PDB-3rgb: Crystal structure of particulate methane monooxygenase from Methy...

ID or keywords:

Entry

Database: PDB / ID: 3rgb

Title

Crystal structure of particulate methane monooxygenase from Methylococcus capsulatus (Bath)

Components

(Methane monooxygenase subunit ...

) x 3

Keywords

OXIDOREDUCTASE /

membrane

Function / homology

Function and homology information

methane monooxygenase (particulate) /

methane monooxygenase complex /

methane monooxygenase activity / methane monooxygenase (soluble) / methane monooxygenase NADH activity / methane monooxygenase NADPH activity / methane metabolic process /

monooxygenase activity /

membrane /

metal ion binding
Similarity search - Function

Biological species

Methylococcus capsulatus (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.8 Å

Authors

Smith, S.M. / Rosenzweig, A.C.

Citation

Journal: Biochemistry / Year: 2011
Title: Crystal Structure and Characterization of Particulate Methane Monooxygenase from Methylocystis species Strain M.
Authors: Smith, S.M. / Rawat, S. / Telser, J. / Hoffman, B.M. / Stemmler, T.L. / Rosenzweig, A.C.

History

Deposition	Apr 8, 2011	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Nov 23, 2011	Provider: repository / Type: Initial release
Revision 1.1	Dec 7, 2011	Group: Database references
Revision 1.2	Feb 21, 2024	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	3rgb.cif.gz	973.6 KB	Display	PDBx/mmCIF format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/rg/3rgb ftp://data.pdbj.org/pub/pdb/validation_reports/rg/3rgb	HTTPS FTP

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Related structure data

Related structure data	3rfrC 1yew 3chx C: citing same article (ref.)
Similar structure data	1yew-d 3rfr-d 4pi0-d 4phz-d 4pi2-d 3chx-d 6rlo-d 6wvv-2 Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#5 - May 2000 Cytochrome c Oxidase similarity (1)

Deposited unit

A: Methane monooxygenase subunit B2

B: Methane monooxygenase subunit A2

C: Methane monooxygenase subunit C2

E: Methane monooxygenase subunit B2

I: Methane monooxygenase subunit B2

J: Methane monooxygenase subunit A2

F: Methane monooxygenase subunit A2

K: Methane monooxygenase subunit C2

G: Methane monooxygenase subunit C2

hetero molecules

325 kDa, 9 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	264.140, 264.140, 150.010
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	94
Space group name H-M	P4₂2₁2

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	I
1	2	E
2	2	I
1	3	B
2	3	J
1	4	F
2	4	J
1	5	C
2	5	K
1	6	G
2	6	K

NCS domain segments:

Component-ID: 1 / Refine code: 1

Dom-ID	Ens-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	HIS	HIS	MET	MET	A	A	33 - 414	33 - 414
2	1	HIS	HIS	MET	MET	I	E	33 - 414	33 - 414
1	2	HIS	HIS	MET	MET	E	D	33 - 414	33 - 414
2	2	HIS	HIS	MET	MET	I	E	33 - 414	33 - 414
1	3	ALA	ALA	GLN	GLN	B	B	7 - 245	7 - 245
2	3	ALA	ALA	GLN	GLN	J	F	7 - 245	7 - 245
1	4	ALA	ALA	GLN	GLN	F	G	7 - 245	7 - 245
2	4	ALA	ALA	GLN	GLN	J	F	7 - 245	7 - 245
1	5	LEU	LEU	LEU	LEU	C	C	45 - 286	45 - 286
2	5	LEU	LEU	LEU	LEU	K	H	45 - 286	45 - 286
1	6	LEU	LEU	MET	MET	G	I	45 - 259	45 - 259
2	6	LEU	LEU	MET	MET	K	H	45 - 259	45 - 259

NCS ensembles :

ID
1
2
3
4
5
6

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Methane monooxygenase subunit ... , 3 types, 9 molecules AEIBJFCKG

#1: Protein	Methane monooxygenase subunit B2 / / pmoB Mass: 46129.746 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Methylococcus capsulatus (bacteria) / Strain: Bath References: UniProt: Q49104, UniProt: G1UBD1*PLUS, methane monooxygenase (soluble)
#2: Protein	Methane monooxygenase subunit A2 / / pmoA Mass: 28445.098 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Methylococcus capsulatus (bacteria) / Strain: Bath References: UniProt: Q607G3, methane monooxygenase (soluble)
#3: Protein	Methane monooxygenase subunit C2 / / pmoC Mass: 33214.180 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Methylococcus capsulatus (bacteria) / Strain: Bath References: UniProt: O05111, UniProt: Q603F1*PLUS, methane monooxygenase (soluble)

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Non-polymers , 4 types, 18 molecules

#4: Chemical	ChemComp-CU / COPPER (II) ION / Copper Mass: 63.546 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cu
#5: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Zn
#6: Chemical	ChemComp-CUA / DINUCLEAR COPPER ION Mass: 127.092 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cu₂
#7: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 4.05 Å³/Da / Density % sol: 69.6 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 8-12% PEG8000, 0.2 M zinc acetate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

ALS

/ Beamline: 5.0.1 / Wavelength: 1.377,1.280

Detector

Type: MARMOSAIC 300 mm CCD / Detector: CCD

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	1.377	1
2	1.28	1

Reflection

Resolution: 2.8→29.46 Å / Num. all: 123120 / Num. obs: 112261 / % possible obs: 91.18 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3

Reflection shell

Resolution: 2.8→2.873 Å / % possible all: 45.47

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Processing

Software

Name	Version	Classification
SOLVE		phasing
REFMAC	5.5.0109	refinement
XDS		data reduction
SCALA		data scaling

Refinement

Method to determine structure:

SAD / Resolution: 2.8→29.46 Å / Cor.coef. F_o:F_c: 0.885 / Cor.coef. F_o:F_c free: 0.857 / SU B: 45.312 / SU ML: 0.357 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.608 / ESU R Free: 0.365 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.29606	5932	5 %	RANDOM
R_work	0.2686	-	-	-
obs	0.26997	112261	91.18 %	-
all	-	123120	-	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 74.167 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.04 Å²	0 Å²	0 Å²
2-	-	0.04 Å²	0 Å²
3-	-	-	-0.08 Å²

Refinement step

Cycle: LAST / Resolution: 2.8→29.46 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	19716	0	18	3	19737

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.015	0.022	20379
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.621	1.93	27822
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.803	5	2424
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	33.594	22.375	897
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	20.863	15	3090
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	17.22	15	126
X-RAY DIFFRACTION	r_chiral_restr	0.122	0.2	3012
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.021	15624
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	0.509	1.5	12132
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	0.998	2	19662
X-RAY DIFFRACTION	r_scbond_it	1.342	3	8247
X-RAY DIFFRACTION	r_scangle_it	2.296	4.5	8160
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-ID	Dom-ID	Auth asym-ID	Number	Type	Rms dev position (Å)	Weight position
1	1	A	3018	tight positional	0.06	0.05
1	2	I	3018	tight positional	0.06	0.05
2	1	E	3018	tight positional	0.06	0.05
2	2	I	3018	tight positional	0.06	0.05
3	1	B	1797	tight positional	0.05	0.05
3	2	J	1797	tight positional	0.05	0.05
4	1	F	1797	tight positional	0.05	0.05
4	2	J	1797	tight positional	0.05	0.05
5	1	C	1760	tight positional	0.04	0.05
5	2	K	1760	tight positional	0.04	0.05
6	1	G	1565	tight positional	0.04	0.05
6	2	K	1565	tight positional	0.04	0.05
1	1	A	3018	tight thermal	0.11	0.5
1	2	I	3018	tight thermal	0.11	0.5
2	1	E	3018	tight thermal	0.11	0.5
2	2	I	3018	tight thermal	0.11	0.5
3	1	B	1797	tight thermal	0.09	0.5
3	2	J	1797	tight thermal	0.09	0.5
4	1	F	1797	tight thermal	0.08	0.5
4	2	J	1797	tight thermal	0.08	0.5
5	1	C	1760	tight thermal	0.06	0.5
5	2	K	1760	tight thermal	0.06	0.5
6	1	G	1565	tight thermal	0.05	0.5
6	2	K	1565	tight thermal	0.05	0.5

LS refinement shell

Resolution: 2.801→2.873 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.497	227	-
R_work	0.501	4053	-
obs	-	-	45.47 %

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°²)	L12 (°²)	L13 (°²)	L22 (°²)	L23 (°²)	L33 (°²)	S11 (Å °)	S12 (Å °)	S13 (Å °)	S21 (Å °)	S22 (Å °)	S23 (Å °)	S31 (Å °)	S32 (Å °)	S33 (Å °)	T11 (Å²)	T12 (Å²)	T13 (Å²)	T22 (Å²)	T23 (Å²)	T33 (Å²)	Origin x (Å)	Origin y (Å)	Origin z (Å)
1	0.9175	-0.6652	-0.1625	1.0311	-0.0271	0.4196	-0.0033	-0.054	-0.0723	0.0479	0.0249	0.0813	-0.0486	-0.0133	-0.0216	0.0675	0.0071	-0.0084	0.1037	0.0271	0.0178	34.93	125.1728	73.5053
2	3.6094	0.1305	0.2609	0.6059	0.0635	0.4553	-0.0218	0.3171	0.108	0.0554	0.069	-0.1533	0.1225	0.0319	-0.0472	0.0888	0.0861	-0.0116	0.1746	0.0459	0.133	62.4959	111.0155	64.8193
3	3.7524	-1.771	0.327	1.9277	0.1289	1.5938	-0.1084	-0.244	0.3919	0.2544	0.1246	-0.3103	-0.1007	-0.0745	-0.0162	0.0914	0.0373	-0.1152	0.1471	-0.0078	0.284	73.0971	127.3594	78.3243
4	1.4884	0.0176	0.8638	0.556	0.2493	1.0393	-0.0196	0.0453	0.1301	0.0158	-0.0141	-0.1493	-0.1176	-0.0108	0.0337	0.0729	-0.0448	-0.0341	0.0645	0.0338	0.065	32.6164	153.2931	41.6825
5	0.4889	-0.0419	-0.0112	0.6122	-0.3857	1.1734	0.0391	0.0263	-0.0688	-0.0383	0.0914	0.1042	0.3097	-0.082	-0.1304	0.1002	-0.0369	-0.0281	0.1481	0.0011	0.0903	30.4984	111.8331	33.5961
6	3.2644	-0.7908	0.3244	0.7545	-0.3	0.9152	-0.0484	-0.2708	0.1321	-0.08	-0.0796	-0.2536	0.2086	0.299	0.128	0.0846	0.0226	0.0726	0.3954	0.0149	0.1375	58.7001	122.5836	22.1735
7	3.5768	-0.5147	-0.9484	0.3416	0.0345	1.5412	-0.0549	0.2131	-0.1205	0.0035	-0.068	-0.2043	-0.0873	0.3207	0.1229	0.1174	-0.1055	-0.0852	0.1783	0.0703	0.3034	62.7471	153.8805	53.2468
8	4.17	0.0387	-1.1477	2.0386	-0.367	2.426	-0.0858	0.1105	-0.1864	-0.1081	-0.042	-0.2791	0.4121	0.116	0.1278	0.2082	0.2321	0.0536	0.4337	-0.0566	0.1646	67.3517	101.4316	28.5977
9	3.0222	0.8339	0.5676	1.8294	0.3179	2.699	-0.1333	0.2502	0.2012	-0.2119	0.0818	-0.1548	-0.0913	0.4103	0.0515	0.1248	-0.1731	0.0908	0.5254	0.1464	0.3891	69.3929	157.8828	30.8542

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	33 - 414
2	X-RAY DIFFRACTION	2	B	7 - 245
3	X-RAY DIFFRACTION	3	C	45 - 286
4	X-RAY DIFFRACTION	3	B	664
5	X-RAY DIFFRACTION	4	E	33 - 414
6	X-RAY DIFFRACTION	5	I	33 - 414
7	X-RAY DIFFRACTION	6	J	7 - 245
8	X-RAY DIFFRACTION	7	F	7 - 245
9	X-RAY DIFFRACTION	8	K	45 - 286
10	X-RAY DIFFRACTION	8	J	664
11	X-RAY DIFFRACTION	9	G	45 - 286
12	X-RAY DIFFRACTION	9	F	664

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Methane monooxygenase subunit ... , 3 types, 9 molecules AEIBJFCKG

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