6CII | pdb_00006cii

Crystal structure of Chlamydomonas reinhardtii THB1 in the cyanomet state

PDB DOI: https://doi.org/10.2210/pdb6CII/pdb

Classification: heme-binding protein
Organism(s): Chlamydomonas reinhardtii
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2018-02-23 Released: 2018-04-25
Deposition Author(s): Martinez, J.E., Schlessman, J.L., Lecomte, J.T.J.
Funding Organization(s): National Science Foundation (NSF, United States)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free:
0.191 (Depositor), 0.191 (DCC)
R-Value Work:
0.163 (Depositor), 0.165 (DCC)
R-Value Observed:
0.166 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 6CII

Ligand Structure Quality Assessment

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

Literature

Control of distal lysine coordination in a monomeric hemoglobin: A role for heme peripheral interactions

Martinez, J.E., Schlessman, J.L., Lecomte, J.T.J.

(2021) J Inorg Biochem 219: 111437

DOI: https://doi.org/10.1016/j.jinorgbio.2021.111437

Macromolecule Content

Total Structure Weight: 15.23 kDa
Atom Count: 1,190
Modeled Residue Count: 124
Deposited Residue Count: 135
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Chlamydomonas reinhardtii THB1	A	135	Chlamydomonas reinhardtii	Mutation(s): 0 Gene Names: THB1, CHLREDRAFT_81856
UniProt
Find proteins for A8JAR4 (Chlamydomonas reinhardtii) Explore A8JAR4 Go to UniProtKB: A8JAR4
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A8JAR4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HEM (Subject of Investigation/LOI) Query on HEM 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]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
CYN (Subject of Investigation/LOI) Query on CYN 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]	CYANIDE ION C N XFXPMWWXUTWYJX-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: 1.70 Å
R-Value Free: 0.191 (Depositor), 0.191 (DCC)
R-Value Work: 0.163 (Depositor), 0.165 (DCC)
R-Value Observed: 0.166 (Depositor)

Space Group: P 4₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.992	α = 90
b = 45.992	β = 90
c = 121.277	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
CrysalisPro	data reduction
CrysalisPro	data scaling
PHENIX	phasing
Coot	model building
PDB_EXTRACT	data extraction

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2018-04-25

Deposition Author(s):

Schlessman, J.L.

Lecomte, J.T.J.

Funding Organization	Location	Grant Number
National Science Foundation (NSF, United States)	United States	MCB-1330488

Revision History (Full details and data files)

Version 1.0: 2018-04-25
Type: Initial release
Version 1.1: 2019-11-27
Changes: Author supporting evidence
Version 1.2: 2021-04-28
Changes: Database references
Version 1.3: 2024-03-13
Changes: Data collection, Database references

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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.