[English] 日本語
Yorodumi
- PDB-4z25: Mimivirus R135 (residues 51-702) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4z25
TitleMimivirus R135 (residues 51-702)
ComponentsPutative GMC-type oxidoreductase R135
KeywordsOXIDOREDUCTASE / GMC oxidoreductase / FAD / fiber
Function / homology
Function and homology information


oxidoreductase activity, acting on CH-OH group of donors / Oxidoreductases / host cell membrane / virion component / flavin adenine dinucleotide binding / membrane / identical protein binding
Similarity search - Function
GMC oxidoreductases signature 2. / Glucose-methanol-choline oxidoreductase / Glucose-methanol-choline oxidoreductase, N-terminal / GMC oxidoreductase / Glucose-methanol-choline oxidoreductase, C-terminal / GMC oxidoreductase / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / FAD/NAD(P)-binding domain superfamily / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / Putative GMC-type oxidoreductase R135
Similarity search - Component
Biological speciesAcanthamoeba polyphaga mimivirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.339 Å
AuthorsKlose, T. / Rossmann, M.G.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI011219 United States
CitationJournal: Structure / Year: 2015
Title: A Mimivirus Enzyme that Participates in Viral Entry.
Authors: Klose, T. / Herbst, D.A. / Zhu, H. / Max, J.P. / Kenttamaa, H.I. / Rossmann, M.G.
History
DepositionMar 28, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 3, 2015Provider: repository / Type: Initial release
Revision 1.1Jun 10, 2015Group: Database references
Revision 1.2Jun 17, 2015Group: Database references
Revision 1.3Sep 13, 2017Group: Author supporting evidence / Database references ...Author supporting evidence / Database references / Derived calculations / Source and taxonomy
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_audit_support / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag ..._citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Putative GMC-type oxidoreductase R135
B: Putative GMC-type oxidoreductase R135
C: Putative GMC-type oxidoreductase R135
D: Putative GMC-type oxidoreductase R135
E: Putative GMC-type oxidoreductase R135
F: Putative GMC-type oxidoreductase R135
G: Putative GMC-type oxidoreductase R135
H: Putative GMC-type oxidoreductase R135
I: Putative GMC-type oxidoreductase R135
J: Putative GMC-type oxidoreductase R135
K: Putative GMC-type oxidoreductase R135
L: Putative GMC-type oxidoreductase R135
hetero molecules


Theoretical massNumber of molelcules
Total (without water)865,69224
Polymers856,26512
Non-polymers9,42712
Water0
1
A: Putative GMC-type oxidoreductase R135
C: Putative GMC-type oxidoreductase R135
hetero molecules


Theoretical massNumber of molelcules
Total (without water)144,2824
Polymers142,7112
Non-polymers1,5712
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7850 Å2
ΔGint-36 kcal/mol
Surface area43280 Å2
MethodPISA
2
B: Putative GMC-type oxidoreductase R135
D: Putative GMC-type oxidoreductase R135
hetero molecules


Theoretical massNumber of molelcules
Total (without water)144,2824
Polymers142,7112
Non-polymers1,5712
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7810 Å2
ΔGint-35 kcal/mol
Surface area43500 Å2
MethodPISA
3
E: Putative GMC-type oxidoreductase R135
I: Putative GMC-type oxidoreductase R135
hetero molecules


Theoretical massNumber of molelcules
Total (without water)144,2824
Polymers142,7112
Non-polymers1,5712
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7720 Å2
ΔGint-36 kcal/mol
Surface area43510 Å2
MethodPISA
4
F: Putative GMC-type oxidoreductase R135
J: Putative GMC-type oxidoreductase R135
hetero molecules


Theoretical massNumber of molelcules
Total (without water)144,2824
Polymers142,7112
Non-polymers1,5712
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7740 Å2
ΔGint-35 kcal/mol
Surface area43440 Å2
MethodPISA
5
G: Putative GMC-type oxidoreductase R135
K: Putative GMC-type oxidoreductase R135
hetero molecules


Theoretical massNumber of molelcules
Total (without water)144,2824
Polymers142,7112
Non-polymers1,5712
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7770 Å2
ΔGint-35 kcal/mol
Surface area43230 Å2
MethodPISA
6
H: Putative GMC-type oxidoreductase R135
hetero molecules

L: Putative GMC-type oxidoreductase R135
hetero molecules


Theoretical massNumber of molelcules
Total (without water)144,2824
Polymers142,7112
Non-polymers1,5712
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_454-x-1,y+1/2,-z-11
Buried area7750 Å2
ΔGint-36 kcal/mol
Surface area43450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)169.974, 154.937, 197.391
Angle α, β, γ (deg.)90.00, 103.56, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
Putative GMC-type oxidoreductase R135


Mass: 71355.430 Da / Num. of mol.: 12 / Fragment: UNP residues 51-702
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acanthamoeba polyphaga mimivirus / Gene: MIMI_R135 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5UPL2, Oxidoreductases
#2: Chemical
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Formula: C27H33N9O15P2 / Comment: FAD*YM

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.92 Å3/Da / Density % sol: 57.87 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: PEG 8000, ammonium nitrate

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0332 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 17, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 3.339→48.57 Å / Num. obs: 141759 / % possible obs: 99.1 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.179 / Net I/σ(I): 9.2
Reflection shellResolution: 3.34→3.46 Å / Rmerge(I) obs: 0.392 / Mean I/σ(I) obs: 4.4 / % possible all: 99.4

-
Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4Z24

4z24


Resolution: 3.339→48.57 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 21.16 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2082 7091 5.01 %Thin shells
Rwork0.1515 ---
obs0.1544 141595 98.09 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.339→48.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms60096 0 636 0 60732
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01262268
X-RAY DIFFRACTIONf_angle_d1.55485032
X-RAY DIFFRACTIONf_dihedral_angle_d12.22622284
X-RAY DIFFRACTIONf_chiral_restr0.0779420
X-RAY DIFFRACTIONf_plane_restr0.00911064
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3391-3.45850.26784730.201712482X-RAY DIFFRACTION90
3.4585-3.59690.26259460.188213351X-RAY DIFFRACTION99
3.5969-3.76050.25634730.180813745X-RAY DIFFRACTION99
3.7605-3.95870.24029460.173913318X-RAY DIFFRACTION99
3.9587-4.20660.20714730.154213816X-RAY DIFFRACTION99
4.2066-4.53120.18529460.135313363X-RAY DIFFRACTION99
4.5312-4.98680.17864730.125113870X-RAY DIFFRACTION99
4.9868-5.70740.19289460.12913360X-RAY DIFFRACTION99
5.7074-7.1870.19644990.134913832X-RAY DIFFRACTION99
7.187-48.57480.15299160.116813367X-RAY DIFFRACTION97

+
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