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- PDB-1fz5: METHANE MONOOXYGENASE HYDROXYLASE, FORM II CRYSTALLIZED ANAEROBIC... -

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Basic information

Entry
Database: PDB / ID: 1fz5
TitleMETHANE MONOOXYGENASE HYDROXYLASE, FORM II CRYSTALLIZED ANAEROBICALLY FROM REDUCED ENZYME
Components(METHANE MONOOXYGENASE COMPONENT A, ...) x 3
KeywordsOXIDOREDUCTASE / dinuclear iron center / monooxygenase
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 / Resolution: 2.4 Å
AuthorsWhittington, D.A. / Lippard, S.J.
CitationJournal: J.Am.Chem.Soc. / Year: 2001
Title: Crystal structures of the soluble methane monooxygenase hydroxylase from Methylococcus capsulatus (Bath) demonstrating geometrical variability at the dinuclear iron active site.
Authors: Whittington, D.A. / Lippard, S.J.
History
DepositionOct 3, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 28, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_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.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_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)251,75910
Polymers251,5676
Non-polymers1924
Water9,440524
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area41130 Å2
ΔGint-216 kcal/mol
Surface area62840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.24, 171.57, 220.52
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 / HYDROXYLASE ALPHA SUBUNIT


Mass: 60719.113 Da / Num. of mol.: 2 / 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 / E.C.1.14.13.25 / HYDROXYLASE BETA SUBUNIT / METHANE MONOOXYGENASE A BETA CHAIN


Mass: 45184.660 Da / Num. of mol.: 2 / 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 / E.C.1.14.13.25 / HYDROXYLASE GAMMA SUBUNIT / SOLUBLE METHANE MONOOXYGENASE HYDROXYLASE COMPONENT GAMMA SUBUNIT


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

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Non-polymers , 3 types, 528 molecules

#4: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 524 / 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: 2.68 Å3/Da / Density % sol: 54.06 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: PEG 8000, CaCl2, MOPS, 1,10-decanedioic acid. pH 7.0, VAPOR DIFFUSION, HANGING DROP at 298 K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
16 %(w/w)PEG80001reservoir
250 mMMOPS1reservoir
3200 mM1reservoirCaCl2
40.01 %sodium azide1reservoir
525 mMMMOH1drop
612.5 %sat1,10-decanedioic acid1dropin H2O
73 %PEG80001drop
825 mMMOPS1drop
9110 mM1dropCaCl2
100.005 %sodium azide1drop

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.98
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 6, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. all: 106519 / Num. obs: 104366 / % possible obs: 97.9 % / Observed criterion σ(I): 2 / Redundancy: 8.7 % / Biso Wilson estimate: 21 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 12.5
Reflection shellResolution: 2.4→2.44 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.47 / % possible all: 97.3
Reflection
*PLUS
Num. measured all: 907358 / Rmerge(I) obs: 0.09
Reflection shell
*PLUS
% possible obs: 97.3 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 2

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Processing

Software
NameClassification
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementResolution: 2.4→46.4 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 20194475.32 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.253 3359 3.5 %RANDOM
Rwork0.218 ---
obs0.218 95134 89.2 %-
all-106519 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 34.14 Å2 / ksol: 0.356 e/Å3
Displacement parametersBiso mean: 44.6 Å2
Baniso -1Baniso -2Baniso -3
1-20.56 Å20 Å20 Å2
2---3.15 Å20 Å2
3----17.42 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.37 Å0.32 Å
Luzzati d res low-6 Å
Luzzati sigma a0.41 Å0.39 Å
Refinement stepCycle: LAST / Resolution: 2.4→46.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17476 0 4 529 18009
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
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_d20.8
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.77
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.111.5
X-RAY DIFFRACTIONc_mcangle_it1.842
X-RAY DIFFRACTIONc_scbond_it1.792
X-RAY DIFFRACTIONc_scangle_it2.682.5
LS refinement shellResolution: 2.4→2.55 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.339 506 3.6 %
Rwork0.322 13400 -
obs--79.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PAPROTEIN.TOP
X-RAY DIFFRACTION2ION.PARAMWATER.TOP
X-RAY DIFFRACTION3WATER_REP.PARAION.TOP
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 46.4 Å / σ(F): 0 / % reflection Rfree: 3.5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 44.6 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg20.8
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.77
X-RAY DIFFRACTIONc_mcbond_it1.5
X-RAY DIFFRACTIONc_scbond_it2
X-RAY DIFFRACTIONc_mcangle_it2
X-RAY DIFFRACTIONc_scangle_it2.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.339 / % reflection Rfree: 3.6 % / Rfactor Rwork: 0.322

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