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- PDB-6d7k: Complex structure of Methane monooxygenase hydroxylase in complex... -

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Basic information

Entry
Database: PDB / ID: 6d7k
TitleComplex structure of Methane monooxygenase hydroxylase in complex with inhibitory subunit
Components(Methane monooxygenase hydroxylase, ...) x 4
Keywordsoxidoreductase/inhibitor / Complex / OXIDOREDUCTASE / oxidoreductase-inhibitor complex
Function / homology
Function and homology information


methane metabolic process / methane monooxygenase [NAD(P)H] activity / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen / monooxygenase activity / metal ion binding
Similarity search - Function
Methane monooxygenase component D / 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 monooxygenase component D / 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
: / FORMIC ACID / HEXANE-1,6-DIOL / MmoD / Methane monooxygenase / Methane monooxygenase / Methane monooxygenase
Similarity search - Component
Biological speciesMethylosinus sporium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsKim, H. / Lee, S.J. / Cho, U.-S.
Funding support United States, Korea, Republic Of, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Center for Research Resources (NIH/NCRR)R01 DK111465 United States
National Research Foundation (NRF, Korea)NRF-2015M3D3A1A01064876 Korea, Republic Of
Citation
Journal: Sci Adv / Year: 2019
Title: MMOD-induced structural changes of hydroxylase in soluble methane monooxygenase.
Authors: Kim, H. / An, S. / Park, Y.R. / Jang, H. / Yoo, H. / Park, S.H. / Lee, S.J. / Cho, U.S.
#1: Journal: To Be Published
Title: The crystal structure of the MMOH-MMOD complex reveals the inhibitory mechanism of MMOD
Authors: Kim, H. / Lee, S.J. / Cho, U.-S.
History
DepositionApr 24, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 26, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Oct 30, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.3Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 4, 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
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.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.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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Methane monooxygenase hydroxylase, MmoX1
B: Methane monooxygenase hydroxylase, MmoY
C: Methane monooxygenase hydroxylase, MmoZ
D: Methane monooxygenase hydroxylase, MmoD
E: Methane monooxygenase hydroxylase, MmoX1
F: Methane monooxygenase hydroxylase, MmoY
G: Methane monooxygenase hydroxylase, MmoZ
H: Methane monooxygenase hydroxylase, MmoD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)275,49716
Polymers274,9468
Non-polymers5528
Water6,107339
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area40450 Å2
ΔGint-202 kcal/mol
Surface area66770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)179.781, 125.776, 126.380
Angle α, β, γ (deg.)90.00, 102.89, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Methane monooxygenase hydroxylase, ... , 4 types, 8 molecules AEBFCGDH

#1: Protein Methane monooxygenase hydroxylase, MmoX1


Mass: 59979.230 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Methylosinus sporium (bacteria) / References: UniProt: Q27RN7
#2: Protein Methane monooxygenase hydroxylase, MmoY


Mass: 45239.246 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Methylosinus sporium (bacteria) / References: UniProt: Q27RN6
#3: Protein Methane monooxygenase hydroxylase, MmoZ


Mass: 19379.207 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Methylosinus sporium (bacteria) / References: UniProt: Q27RN4
#4: Protein Methane monooxygenase hydroxylase, MmoD


Mass: 12875.136 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methylosinus sporium (bacteria) / Gene: mmoD / Production host: Escherichia coli (E. coli) / References: UniProt: Q27RN3

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Non-polymers , 4 types, 347 molecules

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


Mass: 55.845 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe
#6: Chemical ChemComp-HEZ / HEXANE-1,6-DIOL


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2
#7: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CH2O2
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 339 / 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: 2.53 Å3/Da / Density % sol: 55.99 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 10% (w/v) PEG 8000, 20% (v/v) ethylene glycol, 0.02 M of alcohols mix (1,6-hexanediol, 1-butanol, (RS)-1,2-propanediol, 2-propanol, 1,4-butanediol, and 1,3-propanediol), 0.1 M MES/imidazole ...Details: 10% (w/v) PEG 8000, 20% (v/v) ethylene glycol, 0.02 M of alcohols mix (1,6-hexanediol, 1-butanol, (RS)-1,2-propanediol, 2-propanol, 1,4-butanediol, and 1,3-propanediol), 0.1 M MES/imidazole buffer (pH 6.5) and 1,3-butanediol

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Data collection

DiffractionMean temperature: 273 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.987 Å
DetectorType: MAR CCD 130 mm / Detector: CCD / Date: Oct 20, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.59→50 Å / Num. obs: 84164 / % possible obs: 99.5 % / Redundancy: 4.3 % / Rmerge(I) obs: 0.124 / Net I/σ(I): 12.8
Reflection shellResolution: 2.59→2.64 Å / Rmerge(I) obs: 0.793 / % possible all: 98.9

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1MHY

1mhy


Resolution: 2.6→22.289 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.31
RfactorNum. reflection% reflection
Rfree0.2212 4180 5 %
Rwork0.1776 --
obs0.1798 83611 99.37 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.6→22.289 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17401 0 26 339 17766
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00817900
X-RAY DIFFRACTIONf_angle_d0.89124283
X-RAY DIFFRACTIONf_dihedral_angle_d15.17910416
X-RAY DIFFRACTIONf_chiral_restr0.0482516
X-RAY DIFFRACTIONf_plane_restr0.0053134
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.62950.27581360.25072603X-RAY DIFFRACTION99
2.6295-2.66040.27891400.25452646X-RAY DIFFRACTION99
2.6604-2.69280.31551370.23922603X-RAY DIFFRACTION99
2.6928-2.72680.2921400.23082639X-RAY DIFFRACTION99
2.7268-2.76260.28231360.21512625X-RAY DIFFRACTION99
2.7626-2.80040.28631400.21952643X-RAY DIFFRACTION99
2.8004-2.84030.28231390.21212633X-RAY DIFFRACTION99
2.8403-2.88260.29231380.21132624X-RAY DIFFRACTION99
2.8826-2.92760.26121370.21422632X-RAY DIFFRACTION99
2.9276-2.97550.27571380.21512637X-RAY DIFFRACTION99
2.9755-3.02670.27981400.19892641X-RAY DIFFRACTION99
3.0267-3.08160.22681380.20282627X-RAY DIFFRACTION99
3.0816-3.14070.22961400.19222665X-RAY DIFFRACTION100
3.1407-3.20460.23781380.19132624X-RAY DIFFRACTION99
3.2046-3.27410.26291390.19492618X-RAY DIFFRACTION99
3.2741-3.350.26271390.2062644X-RAY DIFFRACTION99
3.35-3.43350.22451410.19692687X-RAY DIFFRACTION100
3.4335-3.5260.25411380.18682627X-RAY DIFFRACTION99
3.526-3.62930.25221400.18252654X-RAY DIFFRACTION100
3.6293-3.74590.19081390.16262646X-RAY DIFFRACTION100
3.7459-3.87910.1861400.16082667X-RAY DIFFRACTION100
3.8791-4.03360.18631400.16052652X-RAY DIFFRACTION100
4.0336-4.2160.19531410.14782677X-RAY DIFFRACTION100
4.216-4.43660.21321380.14632635X-RAY DIFFRACTION100
4.4366-4.71210.18841410.13612671X-RAY DIFFRACTION100
4.7121-5.0720.15371410.14932670X-RAY DIFFRACTION100
5.072-5.57510.20171400.15942670X-RAY DIFFRACTION100
5.5751-6.36540.21421420.17592693X-RAY DIFFRACTION100
6.3654-7.95860.21131430.17912703X-RAY DIFFRACTION100
7.9586-22.28960.18331410.1572675X-RAY DIFFRACTION98

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