[English] 日本語
Yorodumi
- PDB-7s6t: Complex structure of Methane monooxygenase hydroxylase and regula... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7s6t
TitleComplex structure of Methane monooxygenase hydroxylase and regulatory subunit H33A
Components(Methane monooxygenase ...) x 4
KeywordsHYDROLASE / OXIDOREDUCTASE
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
: / Monooxygenase component MmoB/DmpM / Phenol Hydroxylase P2 Protein / Monooxygenase component MmoB/DmpM / Monooxygenase component MmoB/DmpM superfamily / MmoB/DmpM family / Methane monooxygenase, gamma chain / Methane monooxygenase, gamma chain, domain 1 / Methane monooxygenase, gamma chain, domain 2 / Methane monooxygenase, gamma chain superfamily ...: / Monooxygenase component MmoB/DmpM / Phenol Hydroxylase P2 Protein / Monooxygenase component MmoB/DmpM / Monooxygenase component MmoB/DmpM superfamily / MmoB/DmpM family / 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-like / Ferritin-like superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
BENZOIC ACID / : / Methane monooxygenase / Methane monooxygenase regulatory protein B / Methane monooxygenase component A alpha chain / Methane monooxygenase
Similarity search - Component
Biological speciesMethylosinus trichosporium OB3b (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.82 Å
AuthorsJohns, J.C. / Banerjee, R. / Semonis, M.M. / Shi, K. / Aihara, H. / Lipscomb, J.D.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM118030 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM118047 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM08347 United States
CitationJournal: Biochemistry / Year: 2022
Title: X-ray Crystal Structures of Methane Monooxygenase Hydroxylase Complexes with Variants of Its Regulatory Component: Correlations with Altered Reaction Cycle Dynamics.
Authors: Jones, J.C. / Banerjee, R. / Semonis, M.M. / Shi, K. / Aihara, H. / Lipscomb, J.D.
History
DepositionSep 14, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 29, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 19, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Methane monooxygenase component A alpha chain
B: Methane monooxygenase beta chain
C: Methane monooxygenase gamma chain
D: Methane monooxygenase regulatory protein B
E: Methane monooxygenase component A alpha chain
F: Methane monooxygenase beta chain
G: Methane monooxygenase gamma chain
H: Methane monooxygenase regulatory protein B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)279,26064
Polymers275,6898
Non-polymers3,57156
Water40,2642235
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area66050 Å2
ΔGint-104 kcal/mol
Surface area66000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.520, 105.600, 299.980
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain B and (resid 4 through 139 or resid 141...
21(chain F and (resid 4 through 139 or resid 141...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain B and (resid 4 through 139 or resid 141...B4 - 139
121(chain B and (resid 4 through 139 or resid 141...B141 - 320
131(chain B and (resid 4 through 139 or resid 141...B322
141(chain B and (resid 4 through 139 or resid 141...B4 - 1201
151(chain B and (resid 4 through 139 or resid 141...B4 - 1201
161(chain B and (resid 4 through 139 or resid 141...B4 - 1201
171(chain B and (resid 4 through 139 or resid 141...B4 - 1201
181(chain B and (resid 4 through 139 or resid 141...B4 - 1201
191(chain B and (resid 4 through 139 or resid 141...B4 - 1201
211(chain F and (resid 4 through 139 or resid 141...F4 - 139
221(chain F and (resid 4 through 139 or resid 141...F141 - 320
231(chain F and (resid 4 through 139 or resid 141...F322 - 394
241(chain F and (resid 4 through 139 or resid 141...F395
251(chain F and (resid 4 through 139 or resid 141...F4 - 604
261(chain F and (resid 4 through 139 or resid 141...F4 - 604
271(chain F and (resid 4 through 139 or resid 141...F4 - 604
281(chain F and (resid 4 through 139 or resid 141...F4 - 604

-
Components

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

#1: Protein Methane monooxygenase component A alpha chain


Mass: 58971.008 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methylosinus trichosporium OB3b (bacteria)
Gene: CQW49_12480 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A2D2D5X0
#2: Protein Methane monooxygenase beta chain


Mass: 44948.941 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methylosinus trichosporium OB3b (bacteria)
Gene: CQW49_12475 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A2D2D5X7
#3: Protein Methane monooxygenase gamma chain


Mass: 19313.203 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methylosinus trichosporium OB3b (bacteria)
Gene: CQW49_12465 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A2D2D0T0
#4: Protein Methane monooxygenase regulatory protein B


Mass: 14611.542 Da / Num. of mol.: 2 / Mutation: H33A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methylosinus trichosporium OB3b (bacteria)
Gene: CQW49_12470 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A2D2D0T8

-
Non-polymers , 4 types, 2291 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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 50 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical ChemComp-BEZ / BENZOIC ACID


Mass: 122.121 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H6O2
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2235 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestN

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.95 Å3/Da / Density % sol: 58.34 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / Details: 21% PEG3350 and 0.2 M Na2HPO4 pH 6.6

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9791 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 7, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.82→48.51 Å / Num. obs: 289411 / % possible obs: 99.5 % / Redundancy: 5.1 % / Biso Wilson estimate: 28.84 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.094 / Rpim(I) all: 0.046 / Rrim(I) all: 0.105 / Net I/σ(I): 9.3 / Num. measured all: 1472673 / Scaling rejects: 111
Reflection shellResolution: 1.82→1.85 Å / Redundancy: 5.2 % / Rmerge(I) obs: 1.079 / Num. unique obs: 13878 / CC1/2: 0.736 / Rpim(I) all: 0.519 / Rrim(I) all: 1.2 / % possible all: 97.2

-
Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
Aimless0.7.7data scaling
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB entry 7M8Q

7m8q


Resolution: 1.82→48.51 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 17.9 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1722 14175 4.9 %
Rwork0.1462 275111 -
obs0.1475 289286 99.37 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 190.18 Å2 / Biso mean: 31.4446 Å2 / Biso min: 16.34 Å2
Refinement stepCycle: final / Resolution: 1.82→48.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19456 0 222 2241 21919
Biso mean--51.07 42.67 -
Num. residues----2417
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11B3740X-RAY DIFFRACTION4.479TORSIONAL
12F3740X-RAY DIFFRACTION4.479TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.82-1.840.29034280.24988759918796
1.84-1.860.26474680.234691509618100
1.86-1.880.26064750.222791549629100
1.88-1.910.25154820.216290889570100
1.91-1.930.24814960.202291329628100
1.93-1.960.22885020.200190799581100
1.96-1.990.22874700.184691439613100
1.99-2.020.21644320.177691909622100
2.02-2.050.2124530.169991649617100
2.05-2.080.2184430.167791359578100
2.08-2.120.20214570.159591699626100
2.12-2.160.18954710.156891489619100
2.16-2.20.19295070.154491549661100
2.2-2.240.18664750.151590939568100
2.24-2.290.20344690.155191569625100
2.29-2.350.20284890.155191359624100
2.35-2.40.1894750.148991739648100
2.4-2.470.1854650.14791199584100
2.47-2.540.19414840.15269161964599
2.54-2.620.18155330.14819105963899
2.62-2.720.1634690.13759174964399
2.72-2.830.16585040.1399131963599
2.83-2.950.17984970.14429147964499
2.95-3.110.19195000.15179185968599
3.11-3.310.174400.14679265970599
3.31-3.560.16464460.14329244969099
3.56-3.920.14754360.12979292972899
3.92-4.480.13014910.11629243973499
4.48-5.650.13754640.12249377984199
5.65-48.510.14024540.144396461010098

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more