]	L [auth C], O [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain L [auth C] Focus chain O [auth D] Interactions & Density Focus chain L [auth C] Focus chain O [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.75 Å
R-Value Free: 0.188 (Depositor), 0.190 (DCC)
R-Value Work: 0.166 (Depositor), 0.169 (DCC)
R-Value Observed: 0.166 (Depositor)

Diffraction Data:

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.07	α = 90
b = 143.59	β = 111.34
c = 75.85	γ = 90

Software Package:

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

Structure Validation

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Entry History

Deposition Data

Released Date: 2017-06-14

Deposition Author(s):

SSGCID

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History (Full details and data files)

Version 1.0: 2017-06-14
Type: Initial release
Version 1.1: 2017-06-28
Changes: Database references
Version 1.2: 2017-11-22
Changes: Refinement description
Version 1.3: 2023-10-04
Changes: Data collection, Database references, Refinement description