1YEW | pdb_00001yew

Crystal structure of particulate methane monooxygenase

PDB DOI: https://doi.org/10.2210/pdb1YEW/pdb

Classification: OXIDOREDUCTASE, MEMBRANE PROTEIN
Organism(s): Methylococcus capsulatus str. Bath, Methylococcus capsulatus
Expression System: Escherichia coli
Mutation(s): No
Membrane Protein: Yes OPM PDBTM MemProtMD mpstruc

Deposited: 2004-12-28 Released: 2005-02-08
Deposition Author(s): Lieberman, R.L., Rosenzweig, A.C.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free:
0.302 (Depositor), 0.297 (DCC)
R-Value Work:
0.272 (Depositor)
R-Value Observed:
0.273 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of a membrane-bound metalloenzyme that catalyses the biological oxidation of methane.

Lieberman, R.L., Rosenzweig, A.C.

(2005) Nature 434: 177-182

PubMed: 15674245 Search on PubMed
DOI: https://doi.org/10.1038/nature03311
Primary Citation Related Structures:
1YEW

PubMed Abstract:
Particulate methane monooxygenase (pMMO) is an integral membrane metalloenzyme that catalyses the conversion of methane to methanol. Knowledge of how pMMO performs this extremely challenging chemistry may have an impact on the use of methane as an alternative energy source by facilitating the development of new synthetic catalysts. We have determined the structure of pMMO from the methanotroph Methylococcus capsulatus (Bath) to a resolution of 2.8 A. The enzyme is a trimer with an alpha3beta3gamma3 polypeptide arrangement. Two metal centres, modelled as mononuclear copper and dinuclear copper, are located in soluble regions of each pmoB subunit, which resembles cytochrome c oxidase subunit II. A third metal centre, occupied by zinc in the crystal, is located within the membrane. The structure provides new insight into the molecular details of biological methane oxidation.

Organizational Affiliation

Department of Biochemistry, Molecular Biology, and Cell Biology, Northwestern University, Evanston, Illinois 60208, USA.

Macromolecule Content

Total Structure Weight: 314.57 kDa
Atom Count: 19,772
Modeled Residue Count: 2,424
Deposited Residue Count: 2,754
Unique protein chains: 3

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
particulate methane monooxygenase, B subunit	A, D [auth E], G [auth I]	382	Methylococcus capsulatus str. Bath	Mutation(s): 0 EC: 1.14.18.3 Membrane Entity: Yes
UniProt
Find proteins for G1UBD1 (Methylococcus capsulatus (strain ATCC 33009 / NCIMB 11132 / Bath)) Explore G1UBD1 Go to UniProtKB: G1UBD1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	G1UBD1
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
particulate methane monooxygenase, A subunit	B, E [auth F], H [auth J]	247	Methylococcus capsulatus str. Bath	Mutation(s): 0 EC: 1.14.18.3 Membrane Entity: Yes
UniProt
Find proteins for Q607G3 (Methylococcus capsulatus (strain ATCC 33009 / NCIMB 11132 / Bath)) Explore Q607G3 Go to UniProtKB: Q607G3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q607G3
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
particulate methane monooxygenase subunit C2	C, F [auth G], I [auth K]	289	Methylococcus capsulatus	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for O05111 (Methylococcus capsulatus) Explore O05111 Go to UniProtKB: O05111
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O05111
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CUA Query on CUA Download:Ideal Coordinates CCD File SDF format, chain L [auth A] SDF format, chain S [auth E] SDF format, chain V [auth I] MOL2 format, chain L [auth A] MOL2 format, chain S [auth E] MOL2 format, chain V [auth I] mmCIF format, chain L [auth A] mmCIF format, chain S [auth E] mmCIF format, chain V [auth I]	L [auth A], S [auth E], V [auth I]	DINUCLEAR COPPER ION Cu₂ ALKZAGKDWUSJED-UHFFFAOYSA-N		Interactions Focus chain L [auth A] Focus chain S [auth E] Focus chain V [auth I] Interactions & Density Focus chain L [auth A] Focus chain S [auth E] Focus chain V [auth I]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain K [auth A] SDF format, chain N [auth C] SDF format, chain R [auth E] SDF format, chain W [auth K] SDF format, chain T [auth G] SDF format, chain Q [auth E] SDF format, chain P [auth E] SDF format, chain M [auth C] MOL2 format, chain K [auth A] MOL2 format, chain N [auth C] MOL2 format, chain R [auth E] MOL2 format, chain W [auth K] MOL2 format, chain T [auth G] MOL2 format, chain Q [auth E] MOL2 format, chain P [auth E] MOL2 format, chain M [auth C] mmCIF format, chain K [auth A] mmCIF format, chain N [auth C] mmCIF format, chain R [auth E] mmCIF format, chain W [auth K] mmCIF format, chain T [auth G] mmCIF format, chain Q [auth E] mmCIF format, chain P [auth E] mmCIF format, chain M [auth C]	K [auth A] M [auth C] N [auth C] P [auth E] Q [auth E] K [auth A], M [auth C], N [auth C], P [auth E], Q [auth E], R [auth E], T [auth G], W [auth K]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain K [auth A] Focus chain M [auth C] Focus chain N [auth C] Focus chain P [auth E] Focus chain Q [auth E] Focus chain R [auth E] Focus chain T [auth G] Focus chain W [auth K] Interactions & Density Focus chain K [auth A] Focus chain M [auth C] Focus chain N [auth C] Focus chain P [auth E] Focus chain Q [auth E] Focus chain R [auth E] Focus chain T [auth G] Focus chain W [auth K]
CU Query on CU Download:Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain U [auth I] SDF format, chain O [auth E] MOL2 format, chain J [auth A] MOL2 format, chain U [auth I] MOL2 format, chain O [auth E] mmCIF format, chain J [auth A] mmCIF format, chain U [auth I] mmCIF format, chain O [auth E]	J [auth A], O [auth E], U [auth I]	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Focus chain O [auth E] Focus chain U [auth I] Interactions & Density Focus chain J [auth A] Focus chain O [auth E] Focus chain U [auth I]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free: 0.302 (Depositor), 0.297 (DCC)
R-Value Work: 0.272 (Depositor)
R-Value Observed: 0.273 (Depositor)

Space Group: P 4₂ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 264.14	α = 90
b = 264.14	β = 90
c = 150.005	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MAR345	data collection
XDS	data scaling
SOLVE	phasing

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2005-02-08

Deposition Author(s):

Lieberman, R.L.

Rosenzweig, A.C.

Revision History (Full details and data files)

Version 1.0: 2005-02-08
Type: Initial release
Version 1.1: 2008-04-30
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Advisory, Source and taxonomy, Version format compliance
Version 1.3: 2017-10-11
Changes: Refinement description
Version 1.4: 2024-02-14
Changes: Data collection, Database references, Derived calculations, Refinement description