9CBR | pdb_00009cbr

Methionine synthase from Thermus thermophilus HB8, Homocysteine, Folate, and Cobalamin Domains, Catalytic Conformation (Hcy-on)

PDB DOI: https://doi.org/10.2210/pdb9CBR/pdb

Classification: TRANSFERASE
Organism(s): Thermus thermophilus HB8
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2024-06-19 Released: 2025-06-25
Deposition Author(s): Yamada, K., Menjdoza, J., Koutmos, M.
Funding Organization(s): National Science Foundation (NSF, United States)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.38 Å
R-Value Free:
0.217 (Depositor), 0.253 (DCC)
R-Value Work:
0.195 (Depositor), 0.225 (DCC)
R-Value Observed:
0.196 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 3.0 of the entry. See complete history.

Literature

Methionine synthase from Thermus thermophilus HB8, Homocysteine, Folate, and Cobalamin Domains, Catalytic Conformation (Hcy-on)

Menjdoza, J., Yamada, K., Koutmos, M.

To be published.

Macromolecule Content

Total Structure Weight: 97.7 kDa
Atom Count: 7,023
Modeled Residue Count: 867
Deposited Residue Count: 877
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Methionine synthase	A	877	Thermus thermophilus HB8	Mutation(s): 10 Gene Names: TTHA0618 EC: 2.1.1.13
UniProt
Find proteins for Q5SKM5 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SKM5 Go to UniProtKB: Q5SKM5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5SKM5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
B12 (Subject of Investigation/LOI) Query on B12 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]	COBALAMIN C₆₂ H₈₉ Co N₁₃ O₁₄ P LKVIQTCSMMVGFU-DWSMJLPVSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
THG (Subject of Investigation/LOI) Query on THG Download:Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A] mmCIF format, chain G [auth A]	G [auth A]	(6S)-5,6,7,8-TETRAHYDROFOLATE C₁₉ H₂₃ N₇ O₆ MSTNYGQPCMXVAQ-RYUDHWBXSA-N		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]
ZN (Subject of Investigation/LOI) Query on ZN Download:Ideal Coordinates CCD File SDF format, chain B [auth A] SDF format, chain D [auth A] MOL2 format, chain B [auth A] MOL2 format, chain D [auth A] mmCIF format, chain B [auth A] mmCIF format, chain D [auth A]	B [auth A], D [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Focus chain D [auth A] Interactions & Density Focus chain B [auth A] Focus chain D [auth A]
NEH (Subject of Investigation/LOI) Query on NEH Download:Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	F [auth A]	ETHANAMINE C₂ H₇ N QUSNBJAOOMFDIB-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]
K Query on K Download:Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.38 Å
R-Value Free: 0.217 (Depositor), 0.253 (DCC)
R-Value Work: 0.195 (Depositor), 0.225 (DCC)
R-Value Observed: 0.196 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.811	α = 90
b = 115.101	β = 90
c = 120.795	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
DIALS	data reduction
MOLREP	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2025-06-25

Deposition Author(s):

Yamada, K.

Menjdoza, J.

Koutmos, M.

Funding Organization	Location	Grant Number
National Science Foundation (NSF, United States)	United States	1945174

Revision History (Full details and data files)

Version 1.0: 2025-06-25
Type: Initial release
Version 2.0: 2025-09-03
Type: Coordinate replacement
Reason: Model completeness
Changes: Advisory, Atomic model, Author supporting evidence, Data collection, Database references, Derived calculations, Non-polymer description, Polymer sequence, Refinement description, Source and taxonomy, Structure summary
Version 3.0: 2026-05-13
Type: Coordinate replacement
Reason: Model completeness
Changes: Advisory, Atomic model, Author supporting evidence, Data collection, Derived calculations, Non-polymer description, Refinement description, Structure summary