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- PDB-1mty: METHANE MONOOXYGENASE HYDROXYLASE FROM METHYLOCOCCUS CAPSULATUS (BATH) -

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Basic information

Entry
Database: PDB / ID: 1mty
TitleMETHANE MONOOXYGENASE HYDROXYLASE FROM METHYLOCOCCUS CAPSULATUS (BATH)
Components(METHANE MONOOXYGENASE HYDROXYLASE) x 3
KeywordsMONOOXYGENASE / METHANE MONOOXYGENASE / HYDROXYLASE / 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 str. Bath (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsRosenzweig, A.C. / Nordlund, P. / Lippard, S.J. / Frederick, C.A.
Citation
Journal: Proteins / Year: 1997
Title: Crystal structures of the methane monooxygenase hydroxylase from Methylococcus capsulatus (Bath): implications for substrate gating and component interactions.
Authors: Rosenzweig, A.C. / Brandstetter, H. / Whittington, D.A. / Nordlund, P. / Lippard, S.J. / Frederick, C.A.
#1: Journal: Chem.Biol. / Year: 1995
Title: Geometry of the Soluble Methane Monooxygenase Catalytic Diiron Center in Two Oxidation States
Authors: Rosenzweig, A.C. / Nordlund, P. / Takahara, P.M. / Frederick, C.A. / Lippard, S.J.
History
DepositionJul 10, 1996Processing site: BNL
Revision 1.0Apr 21, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 2023Group: Advisory / Database references ...Advisory / Database references / Derived calculations / Other / Refinement description
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_validate_close_contact / 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_database_status.process_site / _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_asym_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 / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_atom_id_1 / _pdbx_validate_close_contact.auth_atom_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_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
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
D: METHANE MONOOXYGENASE HYDROXYLASE
E: METHANE MONOOXYGENASE HYDROXYLASE
B: METHANE MONOOXYGENASE HYDROXYLASE
C: METHANE MONOOXYGENASE HYDROXYLASE
G: METHANE MONOOXYGENASE HYDROXYLASE
H: METHANE MONOOXYGENASE HYDROXYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)245,99810
Polymers245,7746
Non-polymers2234
Water26,8061488
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area41030 Å2
ΔGint-227 kcal/mol
Surface area60640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.700, 109.600, 330.200
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.999971, 0.007615, 4.2E-5), (-0.0029, -0.385979, 0.922503), (0.007041, 0.922476, 0.385989)
Vector: 81.79778, 28.05303, -18.25602)

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Components

#1: Protein METHANE MONOOXYGENASE HYDROXYLASE


Mass: 59241.492 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Methylococcus capsulatus str. Bath (bacteria)
Cellular location: CYTOPLASM / Species: Methylococcus capsulatus / Strain: BATH
References: UniProt: P22869, methane monooxygenase (soluble)
#2: Protein METHANE MONOOXYGENASE HYDROXYLASE


Mass: 44664.988 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Methylococcus capsulatus str. Bath (bacteria)
Cellular location: CYTOPLASM / Species: Methylococcus capsulatus / Strain: BATH
References: UniProt: P18798, methane monooxygenase (soluble)
#3: Protein METHANE MONOOXYGENASE HYDROXYLASE


Mass: 18980.639 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Methylococcus capsulatus str. Bath (bacteria)
Cellular location: CYTOPLASM / Species: Methylococcus capsulatus / Strain: BATH
References: UniProt: P11987, methane monooxygenase (soluble)
#4: Chemical
ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1488 / 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: 2.2 Å3/Da / Density % sol: 44 %
Description: DATA WERE COLLECTED USING THE WEISSENBERG METHOD.
Crystal growpH: 7
Details: 25 MM LI2SO4, 50 MM NH4OAC, 5% PEG 4000, IN 25 MM MOPS PH 7.0 WITH A RESERVOIR OF 20% PEG 4000
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, hanging drop / Details: macroseeding
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 %PEG40001reservoir
225 mM1reservoirLi2SO4
325 mM1reservoirNH4OAc
425 mMMOPS1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 0.9
DetectorType: FUJI / Detector: IMAGE PLATE / Date: Dec 1, 1994
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.7→12 Å / Num. obs: 188161 / % possible obs: 77 % / Observed criterion σ(I): 0 / Redundancy: 2.5 % / Biso Wilson estimate: 13.2 Å2 / Rmerge(I) obs: 0.039 / Rsym value: 0.039 / Net I/σ(I): 20
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.237 / Mean I/σ(I) obs: 20 / Rsym value: 0.237 / % possible all: 75
Reflection shell
*PLUS
% possible obs: 75 %

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1MMO

1mmo


Resolution: 1.7→5 Å / σ(F): 0
RfactorNum. reflection% reflection
Rwork0.183 --
obs0.183 188123 77 %
Displacement parametersBiso mean: 9.1 Å2
Refine analyzeLuzzati coordinate error obs: 0.2 Å / Luzzati d res low obs: 5 Å
Refinement stepCycle: LAST / Resolution: 1.7→5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17389 0 4 1487 18880
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.5
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d21.5
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.5
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 1.7→1.73 Å
RfactorNum. reflection% reflection
Rwork0.245 14013 -
obs--75 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg21.5
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.5
LS refinement shell
*PLUS
Rfactor obs: 0.245

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