6CII

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
R-Value Work: 0.163
R-Value Observed: 0.166

wwPDB Validation 3D Report Full Report

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
Modelled Residue Count: 124
Deposited Residue Count: 135
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

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% Identity50% Identity70% Identity90% Identity95% Identity100% 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]	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]	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
R-Value Work: 0.163
R-Value Observed: 0.166
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

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

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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.