5H6O | pdb_00005h6o

Porphobilinogen deaminase from Vibrio Cholerae

PDB DOI: https://doi.org/10.2210/pdb5H6O/pdb

Classification: TRANSFERASE
Organism(s): Vibrio cholerae
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2016-11-14 Released: 2017-11-15
Deposition Author(s): Funamizu, T., Chen, M., Tanaka, Y., Ishimori, K., Uchida, T.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free:
0.277 (Depositor), 0.281 (DCC)
R-Value Work:
0.236 (Depositor), 0.244 (DCC)
R-Value Observed:
0.238 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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Literature

Porphobilinogen deaminase from Vibrio Cholerae

Funamizu, T., Chen, M., Tanaka, Y., Ishimori, K., Uchida, T.

To be published.

Macromolecule Content

Total Structure Weight: 35.08 kDa
Atom Count: 2,191
Modeled Residue Count: 281
Deposited Residue Count: 317
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Porphobilinogen deaminase	A	317	Vibrio cholerae	Mutation(s): 0 Gene Names: hemC, ERS013197_03721 EC: 2.5.1.61
UniProt
Find proteins for Q9KVM1 (Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)) Explore Q9KVM1 Go to UniProtKB: Q9KVM1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9KVM1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
DPM Query on DPM Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	3-[5-{[3-(2-carboxyethyl)-4-(carboxymethyl)-5-methyl-1H-pyrrol-2-yl]methyl}-4-(carboxymethyl)-1H-pyrrol-3-yl]propanoic acid C₂₀ H₂₄ N₂ O₈ LCAXMKQKEYTFDM-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free: 0.277 (Depositor), 0.281 (DCC)
R-Value Work: 0.236 (Depositor), 0.244 (DCC)
R-Value Observed: 0.238 (Depositor)

Space Group: I 4₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 94.23	α = 90
b = 94.23	β = 90
c = 165.34	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2017-11-15

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2017-11-15
Type: Initial release
Version 1.1: 2023-11-08
Changes: Data collection, Database references, 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.