2ZHZ | pdb_00002zhz

Crystal structure of a pduO-type ATP:cobalamin adenosyltransferase from Burkholderia thailandensis

PDB DOI: https://doi.org/10.2210/pdb2ZHZ/pdb

Classification: TRANSFERASE
Organism(s): Burkholderia thailandensis
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2008-02-12 Released: 2008-07-29
Deposition Author(s): Moon, J.H., Park, A.K., Jang, E.H., Kim, H.S., Chi, Y.M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free:
0.229 (Depositor), 0.229 (DCC)
R-Value Work:
0.201 (Depositor), 0.201 (DCC)
R-Value Observed:
0.211 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Crystal structure of a PduO-type ATP:cobalamin adenosyltransferase from Burkholderia thailandensis.

Moon, J.H., Park, A.K., Jang, E.H., Kim, H.S., Chi, Y.M.

(2008) Proteins 72: 1066-1070

PubMed: 18473361 Search on PubMed
DOI: https://doi.org/10.1002/prot.22084
Primary Citation Related Structures:
2ZHY, 2ZHZ

Organizational Affiliation

Institute of Life Science and Natural Resources, Korea University, Seoul 136-713, Korea.

Macromolecule Content

Total Structure Weight: 59.91 kDa
Atom Count: 4,038
Modeled Residue Count: 494
Deposited Residue Count: 549
Unique protein chains: 1

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP:cob(I)alamin adenosyltransferase, putative	A, B, C	183	Burkholderia thailandensis	Mutation(s): 0 Gene Names: pduO EC: 2.5.1.17 (PDB Primary Data), 2.5.1 (UniProt)
UniProt
Find proteins for Q2SZ09 (Burkholderia thailandensis (strain ATCC 700388 / DSM 13276 / CCUG 48851 / CIP 106301 / E264)) Explore Q2SZ09 Go to UniProtKB: Q2SZ09
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q2SZ09
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ATP Query on ATP Download:Ideal Coordinates CCD File SDF format, chain G [auth B] SDF format, chain H [auth B] MOL2 format, chain G [auth B] MOL2 format, chain H [auth B] mmCIF format, chain G [auth B] mmCIF format, chain H [auth B]	G [auth B], H [auth B]	ADENOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₃ P₃ ZKHQWZAMYRWXGA-KQYNXXCUSA-N		Interactions Focus chain G [auth B] Focus chain H [auth B] Interactions & Density Focus chain G [auth B] Focus chain H [auth B]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain I [auth B] SDF format, chain J [auth C] MOL2 format, chain E [auth A] MOL2 format, chain I [auth B] MOL2 format, chain J [auth C] mmCIF format, chain E [auth A] mmCIF format, chain I [auth B] mmCIF format, chain J [auth C]	E [auth A], I [auth B], J [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain I [auth B] Focus chain J [auth C] Interactions & Density Focus chain E [auth A] Focus chain I [auth B] Focus chain J [auth C]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain F [auth B] MOL2 format, chain D [auth A] MOL2 format, chain F [auth B] mmCIF format, chain D [auth A] mmCIF format, chain F [auth B]	D [auth A], F [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain F [auth B] Interactions & Density Focus chain D [auth A] Focus chain F [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.229 (Depositor), 0.229 (DCC)
R-Value Work: 0.201 (Depositor), 0.201 (DCC)
R-Value Observed: 0.211 (Depositor)

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.907	α = 90
b = 148.174	β = 90
c = 158.096	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
CNS	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data reduction
CNS	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2008-07-29

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2008-07-29
Type: Initial release
Version 1.1: 2011-07-13
Changes: Non-polymer description, Version format compliance
Version 1.2: 2017-10-11
Changes: Refinement description
Version 1.3: 2024-03-13
Changes: Data collection, Database references, Derived calculations