[English] 日本語
Yorodumi
- PDB-1fyz: METHANE MONOOXYGENASE HYDROXYLASE, FORM II REDUCED BY SOAKING -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1fyz
TitleMETHANE MONOOXYGENASE HYDROXYLASE, FORM II REDUCED BY SOAKING
Components(METHANE MONOOXYGENASE COMPONENT A, ...) x 3
KeywordsOXIDOREDUCTASE / 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 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.15 Å
AuthorsWhittington, D.A. / Lippard, S.J.
CitationJournal: J.Am.Chem.Soc. / Year: 2001
Title: Crystal structures of the soluble methane monooxygenase hydroxylase from Methylococcus capsulatus (Bath) demonstrating geometrical variability at the dinuclear iron active site.
Authors: Whittington, D.A. / Lippard, S.J.
History
DepositionOct 3, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 21, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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.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_conn.ptnr2_symmetry / _struct_ref_seq_dif.details / _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)251,91113
Polymers251,5676
Non-polymers3447
Water22,1221228
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area41900 Å2
ΔGint-255 kcal/mol
Surface area63120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.27, 171.66, 221.60
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Cell settingorthorhombic
Space group name H-MP212121

-
Components

-
METHANE MONOOXYGENASE COMPONENT A, ... , 3 types, 6 molecules ABCDEF

#1: Protein METHANE MONOOXYGENASE COMPONENT A, ALPHA CHAIN / E.C.1.14.13.25 / HYDROXYLASE ALPHA SUBUNIT


Mass: 60719.113 Da / Num. of mol.: 2 / 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 / E.C.1.14.13.25 / HYDROXYLASE BETA SUBUNIT / METHANE MONOOXYGENASE A BETA CHAIN


Mass: 45184.660 Da / Num. of mol.: 2 / 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 / E.C.1.14.13.25 / HYDROXYLASE GAMMA SUBUNIT / SOLUBLE METHANE MONOOXYGENASE HYDROXYLASE COMPONENT GAMMA SUBUNIT


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

-
Non-polymers , 3 types, 1235 molecules

#4: Chemical
ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1228 / 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: 2.69 Å3/Da / Density % sol: 54.33 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: PEG 8000, CaCl2, MOPS, 1,10-decanedioic acid. pH 7.0, VAPOR DIFFUSION, HANGING DROP at 298 K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
16 %(w/w)PEG80001reservoir
250 mMMOPS1reservoir
3200 mM1reservoirCaCl2
40.01 %sodium azide1reservoir
525 mMMMOH1drop
612.5 %sat1,10-decanedioic acid1dropin H2O
73 %PEG80001drop
825 mMMOPS1drop
9110 mM1dropCaCl2
100.005 %sodium azide1drop

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1.033
DetectorType: CUSTOM-MADE / Detector: CCD / Date: Feb 9, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 2.15→30 Å / Num. all: 148299 / Num. obs: 145320 / % possible obs: 97.9 % / Observed criterion σ(I): 2 / Redundancy: 14.7 % / Biso Wilson estimate: 14.4 Å2 / Rmerge(I) obs: 0.051 / Net I/σ(I): 21.3
Reflection shellResolution: 2.15→2.23 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.241 / % possible all: 92.2
Reflection
*PLUS
Num. measured all: 2132118
Reflection shell
*PLUS
% possible obs: 92.2 % / Mean I/σ(I) obs: 3.8

-
Processing

Software
NameClassification
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementResolution: 2.15→29.79 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 29598721.57 / Data cutoff low absF: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT METHOD USED
RfactorNum. reflection% reflectionSelection details
Rfree0.23 4903 3.5 %random
Rwork0.189 ---
all-148299 --
obs-138571 93.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 52.779 Å2 / ksol: 0.354488 e/Å3
Displacement parametersBiso mean: 32.9 Å2
Baniso -1Baniso -2Baniso -3
1-15.14 Å20 Å20 Å2
2---4.62 Å20 Å2
3----10.52 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.29 Å0.23 Å
Luzzati d res low-6 Å
Luzzati sigma a0.24 Å0.22 Å
Refinement stepCycle: LAST / Resolution: 2.15→29.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17509 0 7 1232 18748
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_improper_angle_d0.75
X-RAY DIFFRACTIONc_dihedral_angle_d20
X-RAY DIFFRACTIONc_mcbond_it1.771.5
X-RAY DIFFRACTIONc_mcangle_it2.492
X-RAY DIFFRACTIONc_scbond_it3.012
X-RAY DIFFRACTIONc_scangle_it4.012.5
LS refinement shellResolution: 2.15→2.28 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.279 684 3.4 %
Rwork0.242 19500 -
obs--82.6 %
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 3.5 % / Rfactor obs: 0.189 / Rfactor Rfree: 0.23
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 32.9 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg20
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.75
X-RAY DIFFRACTIONc_mcbond_it1.5
X-RAY DIFFRACTIONc_scbond_it2
X-RAY DIFFRACTIONc_mcangle_it2
X-RAY DIFFRACTIONc_scangle_it2.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.279 / % reflection Rfree: 3.4 % / Rfactor Rwork: 0.242

+
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