3I8U | pdb_00003i8u

Crystal structure of PcyA-181,182-dihydrobiliverdin complex

PDB DOI: https://doi.org/10.2210/pdb3I8U/pdb

Classification: OXIDOREDUCTASE
Organism(s): Synechocystis sp. PCC 6803
Expression System: Escherichia coli
Mutation(s): No

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: 1.48 Å
R-Value Free:
0.197 (Depositor), 0.204 (DCC)
R-Value Work:
0.164 (Depositor), 0.173 (DCC)
R-Value Observed:
0.166 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 1.2 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: 2,414
Modeled Residue Count: 243
Deposited Residue Count: 248
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phycocyanobilin:ferredoxin oxidoreductase	A [auth X]	248	Synechocystis sp. PCC 6803	Mutation(s): 0 Gene Names: pcyA, slr0116 EC: 1.3.7.5
UniProt
Find proteins for Q55891 (Synechocystis sp. (strain ATCC 27184 / PCC 6803 / Kazusa)) Explore Q55891 Go to UniProtKB: Q55891
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q55891
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
18B Query on 18B Download:Ideal Coordinates CCD File SDF format, chain B [auth X] MOL2 format, chain B [auth X] mmCIF format, chain B [auth X]	B [auth X]	3-[2-[(Z)-[3-(2-carboxyethyl)-5-[(Z)-(3-ethenyl-4-methyl-5-oxo-pyrrol-2-ylidene)methyl]-4-methyl-pyrrol-2-ylidene]methy l]-5-[(Z)-(4-ethyl-3-methyl-5-oxo-pyrrol-2-ylidene)methyl]-4-methyl-1H-pyrrol-3-yl]propanoic acid C₃₃ H₃₆ N₄ O₆ PSKIZABPQHQTFV-SRVCBVSDSA-N		Interactions Focus chain B [auth X] Interactions & Density Focus chain B [auth X]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.48 Å
R-Value Free: 0.197 (Depositor), 0.204 (DCC)
R-Value Work: 0.164 (Depositor), 0.173 (DCC)
R-Value Observed: 0.166 (Depositor)

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.822	α = 90
b = 95.087	β = 90
c = 42.782	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

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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: 2023-11-01
Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary

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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.