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- PDB-4phz: Crystal structure of particulate methane monooxygenase from Methy... -

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Basic information

Entry
Database: PDB / ID: 4phz
TitleCrystal structure of particulate methane monooxygenase from Methylocystis sp. ATCC 49242 (Rockwell)
Components
  • (Particulate methane monooxygenase subunit ...) x 3
  • unknown peptide
KeywordsOXIDOREDUCTASE / Bacterial Proteins / Binding Sites / Copper / Zinc / Methylocystaceae / Oxygenases / Protein Binding
Function / homology
Function and homology information


Helix hairpin bin / Particulate methane monooxygenase subunit c2. Chain: C / 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 / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 / Helix Hairpins / Jelly Rolls / Up-down Bundle ...Helix hairpin bin / Particulate methane monooxygenase subunit c2. Chain: C / 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 / 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 / Chem-PGT
Similarity search - Component
Biological speciesMethylocystis sp. ATCC 49242 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.59 Å
AuthorsSirajuddin, S. / Rosenzweig, A.C.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM070473 United States
CitationJournal: J.Biol.Chem. / Year: 2014
Title: Effects of zinc on particulate methane monooxygenase activity and structure.
Authors: Sirajuddin, S. / Barupala, D. / Helling, S. / Marcus, K. / Stemmler, T.L. / Rosenzweig, A.C.
History
DepositionMay 7, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 25, 2014Provider: repository / Type: Initial release
Revision 1.1Jul 9, 2014Group: Database references
Revision 1.2Oct 1, 2014Group: Database references
Revision 1.3Apr 6, 2016Group: Source and taxonomy
Revision 1.4Sep 6, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.5Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.6Sep 27, 2023Group: 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_initial_refinement_model / struct_conn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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
Revision 1.7Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
D: unknown peptide
H: unknown peptide
K: Particulate methane monooxygenase subunit C
N: unknown peptide
A: Particulate methane monooxygenase subunit B
B: Particulate methane monooxygenase subunit A
E: Particulate methane monooxygenase subunit B
I: Particulate methane monooxygenase subunit B
F: Particulate methane monooxygenase subunit A
J: Particulate methane monooxygenase subunit A
C: Particulate methane monooxygenase subunit C
G: Particulate methane monooxygenase subunit C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)320,16422
Polymers316,77912
Non-polymers3,38510
Water2,108117
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area66790 Å2
ΔGint-656 kcal/mol
Surface area85670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.462, 184.531, 189.417
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21E
12I
22E
13J
23F
14B
24F
15C
25K
16G
26K

NCS domain segments:

Refine code: 1

Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111HISHISALAALAAE29 - 41629 - 416
211HISHISALAALAEG29 - 41629 - 416
112HISHISALAALAIH29 - 41629 - 416
212HISHISALAALAEG29 - 41629 - 416
113ALAALAILEILEJJ9 - 2529 - 252
213ALAALAILEILEFI9 - 2529 - 252
114ALAALAILEILEBF9 - 2529 - 252
214ALAALAILEILEFI9 - 2529 - 252
115GLUGLUASNASNCK16 - 19616 - 196
215GLUGLUASNASNKC16 - 19616 - 196
125TRPTRPGLUGLUCK226 - 256226 - 256
225TRPTRPGLUGLUKC226 - 256226 - 256
116GLUGLUASNASNGL16 - 19616 - 196
216GLUGLUASNASNKC16 - 19616 - 196
126TRPTRPGLUGLUGL226 - 256226 - 256
226TRPTRPGLUGLUKC226 - 256226 - 256

NCS ensembles :
ID
1
2
3
4
5
6

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Components

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Protein/peptide , 1 types, 3 molecules DHN

#1: Protein/peptide unknown peptide


Mass: 2060.531 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Methylocystis sp. ATCC 49242 (bacteria)

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Particulate methane monooxygenase subunit ... , 3 types, 9 molecules KCGAEIBFJ

#2: Protein Particulate methane monooxygenase subunit C / pmoC


Mass: 29231.023 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Methylocystis sp. ATCC 49242 (bacteria) / References: methane monooxygenase (particulate)
#3: Protein Particulate methane monooxygenase subunit B / pmoB


Mass: 45741.105 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Methylocystis sp. ATCC 49242 (bacteria) / References: methane monooxygenase (particulate)
#4: Protein Particulate methane monooxygenase subunit A / pmoA


Mass: 28560.311 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Methylocystis sp. ATCC 49242 (bacteria) / References: methane monooxygenase (particulate)

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Non-polymers , 3 types, 127 molecules

#5: Chemical
ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cu
#6: Chemical
ChemComp-PGT / (1S)-2-{[{[(2R)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE / PHOSPHATIDYLGLYCEROL / 1-PALMITOYL-2-OLEOYL-SN-GLYCERO-3-[PHOSPHO-RAC-(1-GLYCEROL)](SODIUM SALT)


Mass: 751.023 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C40H79O10P / Comment: phospholipid*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 117 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationN

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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: 3 Å3/Da / Density % sol: 58.99 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 10% PEG3000, 0.1 M sodium cacodylate trihydrate, pH 6.5, 0.2 M magnesium formate

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.37765 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 16, 2011
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.37765 Å / Relative weight: 1
ReflectionResolution: 2.59→50 Å / Num. obs: 93278 / % possible obs: 72.6 % / Redundancy: 14.4 % / Net I/σ(I): 18.9

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Processing

Software
NameVersionClassificationNB
REFMAC5.6.0117refinement
PDB_EXTRACT3.14data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3RFR

3rfr


Resolution: 2.59→50 Å / Cor.coef. Fo:Fc: 0.883 / Cor.coef. Fo:Fc free: 0.827 / SU B: 12.917 / SU ML: 0.276 / Cross valid method: THROUGHOUT / σ(F): 3 / ESU R: 1.391 / ESU R Free: 0.411 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.2887 4678 5 %RANDOM
Rwork0.2367 88600 --
obs0.2393 93278 72.32 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 155.57 Å2 / Biso mean: 42.225 Å2 / Biso min: 5.65 Å2
Baniso -1Baniso -2Baniso -3
1--0.3 Å20 Å20 Å2
2--0.92 Å20 Å2
3----0.61 Å2
Refinement stepCycle: final / Resolution: 2.59→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20526 0 211 117 20854
Biso mean--64.84 23.67 -
Num. residues----2598
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0221350
X-RAY DIFFRACTIONr_angle_refined_deg1.6661.93829106
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.63152583
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.00422.642897
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.147153176
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.19815126
X-RAY DIFFRACTIONr_chiral_restr0.110.23207
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02116137
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION / Type: TIGHT THERMAL / Weight position: 0.5

Ens-IDAuth asym-IDNumberRms dev position (Å)
1A302611.51
2I302611.52
3J19744.06
4B19748.77
5C17318.35
6G17316.17
LS refinement shellResolution: 2.586→2.654 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.494 15 -
Rwork0.432 284 -
all-299 -
obs--3.19 %

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