4C45 | pdb_00004c45

Crystal structure of human pterin-4-alpha-carbinolamine dehydratase 2 (PCBD2)

PDB DOI: https://doi.org/10.2210/pdb4C45/pdb

Classification: LYASE
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2013-08-30 Released: 2013-09-11
Deposition Author(s): Kopec, J., Kiyani, W., Vollmar, M., Shrestha, L., Canning, P., von Delft, F., Burgess-Brown, N., Bountra, C., Arrowsmith, C.H., Edwards, A., Yue, W.W.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.45 Å
R-Value Free:
0.167 (Depositor), 0.179 (DCC)
R-Value Work:
0.144 (Depositor)
R-Value Observed:
0.145 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 4C45

This is version 1.2 of the entry. See complete history.

Literature

Crystal Structure of Human Pterin-4-Alpha- Carbinolamine Dehydratase 2 (Pcbd2)

Kopec, J., Kiyani, W., Vollmar, M., Shrestha, L., Canning, P., von Delft, F., Burgess-Brown, N., Bountra, C., Arrowsmith, C.H., Edwards, A., Yue, W.W.

To be published.

Macromolecule Content

Total Structure Weight: 11.93 kDa
Atom Count: 908
Modeled Residue Count: 99
Deposited Residue Count: 104
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PTERIN-4-ALPHA-CARBINOLAMINE DEHYDRATASE 2	A	104	Homo sapiens	Mutation(s): 0 EC: 4.2.1.96
UniProt & NIH Common Fund Data Resources
Find proteins for Q9H0N5 (Homo sapiens) Explore Q9H0N5 Go to UniProtKB: Q9H0N5
PHAROS: Q9H0N5 GTEx: ENSG00000132570
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9H0N5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EDO Query on EDO 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]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.45 Å
R-Value Free: 0.167 (Depositor), 0.179 (DCC)
R-Value Work: 0.144 (Depositor)
R-Value Observed: 0.145 (Depositor)

Space Group: C 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.547	α = 90
b = 94.044	β = 90
c = 48.33	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2013-09-11

Deposition Author(s):

Burgess-Brown, N.

Arrowsmith, C.H.

Revision History (Full details and data files)

Version 1.0: 2013-09-11
Type: Initial release
Version 1.1: 2018-01-24
Changes: Database references
Version 1.2: 2023-12-20
Changes: Data collection, Database references, Derived calculations, Other, 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.