3I95

Crystal structure of E76Q mutant PcyA-biliverdin complex

PDB DOI: https://doi.org/10.2210/pdb3I95/pdb

Classification: OXIDOREDUCTASE
Organism(s): Synechocystis sp. PCC 6803
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2009-07-10 Released: 2009-10-27
Deposition Author(s): Hagiwara, Y., Sugishima, M., Fukuyama, K.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.40 Å
R-Value Free: 0.192
R-Value Work: 0.175
R-Value Observed: 0.176

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Structural insights into vinyl reduction regiospecificity of phycocyanobilin:ferredoxin oxidoreductase (PcyA).

Hagiwara, Y., Sugishima, M., Khawn, H., Kinoshita, H., Inomata, K., Shang, L., Lagarias, J.C., Takahashi, Y., Fukuyama, K.

To be published.

Macromolecule Content

Total Structure Weight: 28.74 kDa
Atom Count: 2,450
Modelled Residue Count: 243
Deposited Residue Count: 248
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phycocyanobilin:ferredoxin oxidoreductase	A	248	Synechocystis sp. PCC 6803	Mutation(s): 1 Gene Names: pcyA, slr0116
UniProt
Find proteins for Q55891 (Synechocystis sp. (strain PCC 6803 / Kazusa)) Explore Q55891 Go to UniProtKB: Q55891
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q55891
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
BLA Query on BLA Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	BILIVERDINE IX ALPHA C₃₃ H₃₄ N₄ O₆ GWZYPXHJIZCRAJ-SRVCBVSDSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.40 Å
R-Value Free: 0.192
R-Value Work: 0.175
R-Value Observed: 0.176
Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.681	α = 90
b = 95.701	β = 90
c = 42.727	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
SCALEPACK	data scaling

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2009-10-27

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2009-10-27
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2021-11-10
Changes: Database references, Derived calculations
Version 1.3: 2023-11-01
Changes: Data collection, Refinement description

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 R01GM133198.