8I57

Uroporphyrin III (UPIII)-bound CfbA

PDB DOI: https://doi.org/10.2210/pdb8I57/pdb

Classification: BIOSYNTHETIC PROTEIN
Organism(s): Methanocaldococcus jannaschii DSM 2661
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2023-01-24 Released: 2024-01-31
Deposition Author(s): Ogawa, S., Fujishiro, T.
Funding Organization(s): Japan Society for the Promotion of Science (JSPS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.81 Å
R-Value Free: 0.236
R-Value Work: 0.207
R-Value Observed: 0.209

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Substrate selectivity of CfbA

Ogawa, S., Hikita, M., Fujishiro, T.

To be published.

Macromolecule Content

Total Structure Weight: 33.94 kDa
Atom Count: 1,955
Modelled Residue Count: 239
Deposited Residue Count: 286
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Sirohydrochlorin cobaltochelatase	A, B	143	Methanocaldococcus jannaschii DSM 2661	Mutation(s): 0 Gene Names: cbiX, cfbA, MJ0970 EC: 4.99.1.3 (PDB Primary Data), 4.99.1.11 (PDB Primary Data)
UniProt
Find proteins for Q58380 (Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440)) Explore Q58380 Go to UniProtKB: Q58380
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q58380
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
UP3 (Subject of Investigation/LOI) Query on UP3 Download Ideal Coordinates CCD File SDF format, chain C [auth B] MOL2 format, chain C [auth B] mmCIF format, chain C [auth B]	C [auth B]	3,3',3'',3'''-[3,8,13,17-tetrakis(carboxymethyl)porphyrin-2,7,12,18-tetrayl]tetrapropanoic acid C₄₀ H₃₈ N₄ O₁₆ VZVFNUAIRVUCEW-XFMUOGEMSA-N		Interactions Focus chain C [auth B] Interactions & Density Focus chain C [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.81 Å
R-Value Free: 0.236
R-Value Work: 0.207
R-Value Observed: 0.209
Space Group: P 4₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.22	α = 90
b = 68.22	β = 90
c = 82.65	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2024-01-31

Deposition Author(s):

Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science (JSPS)	Japan	19H04639

Revision History (Full details and data files)

Version 1.0: 2024-01-31
Type: Initial release

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.