[English] 日本語
Yorodumi
- PDB-2x2v: Structural basis of a novel proton-coordination type in an F1Fo-A... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2x2v
TitleStructural basis of a novel proton-coordination type in an F1Fo-ATP synthase rotor ring
ComponentsATP SYNTHASE SUBUNIT C
KeywordsMEMBRANE PROTEIN / ION TRANSPORT / ATP SYNTHESIS / TRANSMEMBRANE / CF(0) / MEMBRANE / TRANSPORT / C-RING ROTOR / HYDRONIUM ION / ION BINDING POCKET / HYDROGEN ION TRANSPORT
Function / homology
Function and homology information


proton-transporting ATP synthase complex, coupling factor F(o) / ATP synthesis coupled proton transport / proton-transporting ATP synthase activity, rotational mechanism / lipid binding / integral component of membrane / plasma membrane
ATP synthase, F0 complex, subunit C / V-ATPase proteolipid subunit C-like domain / ATP synthase, F0 complex, subunit C, bacterial/chloroplast / ATP synthase, F0 complex, subunit C, DCCD-binding site / F/V-ATP synthase subunit C superfamily / F1F0 ATP synthase subunit C superfamily / ATP synthase subunit C / ATP synthase c subunit signature.
ATP synthase subunit c
Biological speciesBACILLUS PSEUDOFIRMUS OF4 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsPreiss, L. / Yildiz, O. / Hicks, D.B. / Krulwich, T.A. / Meier, T.
CitationJournal: Plos Biol. / Year: 2010
Title: A New Type of Proton Coordination in an F(1)F(O)- ATP Synthase Rotor Ring.
Authors: Preiss, L. / Yildiz, O. / Hicks, D.B. / Krulwich, T.A. / Meier, T.
Validation Report
SummaryFull reportAbout validation report
History
DepositionJan 18, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 18, 2010Provider: repository / Type: Initial release
Revision 1.1May 7, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: ATP SYNTHASE SUBUNIT C
B: ATP SYNTHASE SUBUNIT C
C: ATP SYNTHASE SUBUNIT C
D: ATP SYNTHASE SUBUNIT C
E: ATP SYNTHASE SUBUNIT C
F: ATP SYNTHASE SUBUNIT C
G: ATP SYNTHASE SUBUNIT C
H: ATP SYNTHASE SUBUNIT C
I: ATP SYNTHASE SUBUNIT C
J: ATP SYNTHASE SUBUNIT C
K: ATP SYNTHASE SUBUNIT C
L: ATP SYNTHASE SUBUNIT C
M: ATP SYNTHASE SUBUNIT C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,63636
Polymers90,83713
Non-polymers4,79923
Water1,51384
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area49870 Å2
ΔGint-577.1 kcal/mol
Surface area24920 Å2
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)74.180, 97.340, 121.240
Angle α, β, γ (deg.)90.00, 104.73, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein/peptide
ATP SYNTHASE SUBUNIT C / / ATP SYNTHASE F(0) SECTOR SUBUNIT C / F-TYPE ATPASE SUBUNIT C / F-ATPASE SUBUNIT C / LIPID-BINDING PROTEIN / OF4 C RING


Mass: 6987.461 Da / Num. of mol.: 13 / Source method: isolated from a natural source / Source: (natural) BACILLUS PSEUDOFIRMUS OF4 (bacteria) / References: UniProt: P22483
#2: Chemical
ChemComp-DPV / dodecyl 2-(trimethylammonio)ethyl phosphate / dodecylphosphocholine


Mass: 351.462 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C17H38NO4P
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Na / Sodium
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 84 / Source method: isolated from a natural source / Formula: H2O / Water

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 4.47 Å3/Da / Density % sol: 72.27 % / Description: NONE
Crystal growpH: 4.3 / Details: pH 4.3

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 2, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→44.951 Å / Num. obs: 57111 / % possible obs: 98.8 % / Observed criterion σ(I): 1.6 / Redundancy: 3.6 % / Biso Wilson estimate: 46.04 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 11.7
Reflection shellResolution: 2.5→2.6 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.98 / Mean I/σ(I) obs: 1.62 / % possible all: 92.8

-
Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2WIE
Resolution: 2.5→44.951 Å / SU ML: 0.33 / σ(F): 1.99 / Phase error: 22.97 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2345 2854 5 %
Rwork0.1876 --
Obs0.1899 57052 98.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 99 Å2 / ksol: 0.456 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--6.4674 Å2-0 Å21.7453 Å2
2--0.0696 Å2-0 Å2
3---6.3978 Å2
Refinement stepCycle: LAST / Resolution: 2.5→44.951 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6372 0 309 84 6765
Refine LS restraints

Refinement-ID: X-RAY DIFFRACTION

TypeDev idealNumber
f_bond_d0.0076721
f_angle_d0.9329126
f_dihedral_angle_d19.5772444
f_chiral_restr0.0531235
f_plane_restr0.0061053
LS refinement shell

Refinement-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.5-2.54310.33471220.3023233387
2.5431-2.58930.25621390.2504264997
2.5893-2.63910.28561450.2315275599
2.6391-2.6930.30371410.2255267299
2.693-2.75160.27161430.212272499
2.7516-2.81560.22551430.1849271299
2.8156-2.8860.23741430.167270499
2.886-2.9640.24671450.156275999
2.964-3.05120.19331440.16212727100
3.0512-3.14960.22531420.15862713100
3.1496-3.26220.24421430.1636271599
3.2622-3.39270.21721450.15292747100
3.3927-3.54710.21051430.15562728100
3.5471-3.7340.19911440.16212735100
3.734-3.96780.23371440.16012736100
3.9678-4.2740.19331450.16252744100
4.274-4.70370.16641450.1452757100
4.7037-5.38330.22631450.19112753100
5.3833-6.77870.26961460.23532777100
6.7787-44.95870.28171470.2324275898
Refinement TLS params.Method: refined / Origin x: 27.9329 Å / Origin y: -17.0887 Å / Origin z: 32.3585 Å
111213212223313233
T0.1582 Å2-0.0047 Å20.1521 Å2-0.1676 Å2-0.0244 Å2--0.1299 Å2
L1.3673 °20.0315 °20.0439 °2-1.1481 °2-0.1096 °2--0.7771 °2
S-0.0372 Å °0.2185 Å °-0.0904 Å °-0.0834 Å °0.021 Å °-0.0937 Å °-0.0112 Å °-0.0098 Å °0.0115 Å °
Refinement TLS groupSelection details: ALL

+
About Yorodumi

-
News

-
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. (see PDBe EMDB page)
  • 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 at PDBe / 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. See below links for details.
  • 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

+
Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.: Omokage search

+
Sep 15, 2016. EM Navigator & Yorodumi renewed

EM Navigator & Yorodumi renewed

  • New versions of EM Navigator and Yorodumi started

Related info.: Changes in new EM Navigator and Yorodumi

+
Aug 31, 2016. New EM Navigator & Yorodumi

New EM Navigator & Yorodumi

  • In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
  • Current version will continue as 'legacy version' for some time.

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi

Read more

-
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.

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