3POT | pdb_00003pot

Structural analysis of a Ni(III)-methyl species in methyl-coenzyme M reductase from Methanothermobacter marburgensis

PDB DOI: https://doi.org/10.2210/pdb3POT/pdb

Classification: TRANSFERASE
Organism(s): Methanothermobacter marburgensis
Mutation(s): No

Deposited: 2010-11-23 Released: 2011-04-13
Deposition Author(s): Cedervall, P.E., Wilmot, C.M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.20 Å
R-Value Free:
0.156 (Depositor), 0.156 (DCC)
R-Value Work:
0.132 (Depositor), 0.132 (DCC)
R-Value Observed:
0.133 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

Literature

Structural Analysis of a Ni-Methyl Species in Methyl-Coenzyme M Reductase from Methanothermobacter marburgensis.

Cedervall, P.E., Dey, M., Li, X., Sarangi, R., Hedman, B., Ragsdale, S.W., Wilmot, C.M.

(2011) J Am Chem Soc 133: 5626-5628

PubMed: 21438550 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1021/ja110492p
Primary Citation Related Structures:
3POT

PubMed Abstract:
We present the 1.2 Å resolution X-ray crystal structure of a Ni-methyl species that is a proposed catalytic intermediate in methyl-coenzyme M reductase (MCR), the enzyme that catalyzes the biological formation of methane. The methyl group is situated 2.1 Å proximal of the Ni atom of the MCR coenzyme F(430). A rearrangement of the substrate channel has been posited to bring together substrate species, but Ni(III)-methyl formation alone does not lead to any observable structural changes in the channel.

Organizational Affiliation

Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, United States.

Macromolecule Content

Total Structure Weight: 277.55 kDa
Atom Count: 22,289
Modeled Residue Count: 2,472
Deposited Residue Count: 2,484
Unique protein chains: 3

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Methyl-coenzyme M reductase I subunit alpha	A, D	550	Methanothermobacter marburgensis	Mutation(s): 0 EC: 2.8.4.1
UniProt
Find proteins for P11558 (Methanothermobacter marburgensis (strain ATCC BAA-927 / DSM 2133 / JCM 14651 / NBRC 100331 / OCM 82 / Marburg)) Explore P11558 Go to UniProtKB: P11558
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P11558
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Methyl-coenzyme M reductase I subunit beta	B, E	443	Methanothermobacter marburgensis	Mutation(s): 0 EC: 2.8.4.1
UniProt
Find proteins for P11560 (Methanothermobacter marburgensis (strain ATCC BAA-927 / DSM 2133 / JCM 14651 / NBRC 100331 / OCM 82 / Marburg)) Explore P11560 Go to UniProtKB: P11560
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P11560
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Methyl-coenzyme M reductase I subunit gamma	C, F	249	Methanothermobacter marburgensis	Mutation(s): 0 EC: 2.8.4.1
UniProt
Find proteins for P11562 (Methanothermobacter marburgensis (strain ATCC BAA-927 / DSM 2133 / JCM 14651 / NBRC 100331 / OCM 82 / Marburg)) Explore P11562 Go to UniProtKB: P11562
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P11562
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 8 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
F43 Query on F43 Download:Ideal Coordinates CCD File SDF format, chain K [auth A] SDF format, chain V [auth D] MOL2 format, chain K [auth A] MOL2 format, chain V [auth D] mmCIF format, chain K [auth A] mmCIF format, chain V [auth D]	K [auth A], V [auth D]	FACTOR 430 C₄₂ H₅₁ N₆ Ni O₁₃ XLFIRMYGVLUNOY-SXMZNAGASA-M		Interactions Focus chain K [auth A] Focus chain V [auth D] Interactions & Density Focus chain K [auth A] Focus chain V [auth D]
TP7 Query on TP7 Download:Ideal Coordinates CCD File SDF format, chain N [auth A] SDF format, chain W [auth D] MOL2 format, chain N [auth A] MOL2 format, chain W [auth D] mmCIF format, chain N [auth A] mmCIF format, chain W [auth D]	N [auth A], W [auth D]	Coenzyme B C₁₁ H₂₂ N O₇ P S JBJSVEVEEGOEBZ-SCZZXKLOSA-N		Interactions Focus chain N [auth A] Focus chain W [auth D] Interactions & Density Focus chain N [auth A] Focus chain W [auth D]
TXZ Query on TXZ Download:Ideal Coordinates CCD File SDF format, chain M [auth A] SDF format, chain X [auth D] MOL2 format, chain M [auth A] MOL2 format, chain X [auth D] mmCIF format, chain M [auth A] mmCIF format, chain X [auth D]	M [auth A], X [auth D]	O-phosphono-N-(6-sulfanylhexanoyl)-L-threonine C₁₀ H₂₀ N O₇ P S PRNNQVAYHYUTOD-APPZFPTMSA-N		Interactions Focus chain M [auth A] Focus chain X [auth D] Interactions & Density Focus chain M [auth A] Focus chain X [auth D]
COM Query on COM Download:Ideal Coordinates CCD File SDF format, chain L [auth A] SDF format, chain Y [auth D] MOL2 format, chain L [auth A] MOL2 format, chain Y [auth D] mmCIF format, chain L [auth A] mmCIF format, chain Y [auth D]	L [auth A], Y [auth D]	1-THIOETHANESULFONIC ACID C₂ H₆ O₃ S₂ ZNEWHQLOPFWXOF-UHFFFAOYSA-N		Interactions Focus chain L [auth A] Focus chain Y [auth D] Interactions & Density Focus chain L [auth A] Focus chain Y [auth D]
06C Query on 06C Download:Ideal Coordinates CCD File SDF format, chain O [auth A] SDF format, chain Z [auth D] MOL2 format, chain O [auth A] MOL2 format, chain Z [auth D] mmCIF format, chain O [auth A] mmCIF format, chain Z [auth D]	O [auth A], Z [auth D]	Iodomethane C H₃ I INQOMBQAUSQDDS-UHFFFAOYSA-N		Interactions Focus chain O [auth A] Focus chain Z [auth D] Interactions & Density Focus chain O [auth A] Focus chain Z [auth D]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain AA [auth D] MOL2 format, chain AA [auth D] mmCIF format, chain AA [auth D]	AA [auth D]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain AA [auth D] Interactions & Density Focus chain AA [auth D]
K Query on K Download:Ideal Coordinates CCD File SDF format, chain P [auth A] MOL2 format, chain P [auth A] mmCIF format, chain P [auth A]	P [auth A]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain P [auth A] Interactions & Density Focus chain P [auth A]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain BA [auth E] SDF format, chain CA [auth E] SDF format, chain DA [auth F] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain Q [auth B] SDF format, chain R [auth B] SDF format, chain S [auth C] SDF format, chain T [auth C] SDF format, chain U [auth D] MOL2 format, chain BA [auth E] MOL2 format, chain CA [auth E] MOL2 format, chain DA [auth F] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth B] MOL2 format, chain S [auth C] MOL2 format, chain T [auth C] MOL2 format, chain U [auth D] mmCIF format, chain BA [auth E] mmCIF format, chain CA [auth E] mmCIF format, chain DA [auth F] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain Q [auth B] mmCIF format, chain R [auth B] mmCIF format, chain S [auth C] mmCIF format, chain T [auth C] mmCIF format, chain U [auth D]	BA [auth E] CA [auth E] DA [auth F] G [auth A] H [auth A] BA [auth E], CA [auth E], DA [auth F], G [auth A], H [auth A], I [auth A], J [auth A], Q [auth B], R [auth B], S [auth C], T [auth C], U [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain BA [auth E] Focus chain CA [auth E] Focus chain DA [auth F] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth C] Focus chain T [auth C] Focus chain U [auth D] Interactions & Density Focus chain BA [auth E] Focus chain CA [auth E] Focus chain DA [auth F] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth C] Focus chain T [auth C] Focus chain U [auth D]

Modified Residues 5 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
AGM Query on AGM	A, D	L-PEPTIDE LINKING	C₇ H₁₇ N₄ O₂		ARG
GL3 Query on GL3	A, D	L-PEPTIDE LINKING	C₂ H₅ N O S		GLY
MGN Query on MGN	A, D	L-PEPTIDE LINKING	C₆ H₁₂ N₂ O₃		GLN
MHS Query on MHS	A, D	L-PEPTIDE LINKING	C₇ H₁₁ N₃ O₂		HIS
SMC Query on SMC	A, D	L-PEPTIDE LINKING	C₄ H₉ N O₂ S		CYS

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.20 Å
R-Value Free: 0.156 (Depositor), 0.156 (DCC)
R-Value Work: 0.132 (Depositor), 0.132 (DCC)
R-Value Observed: 0.133 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 81.886	α = 90
b = 118.165	β = 91.94
c = 122.388	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2011-04-13

Deposition Author(s):

Cedervall, P.E.

Wilmot, C.M.

Revision History (Full details and data files)

Version 1.0: 2011-04-13
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2015-05-20
Changes: Non-polymer description
Version 1.3: 2017-03-29
Changes: Non-polymer description
Version 1.4: 2023-09-06
Changes: Data collection, Database references, Derived calculations, Refinement description

3POT | pdb_00003pot

Structural analysis of a Ni(III)-methyl species in methyl-coenzyme M reductase from Methanothermobacter marburgensis

Literature

Structural Analysis of a Ni-Methyl Species in Methyl-Coenzyme M Reductase from Methanothermobacter marburgensis.

Biological Assembly 1

Macromolecules

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Expand

Entity ID: 2

UniProt

Entity Groups

Sequence Annotations

Expand

Entity ID: 3

UniProt

Entity Groups

Sequence Annotations

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Small Molecules

Experimental Data & Validation

Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Entry History

Deposition Data

Revision History (Full details and data files)