[English] 日本語
Yorodumi
- PDB-4pi0: Crystal structure of particulate methane monooxygenase from Methy... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4pi0
TitleCrystal structure of particulate methane monooxygenase from Methylocystis sp. ATCC 49242 (Rockwell) soaked in copper
Components
  • Particulate methane monooxygenase subunit A
  • Particulate methane monooxygenase subunit B
  • Particulate methane monooxygenase subunit C
  • unknown peptide
KeywordsOXIDOREDUCTASE / Bacterial Proteins / Binding Sites / Copper / Zinc / Methylocystaceae / Oxygenases / Protein Binding
Function / homology
Function and homology information


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 / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 / Helix Hairpins / Jelly Rolls / Up-down Bundle ...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 / 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
Biological speciesMethylocystis sp. ATCC 49242 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.15 Å
AuthorsSirajuddin, S. / Rosenzweig, A.C.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM070473 United States
CitationJournal: J.Biol.Chem. / Year: 2014
Title: Effects of zinc on particulate methane monooxygenase activity and structure.
Authors: Sirajuddin, S. / Barupala, D. / Helling, S. / Marcus, K. / Stemmler, T.L. / Rosenzweig, A.C.
History
DepositionMay 7, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 25, 2014Provider: repository / Type: Initial release
Revision 1.1Jul 9, 2014Group: Database references
Revision 1.2Oct 1, 2014Group: Database references
Revision 1.3Apr 6, 2016Group: Source and taxonomy
Revision 1.4Sep 6, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.5Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.6Sep 27, 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_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.7Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
D: unknown peptide
H: unknown peptide
F: Particulate methane monooxygenase subunit A
K: Particulate methane monooxygenase subunit C
E: Particulate methane monooxygenase subunit B
N: unknown peptide
A: Particulate methane monooxygenase subunit B
I: Particulate methane monooxygenase subunit B
C: Particulate methane monooxygenase subunit C
G: Particulate methane monooxygenase subunit C
J: Particulate methane monooxygenase subunit A
B: Particulate methane monooxygenase subunit A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)317,41618
Polymers317,03412
Non-polymers3816
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area61140 Å2
ΔGint-603 kcal/mol
Surface area86880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.361, 184.739, 188.637
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
11A
21E
12I
22E
13J
23F
14B
24F
15K
25C
16G
26C

NCS domain segments:

Refine code: 1

Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111HISHISALAALAAG29 - 41629 - 416
211HISHISALAALAEE29 - 41629 - 416
112HISHISALAALAIH29 - 41629 - 416
212HISHISALAALAEE29 - 41629 - 416
113GLYGLYILEILEJK11 - 25211 - 252
213GLYGLYILEILEFC11 - 25211 - 252
114GLYGLYILEILEBL11 - 25211 - 252
214GLYGLYILEILEFC11 - 25211 - 252
115GLUGLUPROPROKD16 - 19516 - 195
215GLUGLUPROPROCI16 - 19516 - 195
125TRPTRPGLUGLUKD226 - 256226 - 256
225TRPTRPGLUGLUCI226 - 256226 - 256
116GLUGLUPROPROGJ16 - 19516 - 195
216GLUGLUPROPROCI16 - 19516 - 195
126TRPTRPGLUGLUGJ226 - 256226 - 256
226TRPTRPGLUGLUCI226 - 256226 - 256

NCS ensembles :
ID
1
2
3
4
5
6

-
Components

#1: Protein/peptide unknown peptide


Mass: 2145.636 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Methylocystis sp. ATCC 49242 (bacteria)
#2: Protein Particulate methane monooxygenase subunit A / pmoA


Mass: 28560.311 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Methylocystis sp. ATCC 49242 (bacteria) / References: methane monooxygenase (particulate)
#3: Protein Particulate methane monooxygenase subunit C / pmoC


Mass: 29231.023 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Methylocystis sp. ATCC 49242 (bacteria) / References: methane monooxygenase (particulate)
#4: Protein Particulate methane monooxygenase subunit B / pmoB


Mass: 45741.105 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Methylocystis sp. ATCC 49242 (bacteria) / References: methane monooxygenase (particulate)
#5: Chemical
ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cu
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.33 Å3/Da / Density % sol: 63.04 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 10% PEG3000, 0.1 M sodium cacodylate trihydrate, pH 6.5, 0.2 M magnesium formate dihydrate

-
Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.33765 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 9, 2012
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.33765 Å / Relative weight: 1
ReflectionResolution: 3.15→50 Å / Num. obs: 55808 / % possible obs: 77.8 % / Redundancy: 13.7 % / Net I/σ(I): 21.5

-
Processing

Software
NameVersionClassificationNB
REFMAC5.8.0049refinement
PDB_EXTRACT3.14data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3RFR

3rfr


Resolution: 3.15→50 Å / Cor.coef. Fo:Fc: 0.854 / Cor.coef. Fo:Fc free: 0.795 / SU B: 24.467 / SU ML: 0.424 / Cross valid method: THROUGHOUT / σ(F): 3 / ESU R Free: 0.607 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.2799 2796 5 %RANDOM
Rwork0.2211 53012 --
obs0.2241 55808 78.21 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 227.82 Å2 / Biso mean: 57.517 Å2 / Biso min: 16.97 Å2
Baniso -1Baniso -2Baniso -3
1--0.08 Å2-0 Å2-0 Å2
2--0.52 Å20 Å2
3----0.44 Å2
Refinement stepCycle: final / Resolution: 3.15→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20624 0 6 0 20630
Biso mean--78.93 --
Num. residues----2613
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.01921251
X-RAY DIFFRACTIONr_angle_refined_deg1.6831.9329016
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7352598
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.07622.65902
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.747153185
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.66115126
X-RAY DIFFRACTIONr_chiral_restr0.120.23209
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02116226
X-RAY DIFFRACTIONr_mcbond_it4.5365.59910437
X-RAY DIFFRACTIONr_mcangle_it7.4288.37713020
X-RAY DIFFRACTIONr_scbond_it4.7815.84110814
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION / Type: TIGHT THERMAL / Weight position: 0.5

Ens-IDAuth asym-IDNumberRms dev position (Å)
1A302613.92
2I302613.58
3J19625.04
4B19629.99
5K172310.25
6G17237.88
LS refinement shellResolution: 3.146→3.228 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.624 24 -
Rwork0.344 322 -
all-346 -
obs--6.67 %

+
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