[English] 日本語
Yorodumi
- PDB-2i4r: Crystal structure of the V-type ATP synthase subunit F from Archa... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2i4r
TitleCrystal structure of the V-type ATP synthase subunit F from Archaeoglobus fulgidus. NESG target GR52A.
ComponentsV-type ATP synthase subunit F
KeywordsHYDROLASE / NESG / GR52A / ATP synthesis / Structural Genomics / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium
Function / homology
Function and homology information


proton motive force-driven plasma membrane ATP synthesis / proton-transporting ATP synthase activity, rotational mechanism / ATP binding
Similarity search - Function
ATPase, V1 complex, subunit F / ATPase, V1 complex, subunit F, bacterial/archaeal / ATPase, V1 complex, subunit F / ATPase, V1 complex, subunit F superfamily / ATP synthase (F/14-kDa) subunit / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
V-type ATP synthase subunit F
Similarity search - Component
Biological speciesArchaeoglobus fulgidus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.8 Å
AuthorsVorobiev, S.M. / Su, M. / Seetharaman, J. / Zhao, L. / Fang, Y. / Cunningham, K. / Ma, L.-C. / Xiao, R. / Acton, T.B. / Montelione, G.T. ...Vorobiev, S.M. / Su, M. / Seetharaman, J. / Zhao, L. / Fang, Y. / Cunningham, K. / Ma, L.-C. / Xiao, R. / Acton, T.B. / Montelione, G.T. / Hunt, J.F. / Tong, L. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Crystal structure of the V-type ATP synthase subunit F from Archaeoglobus fulgidus
Authors: Vorobiev, S.M. / Su, M. / Seetharaman, J. / Zhao, L. / Fang, Y. / Cunningham, K. / Ma, L.-C. / Acton, T.B. / Montelione, G.T. / Hunt, J.F. / Tong, L.
History
DepositionAug 22, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 29, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: V-type ATP synthase subunit F
B: V-type ATP synthase subunit F


Theoretical massNumber of molelcules
Total (without water)23,3302
Polymers23,3302
Non-polymers00
Water1629
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: V-type ATP synthase subunit F
B: V-type ATP synthase subunit F

A: V-type ATP synthase subunit F
B: V-type ATP synthase subunit F

A: V-type ATP synthase subunit F
B: V-type ATP synthase subunit F

A: V-type ATP synthase subunit F
B: V-type ATP synthase subunit F


Theoretical massNumber of molelcules
Total (without water)93,3188
Polymers93,3188
Non-polymers00
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_575-x,-y+2,z1
crystal symmetry operation3_556-x,y,-z+11
crystal symmetry operation4_576x,-y+2,-z+11
Buried area10650 Å2
ΔGint-94 kcal/mol
Surface area26950 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)47.398, 77.827, 117.786
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

-
Components

#1: Protein V-type ATP synthase subunit F / V-type ATPase subunit F


Mass: 11664.771 Da / Num. of mol.: 2 / Mutation: I51M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Archaeoglobus fulgidus (archaea) / Gene: atpF / Plasmid: pET15 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) + Magic
References: UniProt: O29102, H+-transporting two-sector ATPase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 9 / 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: 2.33 Å3/Da / Density % sol: 47.15 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 15-20% PEG 1000, 150 mM KH(2)PO(4), 0.1 M MES, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97900, 0.97918, 0.96774
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 13, 2006
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9791
20.979181
30.967741
ReflectionResolution: 2.8→30 Å / Num. all: 10771 / Num. obs: 10674 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4 % / Biso Wilson estimate: 10.2 Å2 / Rmerge(I) obs: 0.062
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 4 % / Rmerge(I) obs: 0.688 / Mean I/σ(I) obs: 2.06 / Num. unique all: 1068 / % possible all: 100

-
Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data collection
DENZOdata reduction
SCALEPACKdata scaling
SHELXDphasing
SHELXEmodel building
SOLVEphasing
RESOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.8→29.14 Å / Rfactor Rfree error: 0.013 / Data cutoff high absF: 205705.82 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.255 380 4.5 %RANDOM
Rwork0.227 ---
obs0.227 8474 81.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 23.8787 Å2 / ksol: 0.257732 e/Å3
Displacement parametersBiso mean: 71.8 Å2
Baniso -1Baniso -2Baniso -3
1-32.15 Å20 Å20 Å2
2--3.86 Å20 Å2
3----36.01 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.37 Å0.36 Å
Luzzati d res low-5 Å
Luzzati sigma a0.75 Å0.5 Å
Refinement stepCycle: LAST / Resolution: 2.8→29.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1197 0 0 9 1206
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d23.8
X-RAY DIFFRACTIONc_improper_angle_d0.99
LS refinement shellResolution: 2.8→2.98 Å / Rfactor Rfree error: 0.071 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.354 25 2.6 %
Rwork0.315 932 -
obs--55.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.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://pdbjlvh1.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