1MMO

CRYSTAL STRUCTURE OF A BACTERIAL NON-HAEM IRON HYDROXYLASE THAT CATALYSES THE BIOLOGICAL OXIDATION OF METHANE

PDB DOI: https://doi.org/10.2210/pdb1MMO/pdb

Classification: OXIDOREDUCTASE (MONOOXYGENASE)
Organism(s): Methylococcus capsulatus
Mutation(s): No

Deposited: 1994-02-22 Released: 1995-02-27
Deposition Author(s): Rosenzweig, A.C., Frederick, C.A., Lippard, S.J., Nordlund, P.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Work: 0.170
R-Value Observed: 0.170

wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of a bacterial non-haem iron hydroxylase that catalyses the biological oxidation of methane.

Rosenzweig, A.C., Frederick, C.A., Lippard, S.J., Nordlund, P.

(1993) Nature 366: 537-543

PubMed: 8255292 Search on PubMed
DOI: https://doi.org/10.1038/366537a0
Primary Citation of Related Structures:
1MMO

PubMed Abstract:
The 2.2 A crystal structure of the 251K alpha 2 beta 2 gamma 2 dimeric hydroxylase protein of methane monooxygenase from Methylococcus capsulatus (Bath) reveals the geometry of the catalytic di-iron core. The two iron atoms are bridged by exogenous hydroxide and acetate ligands and further coordinated by four glutamate residues, two histidine residues and a water molecule. The dinuclear iron centre lies in a hydrophobic active-site cavity for binding methane. An extended canyon runs between alpha beta pairs, which have many long alpha-helices, for possible docking of the reductase and coupling proteins required for catalysis.

Organizational Affiliation

Department of Chemistry, Massachusetts Institute of Technology, Cambridge 02139.

Macromolecule Content

Total Structure Weight: 245.69 kDa
Atom Count: 18,217
Modelled Residue Count: 2,116
Deposited Residue Count: 2,116
Unique protein chains: 3

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
METHANE MONOOXYGENASE HYDROLASE (BETA CHAIN)	A [auth B], B [auth C]	384	Methylococcus capsulatus	Mutation(s): 0 EC: 1.14.13.25
UniProt
Find proteins for P18798 (Methylococcus capsulatus (strain ATCC 33009 / NCIMB 11132 / Bath)) Explore P18798 Go to UniProtKB: P18798
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P18798
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
METHANE MONOOXYGENASE HYDROLASE (ALPHA CHAIN)	C [auth D], D [auth E]	512	Methylococcus capsulatus	Mutation(s): 0 EC: 1.14.13.25
UniProt
Find proteins for P22869 (Methylococcus capsulatus (strain ATCC 33009 / NCIMB 11132 / Bath)) Explore P22869 Go to UniProtKB: P22869
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P22869
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
METHANE MONOOXYGENASE HYDROLASE (GAMMA CHAIN)	E [auth G], F [auth H]	162	Methylococcus capsulatus	Mutation(s): 0 EC: 1.14.13.25
UniProt
Find proteins for P11987 (Methylococcus capsulatus (strain ATCC 33009 / NCIMB 11132 / Bath)) Explore P11987 Go to UniProtKB: P11987
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P11987
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ACY Query on ACY Download Ideal Coordinates CCD File SDF format, chain L [auth E] SDF format, chain I [auth D] MOL2 format, chain L [auth E] MOL2 format, chain I [auth D]	I [auth D], L [auth E]	ACETIC ACID C₂ H₄ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-N		Interactions Focus chain I [auth D] Focus chain L [auth E]
FE Query on FE Download Ideal Coordinates CCD File SDF format, chain G [auth D] SDF format, chain J [auth E] SDF format, chain K [auth E] SDF format, chain H [auth D] MOL2 format, chain G [auth D] MOL2 format, chain J [auth E] MOL2 format, chain K [auth E] MOL2 format, chain H [auth D]	G [auth D], H [auth D], J [auth E], K [auth E]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N		Interactions Focus chain G [auth D] Focus chain H [auth D] Focus chain J [auth E] Focus chain K [auth E]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Work: 0.170
R-Value Observed: 0.170
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.6	α = 90
b = 110.1	β = 90
c = 333.5	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	model building
X-PLOR	refinement
X-PLOR	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 1995-02-27

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 1995-02-27
Type: Initial release
Version 1.1: 2008-03-03
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2017-11-29
Changes: Derived calculations, Other
Version 1.4: 2024-02-14
Changes: Data collection, Database references, Derived calculations