[English] 日本語
Yorodumi
- PDB-1xvc: soluble methane monooxygenase hydroxylase: 8-bromooctanol soaked ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1xvc
Titlesoluble methane monooxygenase hydroxylase: 8-bromooctanol soaked structure
Components(Methane monooxygenase component A ...) x 3
KeywordsOXIDOREDUCTASE / methane / diiron / four-helix bundle / product binding / cavity
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
1-BROMOPENTANE / BROMOMETHANE / BROMIDE ION / : / FORMIC ACID / 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 / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsSazinsky, M.H. / Lippard, S.J.
CitationJournal: J.Am.Chem.Soc. / Year: 2005
Title: Product Bound Structures of the Soluble Methane Monooxygenase Hydroxylase from Methylococcus capsulatus (Bath): Protein Motion in the Alpha-Subunit
Authors: Sazinsky, M.H. / Lippard, S.J.
History
DepositionOct 27, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 3, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 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 / 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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_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 / _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 / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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)252,24215
Polymers251,5676
Non-polymers6759
Water17,114950
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area42610 Å2
ΔGint-233 kcal/mol
Surface area60870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.411, 171.031, 221.434
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

-
Methane monooxygenase component A ... , 3 types, 6 molecules ABCDEF

#1: Protein Methane monooxygenase component A alpha chain / Methane hydroxylase


Mass: 60719.113 Da / Num. of mol.: 2 / Fragment: alpha subunit / 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


Mass: 45184.660 Da / Num. of mol.: 2 / Fragment: beta subunit / 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 / Methane hydroxylase


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

-
Non-polymers , 6 types, 959 molecules

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


Mass: 55.845 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe
#5: Chemical ChemComp-BR / BROMIDE ION / Methane hydroxylase


Mass: 79.904 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Br / References: methane monooxygenase (soluble)
#6: Chemical ChemComp-5BR / 1-BROMOPENTANE


Mass: 151.045 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H11Br
#7: Chemical ChemComp-BMM / BROMOMETHANE


Mass: 94.939 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH3Br
#8: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O2
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 950 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.3 Å3/Da / Density % sol: 55.1 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: MOPS, PEG 8000, NaN3, CaCl2, glycerol, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: May 1, 2002
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. all: 176340 / Num. obs: 176340 / % possible obs: 97.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.3 % / Biso Wilson estimate: 17.8 Å2 / Rmerge(I) obs: 0.074 / Rsym value: 0.074 / Net I/σ(I): 12.8
Reflection shellResolution: 2→2.08 Å / Rmerge(I) obs: 0.262 / Mean I/σ(I) obs: 4.1 / Rsym value: 0.262 / % possible all: 83.7

-
Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1mty

1mty


Resolution: 2→29.79 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 453424.54 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.234 5913 3.5 %RANDOM
Rwork0.206 ---
obs0.206 166594 92 %-
all-176340 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 50.829 Å2 / ksol: 0.34696 e/Å3
Displacement parametersBiso mean: 37 Å2
Baniso -1Baniso -2Baniso -3
1-21.47 Å20 Å20 Å2
2---6.36 Å20 Å2
3----15.11 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.29 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.31 Å0.3 Å
Refinement stepCycle: LAST / Resolution: 2→29.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17317 0 14 953 18284
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
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_d20.1
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.79
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.151.5
X-RAY DIFFRACTIONc_mcangle_it1.732
X-RAY DIFFRACTIONc_scbond_it1.882
X-RAY DIFFRACTIONc_scangle_it2.622.5
LS refinement shellResolution: 2→2.08 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.322 545 3.6 %
Rwork0.308 14747 -
obs--48.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2ION.PARAMWATER.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMION.TOP
X-RAY DIFFRACTION4LIGANDS.PARAMLIGANDS.TOP

+
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