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- PDB-3rfr: Crystal Structure of particulate methane monooxygenase (pMMO) fro... -

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Basic information

Entry
Database: PDB / ID: 3rfr
TitleCrystal Structure of particulate methane monooxygenase (pMMO) from Methylocystis sp. strain M
Components
  • PmoA
  • PmoB
  • PmoC
  • peptide
KeywordsOXIDOREDUCTASE / membrane
Function / homology
Function and homology information


membrane => GO:0016020 / metal ion binding
Similarity search - Function
Particulate methane monooxygenase subunit c2. Chain: C / Helix hairpin bin / particulate methane monooxygenase, chain B / Ammonia/particulate methane monooxygenase, subunit A / Particulate methane monooxygenase, b subunit. Chain: A, domain 3 / Particulate methane monooxygenase, b subunit. Chain: A, domain 1 / Ammonia monooxygenase/particulate methane monooxygenase, subunit A / Ammonia monooxygenase/particulate methane monooxygenase, subunit C / Ammonia/methane monooxygenase, subunit B, hairpin domain superfamily / Ammonia/methane monooxygenase, subunit B, C-terminal ...Particulate methane monooxygenase subunit c2. Chain: C / Helix hairpin bin / particulate methane monooxygenase, chain B / Ammonia/particulate methane monooxygenase, subunit A / Particulate methane monooxygenase, b subunit. Chain: A, domain 3 / Particulate methane monooxygenase, b subunit. Chain: A, domain 1 / Ammonia monooxygenase/particulate methane monooxygenase, subunit A / Ammonia monooxygenase/particulate methane monooxygenase, subunit C / Ammonia/methane monooxygenase, subunit B, hairpin domain superfamily / Ammonia/methane monooxygenase, subunit B, C-terminal / Ammonia monooxygenase/particulate methane monooxygenase, subunit C domain superfamily / Ammonia/particulate methane monooxygenase, subunit A superfamily / Ammonia monooxygenase / Ammonia monooxygenase/methane monooxygenase, subunit C / Ammonia monooxygenase/particulate methane monooxygenase, subunit B / Ammonia/methane monooxygenase, subunitB, N-terminal / Monooxygenase subunit B protein / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 / Helix Hairpins / Jelly Rolls / Up-down Bundle / Immunoglobulin-like / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
COPPER (II) ION / DINUCLEAR COPPER ION / PmoA / PmoB / PmoC
Similarity search - Component
Biological speciesMethylocystis sp. M (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.68 Å
AuthorsSmith, S.M. / Rosenzweig, A.C.
CitationJournal: 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
DepositionApr 6, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 23, 2011Provider: repository / Type: Initial release
Revision 1.1Dec 7, 2011Group: Database references
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 1.3Feb 21, 2024Group: 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_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PmoB
D: peptide
H: peptide
J: PmoA
B: PmoA
F: PmoA
C: PmoC
G: PmoC
K: PmoC
E: PmoB
I: PmoB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)313,54023
Polymers312,69811
Non-polymers84312
Water543
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area60230 Å2
ΔGint-800 kcal/mol
Surface area88340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.718, 178.310, 183.147
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11E
21A
12I
22A
13F
23B
14J
24B
15G
25C
16K
26C

NCS domain segments:

Component-ID: 1 / Refine code: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11HISHISVALVALEJ29 - 41429 - 414
21HISHISVALVALAA29 - 41429 - 414
12HISHISVALVALIK29 - 41429 - 414
22HISHISVALVALAA29 - 41429 - 414
13GLYGLYILEILEFF11 - 25211 - 252
23GLYGLYILEILEBE11 - 25211 - 252
14GLYGLYILEILEJD11 - 25211 - 252
24GLYGLYILEILEBE11 - 25211 - 252
15GLUGLUALAALAGH16 - 25216 - 252
25GLUGLUALAALACG16 - 25216 - 252
16GLUGLUALAALAKI16 - 25216 - 252
26GLUGLUALAALACG16 - 25216 - 252

NCS ensembles :
ID
1
2
3
4
5
6

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Components

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Protein , 3 types, 9 molecules AEIJBFCGK

#1: Protein PmoB


Mass: 45630.996 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Methylocystis sp. M (bacteria) / References: UniProt: Q9KX36
#3: Protein PmoA


Mass: 28648.486 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Methylocystis sp. M (bacteria) / References: UniProt: O06122
#4: Protein PmoC


Mass: 29040.699 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Methylocystis sp. M (bacteria) / References: UniProt: Q9KX37

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Protein/peptide , 1 types, 2 molecules DH

#2: Protein/peptide peptide


Mass: 1368.494 Da / Num. of mol.: 2 / Source method: obtained synthetically

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Non-polymers , 4 types, 15 molecules

#5: Chemical ChemComp-CUA / DINUCLEAR COPPER ION


Mass: 127.092 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cu2
#6: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Zn
#7: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.81 Å3/Da / Density % sol: 56.26 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1 M MES, 18% PEG750 MME, 0.03 M glycyl-glycyl-glycine, 0.01 M zinc sulfate , pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.37765
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 24, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.37765 Å / Relative weight: 1
ReflectionResolution: 2.68→45.79 Å / Num. all: 94159 / Num. obs: 83726 / % possible obs: 88.92 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 12.6 %
Reflection shellResolution: 2.684→2.753 Å / % possible all: 54.44

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.68→45.79 Å / Cor.coef. Fo:Fc: 0.896 / Cor.coef. Fo:Fc free: 0.863 / SU B: 26.805 / SU ML: 0.341 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.907 / ESU R Free: 0.393 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28129 4440 5 %RANDOM
Rwork0.24929 ---
obs0.25094 83726 88.92 %-
all-94159 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 66.477 Å2
Baniso -1Baniso -2Baniso -3
1-0.23 Å20 Å20 Å2
2---0.02 Å20 Å2
3----0.21 Å2
Refinement stepCycle: LAST / Resolution: 2.68→45.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20208 0 13 3 20224
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.02220838
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7351.9328438
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.33252537
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.49222.603899
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.178153146
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.91415132
X-RAY DIFFRACTIONr_chiral_restr0.1270.23121
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02115946
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.631.512633
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.209220379
X-RAY DIFFRACTIONr_scbond_it1.73138205
X-RAY DIFFRACTIONr_scangle_it2.9654.58059
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11E3013tight positional0.060.05
12A3013tight positional0.060.05
21I3013tight positional0.070.05
22A3013tight positional0.070.05
31F1965tight positional0.060.05
32B1965tight positional0.060.05
41J1965tight positional0.070.05
42B1965tight positional0.070.05
51G1696tight positional0.050.05
52C1696tight positional0.050.05
61K1696tight positional0.050.05
62C1696tight positional0.050.05
11E3013tight thermal0.180.5
12A3013tight thermal0.180.5
21I3013tight thermal0.20.5
22A3013tight thermal0.20.5
31F1965tight thermal0.140.5
32B1965tight thermal0.140.5
41J1965tight thermal0.170.5
42B1965tight thermal0.170.5
51G1696tight thermal0.10.5
52C1696tight thermal0.10.5
61K1696tight thermal0.10.5
62C1696tight thermal0.10.5
LS refinement shellResolution: 2.684→2.753 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.462 194 -
Rwork0.435 3740 -
obs--54.44 %
Refinement TLS params.

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

IDL11 (°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)
10.3083-0.1579-0.17860.4060.30551.1326-0.03160.0465-0.01550.2026-0.0093-0.1735-0.11370.04640.04090.315-0.0103-0.06370.02160.00840.17756.047423.490947.3555
20000000000000000.1643000.164300.1643000
30.1008-0.16260.27780.3791-0.3211.05070.04540.0092-0.0504-0.1602-0.02990.0973-0.0656-0.0297-0.01550.14950.0851-0.05410.1621-0.02490.264538.9065-22.195921.5745
40.4393-0.09040.43590.45430.07160.8920.04260.11210.0037-0.0177-0.0768-0.16060.02880.03610.03430.1888-0.00010.020.20470.0090.248257.69915.669417.1718
50.5815-0.14440.47520.8041-0.08831.29950.08070.1356-0.0610.1173-0.0390.0297-0.1194-0.1263-0.04170.09850.10750.02140.2672-0.00340.173817.557713.545931.5343
60.58480.1261.04750.65410.88042.8420.0260.13620.04070.0055-0.0518-0.0719-0.06960.03950.02580.25510.007-0.02660.10390.02340.112541.298433.779613.3686
70.6066-0.71630.73571.8516-0.38153.05330.16620.0776-0.2445-0.1432-0.23030.2410.1115-0.22940.06420.05980.059-0.08360.3655-0.07330.2086.4085-6.785123.4098
81.0518-0.00171.07090.6679-0.49822.84270.0013-0.03730.0465-0.0482-0.0807-0.0678-0.07840.17610.07940.22070.14690.00540.2246-0.01610.094556.5211-18.12554.8981
90.5598-0.66390.13370.8004-0.23290.7305-0.1359-0.114-0.01430.14380.13460.02840.0617-0.19050.00130.20440.06490.03380.14480.02240.127124.3098-3.079257.0189
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A29 - 414
2X-RAY DIFFRACTION3J11 - 252
3X-RAY DIFFRACTION4B11 - 252
4X-RAY DIFFRACTION5F11 - 252
5X-RAY DIFFRACTION6C16 - 252
6X-RAY DIFFRACTION7G16 - 252
7X-RAY DIFFRACTION8K16 - 252
8X-RAY DIFFRACTION9E29 - 414

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