[English] 日本語
Yorodumi
- PDB-3chx: Crystal structure of Methylosinus trichosporium OB3b particulate ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3chx
TitleCrystal structure of Methylosinus trichosporium OB3b particulate methane monooxygenase (pMMO)
Components
  • 20-residue peptide
  • 26-residue peptide
  • PmoA
  • PmoB
  • PmoC
KeywordsMEMBRANE PROTEIN / METHANE / BETA BARREL
Function / homology
Function and homology information


metal ion binding / membrane
Similarity search - Function
Helix hairpin bin / Particulate methane monooxygenase subunit c2. Chain: C / particulate methane monooxygenase, chain B / Ammonia/particulate methane monooxygenase, subunit A / Particulate methane monooxygenase, b subunit. Chain: A, domain 3 / Particulate methane monooxygenase, b subunit. Chain: A, domain 1 / Ammonia monooxygenase/particulate methane monooxygenase, subunit A / Ammonia monooxygenase/particulate methane monooxygenase, subunit C / Ammonia/methane monooxygenase, subunit B, hairpin domain superfamily / Ammonia/methane monooxygenase, subunit B, C-terminal ...Helix hairpin bin / Particulate methane monooxygenase subunit c2. Chain: C / particulate methane monooxygenase, chain B / Ammonia/particulate methane monooxygenase, subunit A / Particulate methane monooxygenase, b subunit. Chain: A, domain 3 / Particulate methane monooxygenase, b subunit. Chain: A, domain 1 / Ammonia monooxygenase/particulate methane monooxygenase, subunit A / Ammonia monooxygenase/particulate methane monooxygenase, subunit C / Ammonia/methane monooxygenase, subunit B, hairpin domain superfamily / Ammonia/methane monooxygenase, subunit B, C-terminal / Ammonia monooxygenase/particulate methane monooxygenase, subunit C domain superfamily / Ammonia/particulate methane monooxygenase, subunit A superfamily / Ammonia monooxygenase / Ammonia monooxygenase/methane monooxygenase, subunit C / Ammonia monooxygenase/particulate methane monooxygenase, subunit B / Ammonia/methane monooxygenase, subunitB, N-terminal / Monooxygenase subunit B protein / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 / Helix Hairpins / Jelly Rolls / Up-down Bundle / Immunoglobulin-like / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
COPPER (II) ION / PmoA / PmoB / PmoC
Similarity search - Component
Biological speciesMethylosinus trichosporium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.9 Å
AuthorsHakemian, A.S.
CitationJournal: Biochemistry / Year: 2008
Title: The metal centers of particulate methane monooxygenase from Methylosinus trichosporium OB3b.
Authors: Hakemian, A.S. / Kondapalli, K.C. / Telser, J. / Hoffman, B.M. / Stemmler, T.L. / Rosenzweig, A.C.
History
DepositionMar 10, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 15, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 30, 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 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_seq_id / _struct_conn.ptnr2_label_asym_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: PmoB
B: PmoA
C: PmoC
D: 20-residue peptide
M: 26-residue peptide
E: PmoB
F: PmoA
G: PmoC
H: 20-residue peptide
N: 26-residue peptide
I: PmoB
J: PmoA
K: PmoC
L: 20-residue peptide
O: 26-residue peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)314,61524
Polymers314,04315
Non-polymers5729
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area55700 Å2
ΔGint-583.7 kcal/mol
Surface area92180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.810, 184.070, 203.900
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain: (Details: chain AAAA,CCCC, using strict)
NCS oper:
IDCodeMatrixVector
1given(-0.3077, 0.6681, 0.6774), (0.3198, 0.7432, -0.5877), (-0.8961, 0.0358, -0.4424)-38.1565, 31.0754, 71.0417
2given(-0.3017, 0.3127, -0.9007), (0.6666, 0.7446, 0.0352), (0.6816, -0.5898, -0.4331)42.6907, 0.284, 75.2426

-
Components

-
Protein , 3 types, 9 molecules AEIBFJCGK

#1: Protein PmoB


Mass: 43181.145 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methylosinus trichosporium (bacteria) / Gene: pmoB / References: UniProt: Q9KX50
#2: Protein PmoA


Mass: 28524.338 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methylosinus trichosporium (bacteria) / Gene: pmoA / References: UniProt: Q50541
#3: Protein PmoC


Mass: 29024.742 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methylosinus trichosporium (bacteria) / Gene: pmoC / References: UniProt: Q9KX51

-
Protein/peptide , 2 types, 6 molecules DHLMNO

#4: Protein/peptide 20-residue peptide


Mass: 1720.111 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methylosinus trichosporium (bacteria)
#5: Protein/peptide 26-residue peptide


Mass: 2230.741 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methylosinus trichosporium (bacteria)

-
Non-polymers , 1 types, 9 molecules

#6: Chemical
ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Cu

-
Details

Sequence detailsAUTHORS STATE THAT IT WAS NOT POSSIBLE TO ASSIGN PEPTIDES IN CHAINS D,H,L.M,N, AND O TO A ...AUTHORS STATE THAT IT WAS NOT POSSIBLE TO ASSIGN PEPTIDES IN CHAINS D,H,L.M,N, AND O TO A PARTICULAR SEQUENCE OR CHAIN.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.4 Å3/Da / Density % sol: 63.83 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1 M cacodylate, 10% PEG3000, 0.25 M manganese chloride, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.9794 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 20, 2005
RadiationMonochromator: double crystal monochromator and K-B pair of biomorph mirrors for vertical and horizontal focusing
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 3.9→37.969 Å / Num. obs: 39753 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.4 % / Rmerge(I) obs: 0.086 / Rsym value: 0.086 / Net I/σ(I): 7.5
Reflection shellResolution: 3.9→4.11 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.376 / Mean I/σ(I) obs: 2 / Num. measured all: 43098 / Num. unique all: 5723 / Rsym value: 0.376 / % possible all: 100

-
Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3.7 Å37.94 Å
Translation3.7 Å37.94 Å

-
Processing

Software
NameVersionClassificationNB
SCALAdata scaling
PHASERphasing
CNSrefinement
PDB_EXTRACT3.004data extraction
Blu-Icedata collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1YEW

1yew


Resolution: 3.9→38 Å / FOM work R set: 0.623 / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.377 3992 10 %random
Rwork0.342 ---
all-39875 --
obs-39694 99.9 %-
Solvent computationBsol: 114.657 Å2
Displacement parametersBiso mean: 141.814 Å2
Baniso -1Baniso -2Baniso -3
1--2.942 Å20 Å20 Å2
2---84.918 Å20 Å2
3---87.86 Å2
Refinement stepCycle: LAST / Resolution: 3.9→38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18936 0 9 0 18945
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_angle_deg1.864
Refine LS restraints NCSRms: 0 / Type: strict / Weight: 300
LS refinement shellResolution: 3.9→4.04 Å
RfactorNum. reflection% reflection
Rfree0.534 403 -
Rwork0.556 --
obs-3764 96 %
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:ion.param

+
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