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- PDB-1xmf: Structure of Mn(II)-Soaked Apo Methane Monooxygenase Hydroxylase ... -

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Basic information

Entry
Database: PDB / ID: 1xmf
TitleStructure of Mn(II)-Soaked Apo Methane Monooxygenase Hydroxylase Crystals from M. capsulatus (Bath)
Components(Methane monooxygenase component A ...) x 3
KeywordsOXIDOREDUCTASE / dimanganese / MMOH / diiron / methane / four-helix bundle
Function / homology
Function and homology information


methane metabolic process / methane monooxygenase (soluble) / methane monooxygenase [NAD(P)H] activity / one-carbon metabolic process / metal ion binding
Similarity search - Function
Methane monooxygenase, gamma chain, domain 1 / Methane monooxygenase, gamma chain, domain 2 / Methane monooxygenase, gamma chain / Methane monooxygenase, gamma chain, domain 1 / Methane monooxygenase, gamma chain, domain 2 / Methane monooxygenase, gamma chain superfamily / : / : / Methane monooxygenase, hydrolase gamma chain / Methane/phenol monooxygenase, hydroxylase component ...Methane monooxygenase, gamma chain, domain 1 / Methane monooxygenase, gamma chain, domain 2 / Methane monooxygenase, gamma chain / Methane monooxygenase, gamma chain, domain 1 / Methane monooxygenase, gamma chain, domain 2 / Methane monooxygenase, gamma chain superfamily / : / : / Methane monooxygenase, hydrolase gamma chain / Methane/phenol monooxygenase, hydroxylase component / Propane/methane/phenol/toluene hydroxylase / Methane/Phenol/Alkene Hydroxylase / Ribonucleotide Reductase, subunit A / Ribonucleotide Reductase, subunit A / Monooxygenase / Ribonucleotide reductase-like / Ferritin-like superfamily / Up-down Bundle / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
: / Methane monooxygenase component A gamma chain / Methane monooxygenase component A beta chain / Methane monooxygenase component A alpha chain
Similarity search - Component
Biological speciesMethylococcus capsulatus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.32 Å
AuthorsSazinsky, M.H. / Merkx, M. / Cadieux, E. / Tang, S. / Lippard, S.J.
CitationJournal: Biochemistry / Year: 2004
Title: Preparation and X-ray Structures of Metal-Free, Dicobalt and Dimanganese Forms of Soluble Methane Monooxygenase Hydroxylase from Methylococcus capsulatus (Bath)
Authors: Sazinsky, M.H. / Merkx, M. / Cadieux, E. / Tang, S. / Lippard, S.J.
History
DepositionOct 2, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 18, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Aug 23, 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 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / 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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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_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_ref_seq_dif.details / _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: Methane monooxygenase component A alpha chain
B: Methane monooxygenase component A alpha chain
C: Methane monooxygenase component A beta chain
D: Methane monooxygenase component A beta chain
E: Methane monooxygenase component A gamma chain
F: Methane monooxygenase component A gamma chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)251,53814
Polymers251,1586
Non-polymers3808
Water20,0511113
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area41760 Å2
ΔGint-227 kcal/mol
Surface area60610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.820, 171.679, 220.275
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Cell settingorthorhombic
Space group name H-MP212121

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Components

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Methane monooxygenase component A ... , 3 types, 6 molecules ABCDEF

#1: Protein Methane monooxygenase component A alpha chain / E.C.1.14.13.25 / Methane hydroxylase alpha chain


Mass: 60719.113 Da / Num. of mol.: 2 / Fragment: alpha subunit / Source method: isolated from a natural source / Details: gene MMOX / Source: (natural) Methylococcus capsulatus (bacteria) / Strain: Bath
References: UniProt: P22869, methane monooxygenase (soluble)
#2: Protein Methane monooxygenase component A beta chain / E.C.1.14.13.25 / Methane hydroxylase beta chain


Mass: 45111.504 Da / Num. of mol.: 2 / Fragment: beta subunit / Source method: isolated from a natural source / Details: gene MMOY / Source: (natural) Methylococcus capsulatus (bacteria) / Strain: Bath
References: UniProt: P18798, methane monooxygenase (soluble)
#3: Protein Methane monooxygenase component A gamma chain / E.C.1.14.13.25 / Methane hydroxylase gamma chain


Mass: 19748.537 Da / Num. of mol.: 2 / Fragment: gamma subunit / Source method: isolated from a natural source / Details: gene MMOZ / Source: (natural) Methylococcus capsulatus (bacteria) / Strain: Bath
References: UniProt: P11987, methane monooxygenase (soluble)

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Non-polymers , 3 types, 1121 molecules

#4: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#5: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1113 / 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: 2.59 Å3/Da / Density % sol: 52.2 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: MOPS, CaCl2, PEG8000, glycerol, azide, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: May 1, 2002
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 2.3→30 Å / Num. all: 132599 / Num. obs: 117119 / % possible obs: 91.7 % / Observed criterion σ(I): 1 / Redundancy: 2.3 % / Biso Wilson estimate: 19.1 Å2 / Rmerge(I) obs: 0.058 / Rsym value: 0.058 / Net I/σ(I): 11.3
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.295 / Mean I/σ(I) obs: 2.8 / Rsym value: 0.295 / % possible all: 90.7

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Processing

Software
NameClassification
MAR345data collection
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB 1FZ1

1fz1


Resolution: 2.32→28.76 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 415690.79 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.263 3543 3.6 %RANDOM
Rwork0.219 ---
all0.209 98559 --
obs0.2191 98559 84.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 38.0333 Å2 / ksol: 0.330296 e/Å3
Displacement parametersBiso mean: 43.2 Å2
Baniso -1Baniso -2Baniso -3
1-23.44 Å20 Å20 Å2
2---5.85 Å20 Å2
3----17.59 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.38 Å0.31 Å
Luzzati d res low-5 Å
Luzzati sigma a0.44 Å0.4 Å
Refinement stepCycle: LAST / Resolution: 2.32→28.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17315 0 8 1113 18436
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d20.2
X-RAY DIFFRACTIONc_improper_angle_d0.75
X-RAY DIFFRACTIONc_mcbond_it1.161.5
X-RAY DIFFRACTIONc_mcangle_it1.882
X-RAY DIFFRACTIONc_scbond_it1.72
X-RAY DIFFRACTIONc_scangle_it2.442.5
LS refinement shellResolution: 2.32→2.47 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.344 506 3.5 %
Rwork0.32 14063 -
obs--75.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2ION.PARAMWATER.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMION.TOP

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