[English] 日本語
Yorodumi
- PDB-6o1z: Structure of pCW3 conjugation coupling protein TcpA hexagonal cry... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6o1z
TitleStructure of pCW3 conjugation coupling protein TcpA hexagonal crystal form
ComponentsDNA translocase coupling protein
KeywordsTRANSLOCASE / ATPase / Conjugation
Function / homologyFtsK domain / FtsK/SpoIIIE family / FtsK domain profile. / DNA binding / P-loop containing nucleoside triphosphate hydrolase / ATP binding / membrane / identical protein binding / Probable DNA translocase coupling protein
Function and homology information
Biological speciesClostridium perfringens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsTraore, D.A.K. / Ahktar, N. / Torres, V.T. / Adams, V. / Coulibaly, F. / Panjikar, S. / Caradoc-Davies, T.T. / Rood, J.I. / Whisstock, J.C.
Funding support Australia, 1items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)GNT1104502 Australia
CitationJournal: To be published
Title: Structure of pCW3 conjugation coupling protein TcpA
Authors: Traore, D.A.K. / Whisstock, J.C.
History
DepositionFeb 22, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 4, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 11, 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: DNA translocase coupling protein


Theoretical massNumber of molelcules
Total (without water)41,1661
Polymers41,1661
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)108.500, 108.500, 148.990
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number177
Space group name H-MP622

-
Components

#1: Protein DNA translocase coupling protein


Mass: 41166.328 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium perfringens (bacteria) / Gene: tcpA, pCW3_0030 / Production host: Escherichia coli (E. coli) / References: UniProt: Q1PLI0

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.12 Å3/Da / Density % sol: 60.56 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 25 % (w/v) PEG 3350, 0.1 M NaCitrate pH 5.5

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 12, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 3.1→46.98 Å / Num. obs: 9949 / % possible obs: 100 % / Redundancy: 13.9 % / Biso Wilson estimate: 89.6 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.137 / Rpim(I) all: 0.038 / Rrim(I) all: 0.143 / Net I/σ(I): 13.7 / Num. measured all: 138765 / Scaling rejects: 101
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
3.1-3.3114.41.1372511617450.8860.311.182.6100
8.77-46.9812.10.04262085130.9990.0120.04440.699.1

-
Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
SCALA3.3.21data scaling
PDB_EXTRACT3.24data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6O1X

6o1x


Resolution: 3.1→46.98 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.877 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.457
RfactorNum. reflection% reflectionSelection details
Rfree0.275 492 4.95 %RANDOM
Rwork0.197 ---
obs0.201 9946 99.8 %-
Displacement parametersBiso max: 205.16 Å2 / Biso mean: 115.29 Å2 / Biso min: 60.1 Å2
Baniso -1Baniso -2Baniso -3
1-15.999 Å20 Å20 Å2
2--15.999 Å20 Å2
3----31.998 Å2
Refine analyzeLuzzati coordinate error obs: 0.41 Å
Refinement stepCycle: final / Resolution: 3.1→46.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2854 0 0 0 2854
Num. residues----360
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1073SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes487HARMONIC5
X-RAY DIFFRACTIONt_it2897HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion387SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3397SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d2897HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg3895HARMONIC21.28
X-RAY DIFFRACTIONt_omega_torsion2.84
X-RAY DIFFRACTIONt_other_torsion23.38
LS refinement shellResolution: 3.1→3.15 Å / Rfactor Rfree error: 0 / Total num. of bins used: 24
RfactorNum. reflection% reflection
Rfree0.3972 20 4.82 %
Rwork0.2182 395 -
all0.2256 415 -
obs--99.29 %
Refinement TLS params.Method: refined / Origin x: 4.6463 Å / Origin y: 32.0675 Å / Origin z: 32.488 Å
111213212223313233
T-0.1742 Å2-0.051 Å2-0.0493 Å2--0.3749 Å2-0.0739 Å2--0.376 Å2
L2.1992 °20.0472 °2-0.1523 °2-1.7755 °2-0.9447 °2--1.032 °2
S0.0278 Å °-0.6363 Å °-0.0324 Å °0.889 Å °-0.1205 Å °0.1128 Å °-0.1323 Å °0.0153 Å °0.0927 Å °
Refinement TLS groupSelection details: { A|* }

+
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