3DMI

Crystallization and Structural Analysis of Cytochrome c6 from the Diatom Phaeodactylum tricornutum at 1.5 A resolution

PDB DOI: https://doi.org/10.2210/pdb3DMI/pdb

Classification: ELECTRON TRANSPORT
Organism(s): Phaeodactylum tricornutum
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2008-07-01 Released: 2009-03-17
Deposition Author(s): Akazaki, H., Kawai, F., Hosokawa, M., Hama, T., Hirano, T., Lim, B.-K., Sakurai, N., Hakamata, W., Park, S.-Y., Nishio, T., Oku, T.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free: 0.202
R-Value Work: 0.164
R-Value Observed: 0.166

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.2 of the entry. See complete history.

Literature

Crystallization and structural analysis of cytochrome c(6) from the diatom Phaeodactylum tricornutum at 1.5 A resolution.

Akazaki, H., Kawai, F., Hosokawa, M., Hama, T., Chida, H., Hirano, T., Lim, B.K., Sakurai, N., Hakamata, W., Park, S.Y., Nishio, T., Oku, T.

(2009) Biosci Biotechnol Biochem 73: 189-191

PubMed: 19129656 Search on PubMed
DOI: https://doi.org/10.1271/bbb.80472
Primary Citation of Related Structures:
3DMI

PubMed Abstract:
We determined for the first time the crystal structure of diatom cytochrome c(6) from Phaeodactylum tricornutum at 1.5 A resolution. The overall structure of the protein was classified as a class I c-type cytochrome. The physicochemical properties of the protein were examined by denaturation with guanidine hydrochloride and urea, and compared with those of other algal cytochrome c(6).

Organizational Affiliation

Bio-Organic Chemistry Laboratory, Graduate School of Bioresource Sciences, Nihon University.

Macromolecule Content

Total Structure Weight: 9.72 kDa
Atom Count: 783
Modelled Residue Count: 87
Deposited Residue Count: 88
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
cytochrome c6	A	88	Phaeodactylum tricornutum	Mutation(s): 0 Gene Names: pet J
UniProt
Find proteins for Q8GTB5 (Phaeodactylum tricornutum) Explore Q8GTB5 Go to UniProtKB: Q8GTB5
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8GTB5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HEC Query on HEC Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A]	C [auth A]	HEME C C₃₄ H₃₄ Fe N₄ O₄ HXQIYSLZKNYNMH-LJNAALQVSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-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: 1.50 Å
R-Value Free: 0.202
R-Value Work: 0.164
R-Value Observed: 0.166
Space Group: I 2 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.385	α = 90
b = 80.385	β = 90
c = 80.385	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data collection
HKL-2000	data reduction
SCALEPACK	data scaling
MOLREP	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2009-03-17

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2009-03-17
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 2.0: 2019-10-02
Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
Version 2.1: 2019-11-06
Changes: Data collection, Database references
Version 2.2: 2023-11-01
Changes: Data collection, Database references, Derived calculations, Refinement description