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- PDB-1xvc: soluble methane monooxygenase hydroxylase: 8-bromooctanol soaked ... -

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Basic information

Entry
Database: PDB / ID: 1xvc
Titlesoluble methane monooxygenase hydroxylase: 8-bromooctanol soaked structure
Components(Methane monooxygenase component A ...) x 3
KeywordsOXIDOREDUCTASE / methane / diiron / four-helix bundle / product binding / cavity
Function / homology
Function and homology information


methane metabolic process / methane monooxygenase (soluble) / : / : / 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 / Propane/methane/phenol/toluene hydroxylase / Methane/Phenol/Alkene Hydroxylase ...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
1-BROMOPENTANE / BROMOMETHANE / BROMIDE ION / : / FORMIC ACID / 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 Å
AuthorsSazinsky, M.H. / Lippard, S.J.
CitationJournal: J.Am.Chem.Soc. / Year: 2005
Title: Product Bound Structures of the Soluble Methane Monooxygenase Hydroxylase from Methylococcus capsulatus (Bath): Protein Motion in the Alpha-Subunit
Authors: Sazinsky, M.H. / Lippard, S.J.
History
DepositionOct 27, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 3, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 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_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_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_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_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)252,24215
Polymers251,5676
Non-polymers6759
Water17,114950
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area42610 Å2
ΔGint-233 kcal/mol
Surface area60870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.411, 171.031, 221.434
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
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 / Methane hydroxylase


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


Mass: 45184.660 Da / Num. of mol.: 2 / Fragment: beta subunit / Source method: isolated from a natural source / Source: (natural) Methylococcus capsulatus (bacteria)
References: UniProt: P18798, methane monooxygenase (soluble)
#3: Protein Methane monooxygenase component A gamma chain / Methane hydroxylase


Mass: 19879.732 Da / Num. of mol.: 2 / Fragment: gamma subunit / Source method: isolated from a natural source / Source: (natural) Methylococcus capsulatus (bacteria)
References: UniProt: P11987, methane monooxygenase (soluble)

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Non-polymers , 6 types, 959 molecules

#4: Chemical
ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe
#5: Chemical ChemComp-BR / BROMIDE ION / Methane hydroxylase


Mass: 79.904 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Br / References: methane monooxygenase (soluble)
#6: Chemical ChemComp-5BR / 1-BROMOPENTANE


Mass: 151.045 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H11Br
#7: Chemical ChemComp-BMM / BROMOMETHANE


Mass: 94.939 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH3Br
#8: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O2
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 950 / 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: 2.3 Å3/Da / Density % sol: 55.1 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: MOPS, PEG 8000, NaN3, CaCl2, glycerol, 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: BL11-1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: May 1, 2002
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. all: 176340 / Num. obs: 176340 / % possible obs: 97.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.3 % / Biso Wilson estimate: 17.8 Å2 / Rmerge(I) obs: 0.074 / Rsym value: 0.074 / Net I/σ(I): 12.8
Reflection shellResolution: 2→2.08 Å / Rmerge(I) obs: 0.262 / Mean I/σ(I) obs: 4.1 / Rsym value: 0.262 / % possible all: 83.7

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Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1mty

1mty


Resolution: 2→29.79 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 453424.54 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.234 5913 3.5 %RANDOM
Rwork0.206 ---
obs0.206 166594 92 %-
all-176340 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 50.829 Å2 / ksol: 0.34696 e/Å3
Displacement parametersBiso mean: 37 Å2
Baniso -1Baniso -2Baniso -3
1-21.47 Å20 Å20 Å2
2---6.36 Å20 Å2
3----15.11 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.29 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.31 Å0.3 Å
Refinement stepCycle: LAST / Resolution: 2→29.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17317 0 14 953 18284
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d20.1
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.79
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.151.5
X-RAY DIFFRACTIONc_mcangle_it1.732
X-RAY DIFFRACTIONc_scbond_it1.882
X-RAY DIFFRACTIONc_scangle_it2.622.5
LS refinement shellResolution: 2→2.08 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.322 545 3.6 %
Rwork0.308 14747 -
obs--48.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2ION.PARAMWATER.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMION.TOP
X-RAY DIFFRACTION4LIGANDS.PARAMLIGANDS.TOP

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