[English] 日本語
Yorodumi
- PDB-1d8s: ESCHERICHIA COLI F1 ATPASE -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1d8s
TitleESCHERICHIA COLI F1 ATPASE
Components
  • F1 ATPASE (ALPHA SUBUNIT)
  • F1 ATPASE (BETA SUBUNIT)
  • F1 ATPASE (GAMMA SUBUNIT)
KeywordsHYDROLASE
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 4.4 Å
AuthorsHausrath, A.C. / Gruber, G. / Matthews, B.W. / Capaldi, R.A.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 1999
Title: Structural features of the gamma subunit of the Escherichia coli F(1) ATPase revealed by a 4.4-A resolution map obtained by x-ray crystallography.
Authors: Hausrath, A.C. / Gruber, G. / Matthews, B.W. / Capaldi, R.A.
#1: Journal: FEBS Lett. / Year: 1997
Title: An Improved Purification of ECF1 and ECF1F0 by Using a Cytochrome bo-Deficient Strain of Escherichia coli Facilitates Crystallization of These Complexes
Authors: Gruber, G. / Hausrath, A.C. / Sagermann, M. / Capaldi, R.A.
History
DepositionOct 25, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 3, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 22, 2020Group: Data collection / Other / Refinement description / Category: diffrn / pdbx_database_status / software
Item: _diffrn.ambient_pressure / _diffrn.ambient_temp ..._diffrn.ambient_pressure / _diffrn.ambient_temp / _pdbx_database_status.status_code_sf / _software.name
Revision 1.4Feb 7, 2024Group: Database references / Category: database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: F1 ATPASE (ALPHA SUBUNIT)
B: F1 ATPASE (ALPHA SUBUNIT)
C: F1 ATPASE (ALPHA SUBUNIT)
D: F1 ATPASE (BETA SUBUNIT)
E: F1 ATPASE (BETA SUBUNIT)
F: F1 ATPASE (BETA SUBUNIT)
G: F1 ATPASE (GAMMA SUBUNIT)


Theoretical massNumber of molelcules
Total (without water)263,1857
Polymers263,1857
Non-polymers00
Water00
1
A: F1 ATPASE (ALPHA SUBUNIT)
D: F1 ATPASE (BETA SUBUNIT)
G: F1 ATPASE (GAMMA SUBUNIT)


Theoretical massNumber of molelcules
Total (without water)99,8823
Polymers99,8823
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: F1 ATPASE (ALPHA SUBUNIT)
E: F1 ATPASE (BETA SUBUNIT)


Theoretical massNumber of molelcules
Total (without water)81,6522
Polymers81,6522
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: F1 ATPASE (ALPHA SUBUNIT)
F: F1 ATPASE (BETA SUBUNIT)


Theoretical massNumber of molelcules
Total (without water)81,6522
Polymers81,6522
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)180.680, 197.520, 237.900
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

-
Components

#1: Protein F1 ATPASE (ALPHA SUBUNIT)


Mass: 41889.645 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: pAN45 / Production host: Escherichia coli (E. coli) / Strain (production host): GO104 / References: EC: 3.6.1.34
#2: Protein F1 ATPASE (BETA SUBUNIT)


Mass: 39762.000 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: pAN45 / Production host: Escherichia coli (E. coli) / Strain (production host): GO104 / References: EC: 3.6.1.34
#3: Protein F1 ATPASE (GAMMA SUBUNIT)


Mass: 18230.410 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: pAN45 / Production host: Escherichia coli (E. coli) / Strain (production host): GO104 / References: EC: 3.6.1.34
Sequence detailsTHIS MODEL WAS CONSTRUCTED FROM A LOW-RESOLUTION MAP. ONLY BACKBONE ATOMS HAVE BEEN MODELLED. IT IS ...THIS MODEL WAS CONSTRUCTED FROM A LOW-RESOLUTION MAP. ONLY BACKBONE ATOMS HAVE BEEN MODELLED. IT IS NOT POSSIBLE TO UNAMBIGUOUSLY DETERMINE THE SEQUENCE REGISTER. EVERY AMINO ACID IS LABELLED UNK. THE RESIDUE NUMBERING IS AMBIGOUS FOR ALL CHAINS. THE SEQUENCE OF THE ALPHA SUBUNIT (CHAINS A,B,C) IS: (SWS|P00822|ATPA_ECOLI) MQLNSTEISELIKQRIAQFNVVSEAHNEGTIVSVSDGVIRIHGLADCMQGEMI SLPGNRYAIALNLERDSVGAVVMGPYADLAEGMKVKCTGRILEVPVGRGLLGR VVNTLGAPIDGKGPLDHDGFSAVEAIAPGVIERQSVDQPVQTGYKAVDSMIPI GRGQRELIIGDRQTGKTALAIDAIINQRDSGIKCIYVAIGQKASTISNVVRKLE EHGALANTIVVVATASESAALQYLAPYAGCAMGEYFRDRGEDALIIYDDLSKQA VAYRQISLLLRRPPGREAFPGDVFYLHSRLLERAARVNAEYVEAFTKGEVKGKT GSLTALPIIETQAGDVSAFVPTNVISITDGQIFLETNLFNAGIRPAVNPGISVS RVGGAAQTKIMKKLSGGIRTALAQYRELAAFSQFASDLDDATRKQLDHGQKVTE LLKQKQYAPMSVAQQSLVLFAAERGYLADVELSKIGSFEAALLAYVDRDHAPLM QEINQTGGYNDEIEGKLKGILDSFKATQSW THE SEQUENCE OF THE BETA SUBUNIT (CHAINS D,E,F) IS: (SWS|P00824|ATPB_ECOLI) MATGKIVQVIGAVVDVEFPQDAVPRVYDALEVQNGNERLVLEVQQQLGGGIVRT IAMGSSDGLRRGLDVKDLEHPIEVPVGKATLGRIMNVLGEPVDMKGEIGEEERW AIHRAAPSYEELSNSQELLETGIKVIDLMCPFAKGGKVGLFGGAGVGKTVNMME LIRNIAIEHSGYSVFAGVGERTREGNDFYHEMTDSNVIDKVSLVYGQMNEPPGN RLRVALTGLTMAEKFRDEGRDVLLFVDNIYRYTLAGTEVSALLGRMPSAVGYQP TLAEEMGVLQERITSTKTGSITSVQAVYVPADDLTDPSPATTFAHLDATVVLSR QIASLGIYPAVDPLDSTSRQLDPLVVGQEHYDTARGVQSILQRYQELKDIIAIL GMDELSEEDKLVVARARKIQRFLSQPFFVAEVFTGSPGKYVSLKDTIRGFKGIM EGEYDHLPEQAFYMVGSIEEAVEKAKKL THE SEQUENCE OF THE GAMMA SUBUNIT (CHAIN G) IS: (SWS|P00837|ATPG_ECOLI) MAGAKEIRSKIASVQNTQKITKAMEMVAASKMRKSQDRMAASRPYAETMRKVIG HLAHGNLEYKHPYLEDRDVKRVGYLVVSTDRGLCGGLNINLFKKLLAEMKTWTD KGVQCDLAMIGSKGVSFFNSVGGNVVAQVTGMGDNPSLSELIGPVKVMLQAYDE GRLDKLYIVSNKFINTMSQVPTISQLLPLPASDDDDLKHKSWDYLYEPDPKALL DTLLRRYVESQVYQGVVENLASEQAARMVAMKAATDNGGSLIKELQLVYNKARQ ASITQELTEIVSGAAAV

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 4.03 Å3/Da / Density % sol: 69.5 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: Tris, PEG 8000, glycerol, NaCl, MgSO4, LiSO4, NaN3, EDTA, AMP-PNP, ATP, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal grow
*PLUS
Temperature: 25 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlprotein1drop
2110 mMTris-HCl1drop
310 %glycerol1drop
4100 mM1dropNaCl
510 mM1dropMgSO4
640 mM1dropLi2SO4
70.05 %1dropNaN3
80.1 MEDTA1drop
95 mMadenylylimidodiphosphate1drop
100.1 MATP1drop
118.0 %PEG80001drop
1235 %satammonium sulfate1reservoir

-
Data collection

DiffractionAmbient pressure: 101 kPa / Mean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.98
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 4.4→25 Å / Num. all: 89801 / Num. obs: 17553 / % possible obs: 64.5 % / Redundancy: 5.1 % / Rmerge(I) obs: 0.122 / Net I/σ(I): 3.7
Reflection shellResolution: 4.4→4.44 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.358 / Num. unique all: 0 / % possible all: 53.6
Reflection
*PLUS
Num. measured all: 89801
Reflection shell
*PLUS
% possible obs: 53.6 % / Mean I/σ(I) obs: 2.1

-
Processing

Software
NameVersionClassification
AMoREphasing
TNTrefinement
MOSFLMdata reduction
SCALA(SCALA)data scaling
RefinementResolution: 4.4→25 Å / Stereochemistry target values: TNT PROTGEO 1.0
Details: Only rigid body refinement was carried out. The model consists of backbone atoms only.
RfactorNum. reflection% reflection
all0.404 27196 -
obs-17529 64 %
Refinement stepCycle: LAST / Resolution: 4.4→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12283 0 0 0 12283
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_angle_deg0.107
X-RAY DIFFRACTIONt_bond_d3.02

+
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