[English] 日本語
Yorodumi
- PDB-3ea0: Crystal Structure of ParA Family ATPase from Chlorobium tepidum TLS -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3ea0
TitleCrystal Structure of ParA Family ATPase from Chlorobium tepidum TLS
ComponentsATPase, ParA family
KeywordsHYDROLASE / alpha-beta-alpha sandwich / structural genomics / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


negative regulation of cell division / cytoplasmic side of plasma membrane / ATP hydrolysis activity / ATP binding / metal ion binding / cytosol
Similarity search - Function
: / AAA domain / AAA domain / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / ATPase, ParA family
Similarity search - Component
Biological speciesChlorobium tepidum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 Å
AuthorsKim, Y. / Tesar, C. / Clancy, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal Structure of ParA Family ATPase from Chlorobium tepidum TLS
Authors: Kim, Y. / Tesar, C. / Clancy, S. / Joachimiak, A.
History
DepositionAug 24, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 23, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: ATPase, ParA family
B: ATPase, ParA family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,0716
Polymers54,0082
Non-polymers1,0634
Water2,018112
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4680 Å2
ΔGint-30 kcal/mol
Surface area19870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.572, 67.032, 134.786
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein ATPase, ParA family


Mass: 27004.229 Da / Num. of mol.: 2 / Fragment: residues 36-277
Source method: isolated from a genetically manipulated source
Details: N-terminal 6 His tag with TEV protease cut site / Source: (gene. exp.) Chlorobium tepidum (bacteria) / Strain: TLS / Gene: CT0433 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE3 / References: UniProt: Q8KF94
#2: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 112 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.12 Å3/Da / Density % sol: 41.84 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2M MgCl2, 0.1M BisTris pH6.5, 25 % PEG3350, VAPOR DIFFUSION, SITTING DROP, temperature 295K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 21, 2008 / Details: mirrors
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.2→40.45 Å / Num. obs: 44390 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.8 % / Biso Wilson estimate: 32.49 Å2 / Rmerge(I) obs: 0.138 / Net I/σ(I): 6.8
Reflection shellResolution: 2.2→2.24 Å / Redundancy: 7.7 % / Rmerge(I) obs: 0.658 / Mean I/σ(I) obs: 2.8 / Num. unique all: 1122 / % possible all: 95.2

-
Processing

Software
NameVersionClassification
SBC-Collectdata collection
HKL-3000data collection
HKL-3000phasing
MLPHAREphasing
DMmodel building
SHELXDphasing
RESOLVEmodel building
Cootmodel building
PHENIX(phenix.refine)refinement
HKL-3000data reduction
HKL-3000data scaling
DMphasing
RESOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.2→40.45 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: MLHL / Details: number of reflections contains both F+ and F-.
RfactorNum. reflection% reflectionSelection details
Rfree0.2516 2279 5.13 %Random
Rwork0.1941 ---
all0.197 44390 --
obs0.197 44390 98.76 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 50.308 Å2 / ksol: 0.316 e/Å3
Displacement parametersBiso mean: 48.27 Å2
Baniso -1Baniso -2Baniso -3
1-17.391 Å2-0 Å2-0 Å2
2---14.6967 Å20 Å2
3----2.6943 Å2
Refinement stepCycle: LAST / Resolution: 2.2→40.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3722 0 64 112 3898
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONf_bond_d0.008
X-RAY DIFFRACTIONf_angle_deg1.145
X-RAY DIFFRACTIONf_dihedral_angle_d20.77
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
2.2-2.24780.28861470.26312398254590
2.2478-2.30010.33461500.26122541269196
2.3001-2.35760.27511420.23772590273298
2.3576-2.42140.26691400.24422672281299
2.4214-2.49260.35751290.23626552784100
2.4926-2.57310.29071450.222826692814100
2.5731-2.6650.27351530.212926812834100
2.665-2.77170.271480.210526452793100
2.7717-2.89780.29311280.209226712799100
2.8978-3.05050.2621430.204826542797100
3.0505-3.24160.28441220.202426902812100
3.2416-3.49170.22971760.179626122788100
3.4917-3.84290.20331460.158426682814100
3.8429-4.39840.23311360.159726772813100
4.3984-5.53920.23411540.167626512805100
5.5392-40.45660.21391200.18392637275798
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.59630.0767-0.09442.328-0.41481.11130.0890.0217-0.01660.08580.07670.09280.16530.0086-0.1710.29450.02360.00860.2009-0.00390.187424.859-13.322850.7381
20.75710.4063-0.18873.5575-0.40931.5825-0.05240.0477-0.02360.08270.1261-0.21790.02650.0681-0.07330.17020.02180.03040.1958-0.05740.187735.614313.178252.0623
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B

+
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