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- PDB-1mhz: METHANE MONOOXYGENASE HYDROXYLASE -

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Basic information

Entry
Database: PDB / ID: 1mhz
TitleMETHANE MONOOXYGENASE HYDROXYLASE
Components(METHANE MONOOXYGENASE HYDROXYLASE) x 3
KeywordsOXIDOREDUCTASE / MONOOXYGENASE / NADP / ONE-CARBON METABOLISM
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 alpha chain / Methane monooxygenase component A beta chain / Methane monooxygenase component A gamma chain
Similarity search - Component
Biological speciesMethylosinus trichosporium (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsElango, N. / Radhakrishnan, R. / Froland, W.A. / Waller, B.J. / Earhart, C.A. / Lipscomb, J.D. / Ohlendorf, D.H.
CitationJournal: Protein Sci. / Year: 1997
Title: Crystal structure of the hydroxylase component of methane monooxygenase from Methylosinus trichosporium OB3b
Authors: Elango, N. / Radhakrishnan, R. / Froland, W.A. / Wallar, B.J. / Earhart, C.A. / Lipscomb, J.D. / Ohlendorf, D.H.
History
DepositionOct 21, 1996Processing site: BNL
Revision 1.0May 15, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.4Dec 21, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...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
Revision 1.5Aug 9, 2023Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 1.6May 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
B: METHANE MONOOXYGENASE HYDROXYLASE
D: METHANE MONOOXYGENASE HYDROXYLASE
G: METHANE MONOOXYGENASE HYDROXYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,1495
Polymers124,0373
Non-polymers1122
Water724
1
B: METHANE MONOOXYGENASE HYDROXYLASE
D: METHANE MONOOXYGENASE HYDROXYLASE
G: METHANE MONOOXYGENASE HYDROXYLASE
hetero molecules

B: METHANE MONOOXYGENASE HYDROXYLASE
D: METHANE MONOOXYGENASE HYDROXYLASE
G: METHANE MONOOXYGENASE HYDROXYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)248,29810
Polymers248,0746
Non-polymers2234
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_586x,-y+3,-z+11
Buried area39750 Å2
ΔGint-208 kcal/mol
Surface area61170 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)293.380, 64.010, 143.650
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein METHANE MONOOXYGENASE HYDROXYLASE


Mass: 45165.145 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Methylosinus trichosporium (bacteria)
References: UniProt: P27354, methane monooxygenase (soluble)
#2: Protein METHANE MONOOXYGENASE HYDROXYLASE


Mass: 59513.691 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Methylosinus trichosporium (bacteria)
References: UniProt: P27353, methane monooxygenase (soluble)
#3: Protein METHANE MONOOXYGENASE HYDROXYLASE


Mass: 19358.285 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Methylosinus trichosporium (bacteria)
References: UniProt: P27355, methane monooxygenase (soluble)
#4: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / 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: 2.72 Å3/Da / Density % sol: 55 %
Crystal growDetails: COMPONENT B WAS PRESENT IN THE CRYSTALLIZATION. SEE JRNL REFERENCE FOR DETAILS.
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Details: used to seeding, Froland, W.A., (1994) J. Mol. Biol., 236, 379.
PH range low: 7.8 / PH range high: 7.4
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
12.5-3.5 mg/mlMMOH1drop
250 mMsodium phosphate/citrate1drop
39-11 %PEG20001drop
418-22 %PEG20001reservoir

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Data collection

DiffractionMean temperature: 291 K
Diffraction sourceWavelength: 1.5418
DetectorType: SIEMENS / Detector: AREA DETECTOR / Date: Mar 18, 1996
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.7→5 Å / Num. obs: 33478 / % possible obs: 89.3 % / Observed criterion σ(I): 1 / Redundancy: 5 % / Rmerge(I) obs: 0.094 / Net I/σ(I): 6.18
Reflection
*PLUS
Num. measured all: 177040

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
XENGENdata reduction
X-PLOR3.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1MHY

1mhy


Resolution: 2.7→5 Å / σ(F): 2
Details: BOTH MMOH AND COMPONENT B WERE PRESENT IN THE CRYSTALLIZATION. HOWEVER THE ELECTRON DENSITY MAP DID NOT SHOW ANY FEATURE TO THE EFFECT OF COMPONENT B BEING PRESENT IN THE CRYSTAL. SEE JRNL REFERENCE FOR DETAILS.
RfactorNum. reflection% reflection
Rwork0.152 --
obs0.152 22264 89.3 %
Displacement parametersBiso mean: 22.17 Å2
Refine analyzeLuzzati coordinate error obs: 0.19 Å / Luzzati d res low obs: 5 Å
Refinement stepCycle: LAST / Resolution: 2.7→5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8597 0 2 4 8603
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.013
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_deg1.61
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d21.39
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.54
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
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Rfactor all: 0.178
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg21.39
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.54

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