7TM8 | pdb_00007tm8

Crystal structure of Bifunctional adenosylcobalamin biosynthesis protein from Klebsiella pneumoniae

PDB DOI: https://doi.org/10.2210/pdb7TM8/pdb

Classification: TRANSFERASE
Organism(s): Klebsiella pneumoniae subsp. pneumoniae HS11286
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2022-01-19 Released: 2022-02-02
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.65 Å
R-Value Free:
0.205 (Depositor), 0.204 (DCC)
R-Value Work:
0.177 (Depositor), 0.177 (DCC)
R-Value Observed:
0.178 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of Bifunctional adenosylcobalamin biosynthesis protein from Klebsiella pneumoniae

Liu, L., Lovell, S., Battaile, K.P., Tillery, L., Shek, R., Craig, J.K., Barrett, L.K., Van Voorhis, W.C.

To be published.

Macromolecule Content

Total Structure Weight: 63.06 kDa
Atom Count: 4,381
Modeled Residue Count: 502
Deposited Residue Count: 567
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bifunctional adenosylcobalamin biosynthesis protein	A, B, C	189	Klebsiella pneumoniae subsp. pneumoniae HS11286	Mutation(s): 1 Gene Names: KPHS_42470 EC: 2.7.1.156 (PDB Primary Data), 2.7.7.62 (PDB Primary Data)
UniProt
Find proteins for A0A0H3GSH0 (Klebsiella pneumoniae subsp. pneumoniae (strain HS11286)) Explore A0A0H3GSH0 Go to UniProtKB: A0A0H3GSH0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A0H3GSH0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain J [auth C] SDF format, chain I [auth C] SDF format, chain H [auth B] SDF format, chain G [auth B] SDF format, chain F [auth A] SDF format, chain E [auth A] SDF format, chain D [auth A] MOL2 format, chain J [auth C] MOL2 format, chain I [auth C] MOL2 format, chain H [auth B] MOL2 format, chain G [auth B] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] mmCIF format, chain J [auth C] mmCIF format, chain I [auth C] mmCIF format, chain H [auth B] mmCIF format, chain G [auth B] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A]	D [auth A] E [auth A] F [auth A] G [auth B] H [auth B] D [auth A], E [auth A], F [auth A], G [auth B], H [auth B], I [auth C], J [auth C]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth B] Focus chain H [auth B] Focus chain I [auth C] Focus chain J [auth C] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth B] Focus chain H [auth B] Focus chain I [auth C] Focus chain J [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.65 Å
R-Value Free: 0.205 (Depositor), 0.204 (DCC)
R-Value Work: 0.177 (Depositor), 0.177 (DCC)
R-Value Observed: 0.178 (Depositor)

Diffraction Data:

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.138	α = 90
b = 63.279	β = 90
c = 131.599	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
Aimless	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2022-02-02

Deposition Author(s):

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	HHSN272201700059C

Revision History (Full details and data files)

Version 1.0: 2022-02-02
Type: Initial release
Version 1.1: 2023-10-18
Changes: Data collection, Refinement description

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.