[English] 日本語
Yorodumi
- PDB-1w2e: The Crystal Structure of the Bacterial Cell Division Protein ZapA -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1w2e
TitleThe Crystal Structure of the Bacterial Cell Division Protein ZapA
ComponentsZAPA
KeywordsBACTERIAL CELL DIVISION / FTSZ MODULATOR
Function / homology
Function and homology information


septin ring assembly / cell septum / division septum assembly / FtsZ-dependent cytokinesis / cell division site / cytosol
Similarity search - Function
Cell division protein ZapA protomer, N-terminal domain / Cell division protein ZapA, N-terminal / Cell division protein ZapA-like / Cell division protein ZapA-like superfamily / Cell division protein ZapA / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #50 / Double Stranded RNA Binding Domain / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / 2-Layer Sandwich ...Cell division protein ZapA protomer, N-terminal domain / Cell division protein ZapA, N-terminal / Cell division protein ZapA-like / Cell division protein ZapA-like superfamily / Cell division protein ZapA / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #50 / Double Stranded RNA Binding Domain / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Cell division protein ZapA
Similarity search - Component
Biological speciesPSEUDOMONAS AERUGINOSA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.8 Å
AuthorsLow, H.H. / Moncrieffe, M.C. / Lowe, J.
CitationJournal: J.Mol.Biol. / Year: 2004
Title: The Crystal Structure of Zapa and its Modulation of Ftsz Polymerisation
Authors: Low, H.H. / Moncrieffe, M.C. / Lowe, J.
History
DepositionJul 1, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 19, 2004Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 24, 2018Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name ..._entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain / _entity_src_gen.pdbx_host_org_variant
Revision 1.4Oct 23, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: ZAPA
B: ZAPA


Theoretical massNumber of molelcules
Total (without water)23,6282
Polymers23,6282
Non-polymers00
Water21612
1
A: ZAPA
B: ZAPA

A: ZAPA
B: ZAPA


Theoretical massNumber of molelcules
Total (without water)47,2554
Polymers47,2554
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
MethodPQS
Unit cell
Length a, b, c (Å)105.960, 105.960, 36.260
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

-
Components

#1: Protein ZAPA / HYPOTHETICAL PROTEIN PA5227


Mass: 11813.772 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PSEUDOMONAS AERUGINOSA (bacteria) / Strain: PA01-LAC / Plasmid: PHIS17 / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / Variant (production host): C41 / References: UniProt: Q9HTW3
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.15 Å3/Da / Density % sol: 43 %

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX14.2 / Wavelength: 0.97
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.8→74.33 Å / Num. obs: 5317 / % possible obs: 99.5 % / Observed criterion σ(I): 0 / Redundancy: 12.1 % / Biso Wilson estimate: 65.699 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 47.5
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 12.6 % / Rmerge(I) obs: 0.06 / Mean I/σ(I) obs: 31.5 / % possible all: 99.5

-
Processing

SoftwareName: CNS / Classification: refinement
RefinementMethod to determine structure: MAD / Resolution: 2.8→74.33 Å / Data cutoff high absF: 10000 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.2888 280 5.1 %
Rwork0.24 --
obs0.24 5406 99.3 %
Solvent computationBsol: 39.4988 Å2 / ksol: 0.357469 e/Å3
Displacement parametersBiso mean: 53.711 Å2
Baniso -1Baniso -2Baniso -3
1--2.267 Å20 Å20 Å2
2---2.267 Å20 Å2
3---4.535 Å2
Refinement stepCycle: LAST / Resolution: 2.8→74.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1453 0 0 12 1465
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.199
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.8→2.93 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.3745 -5 %
Rwork0.3293 609 -
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1PROTEIN_REP.PARAM
X-RAY DIFFRACTION2WATER_REP.PARAM

+
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