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- PDB-4pi0: Crystal structure of particulate methane monooxygenase from Methy... -

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Basic information

Entry
Database: PDB / ID: 4pi0
TitleCrystal structure of particulate methane monooxygenase from Methylocystis sp. ATCC 49242 (Rockwell) soaked in copper
Components
  • Particulate methane monooxygenase subunit AMethane monooxygenase (particulate)
  • Particulate methane monooxygenase subunit BMethane monooxygenase (particulate)
  • Particulate methane monooxygenase subunit CMethane monooxygenase (particulate)
  • unknown peptide
KeywordsOXIDOREDUCTASE / Bacterial Proteins / Binding Sites / Copper / Zinc / Methylocystaceae / Oxygenases / Protein Binding
Function / homology
Function and homology information


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 / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 / Helix Hairpins / Jelly Rolls / Up-down Bundle ...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 / 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
Biological speciesMethylocystis sp. ATCC 49242 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.15 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

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


Theoretical massNumber of molelcules
Total (without water)317,41618
Polymers317,03412
Non-polymers3816
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area61140 Å2
ΔGint-603 kcal/mol
Surface area86880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.361, 184.739, 188.637
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
15K
25C
16G
26C

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
111HISHISALAALAAG29 - 41629 - 416
211HISHISALAALAEE29 - 41629 - 416
112HISHISALAALAIH29 - 41629 - 416
212HISHISALAALAEE29 - 41629 - 416
113GLYGLYILEILEJK11 - 25211 - 252
213GLYGLYILEILEFC11 - 25211 - 252
114GLYGLYILEILEBL11 - 25211 - 252
214GLYGLYILEILEFC11 - 25211 - 252
115GLUGLUPROPROKD16 - 19516 - 195
215GLUGLUPROPROCI16 - 19516 - 195
125TRPTRPGLUGLUKD226 - 256226 - 256
225TRPTRPGLUGLUCI226 - 256226 - 256
116GLUGLUPROPROGJ16 - 19516 - 195
216GLUGLUPROPROCI16 - 19516 - 195
126TRPTRPGLUGLUGJ226 - 256226 - 256
226TRPTRPGLUGLUCI226 - 256226 - 256

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein/peptide unknown peptide


Mass: 2145.636 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Methylocystis sp. ATCC 49242 (bacteria)
#2: Protein Particulate methane monooxygenase subunit A / Methane monooxygenase (particulate) / 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)
#3: Protein Particulate methane monooxygenase subunit C / Methane monooxygenase (particulate) / 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)
#4: Protein Particulate methane monooxygenase subunit B / Methane monooxygenase (particulate) / 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)
#5: Chemical
ChemComp-CU / COPPER (II) ION / Copper


Mass: 63.546 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cu

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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: 3.33 Å3/Da / Density % sol: 63.04 %
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 dihydrate

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.33765 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 9, 2012
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.33765 Å / Relative weight: 1
ReflectionResolution: 3.15→50 Å / Num. obs: 55808 / % possible obs: 77.8 % / Redundancy: 13.7 % / Net I/σ(I): 21.5

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Processing

Software
NameVersionClassificationNB
REFMAC5.8.0049refinement
PDB_EXTRACT3.14data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3RFR

3rfr


Resolution: 3.15→50 Å / Cor.coef. Fo:Fc: 0.854 / Cor.coef. Fo:Fc free: 0.795 / SU B: 24.467 / SU ML: 0.424 / Cross valid method: THROUGHOUT / σ(F): 3 / ESU R Free: 0.607 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.2799 2796 5 %RANDOM
Rwork0.2211 53012 --
obs0.2241 55808 78.21 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 227.82 Å2 / Biso mean: 57.517 Å2 / Biso min: 16.97 Å2
Baniso -1Baniso -2Baniso -3
1--0.08 Å2-0 Å2-0 Å2
2--0.52 Å20 Å2
3----0.44 Å2
Refinement stepCycle: final / Resolution: 3.15→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20624 0 6 0 20630
Biso mean--78.93 --
Num. residues----2613
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.01921251
X-RAY DIFFRACTIONr_angle_refined_deg1.6831.9329016
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7352598
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.07622.65902
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.747153185
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.66115126
X-RAY DIFFRACTIONr_chiral_restr0.120.23209
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02116226
X-RAY DIFFRACTIONr_mcbond_it4.5365.59910437
X-RAY DIFFRACTIONr_mcangle_it7.4288.37713020
X-RAY DIFFRACTIONr_scbond_it4.7815.84110814
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)
1A302613.92
2I302613.58
3J19625.04
4B19629.99
5K172310.25
6G17237.88
LS refinement shellResolution: 3.146→3.228 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.624 24 -
Rwork0.344 322 -
all-346 -
obs--6.67 %

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