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- PDB-1f47: THE BACTERIAL CELL-DIVISION PROTEIN ZIPA AND ITS INTERACTION WITH... -

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Basic information

Entry
Database: PDB / ID: 1f47
TitleTHE BACTERIAL CELL-DIVISION PROTEIN ZIPA AND ITS INTERACTION WITH AN FTSZ FRAGMENT REVEALED BY X-RAY CRYSTALLOGRAPHY
Components
  • CELL DIVISION PROTEIN FTSZ
  • CELL DIVISION PROTEIN ZIPA
KeywordsCELL CYCLE / cell division zipa / CELL DIVISiON ftsz / SEPARATION / INNER MEMBRANE / TRANSMEMBRANE
Function / homology
Function and homology information


divisome complex / division septum assembly / FtsZ-dependent cytokinesis / cell division site / protein polymerization / cell division / GTPase activity / GTP binding / protein homodimerization activity / identical protein binding ...divisome complex / division septum assembly / FtsZ-dependent cytokinesis / cell division site / protein polymerization / cell division / GTPase activity / GTP binding / protein homodimerization activity / identical protein binding / plasma membrane / cytoplasm
Similarity search - Function
Cell Division Protein Zipa; Chain: A, / ZipA, C-terminal FtsZ-binding domain / ZipA, C-terminal FtsZ-binding domain / Cell division protein ZipA / ZipA, C-terminal FtsZ-binding domain superfamily / ZipA, C-terminal FtsZ-binding domain / ZipA, C-terminal domain (FtsZ-binding) / Cell division protein FtsZ / Cell division protein FtsZ, conserved site / Cell division protein FtsZ, C-terminal ...Cell Division Protein Zipa; Chain: A, / ZipA, C-terminal FtsZ-binding domain / ZipA, C-terminal FtsZ-binding domain / Cell division protein ZipA / ZipA, C-terminal FtsZ-binding domain superfamily / ZipA, C-terminal FtsZ-binding domain / ZipA, C-terminal domain (FtsZ-binding) / Cell division protein FtsZ / Cell division protein FtsZ, conserved site / Cell division protein FtsZ, C-terminal / FtsZ family, C-terminal domain / FtsZ protein signature 1. / FtsZ protein signature 2. / Tubulin-like protein FtsZ/CetZ / Tubulin/FtsZ family, C-terminal domain / Tubulin/FtsZ-like, C-terminal domain / Tubulin/FtsZ, C-terminal / Tubulin/FtsZ, 2-layer sandwich domain / Tubulin/FtsZ family, GTPase domain / Tubulin/FtsZ family, GTPase domain / Tubulin/FtsZ, GTPase domain / Tubulin/FtsZ, GTPase domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Cell division protein FtsZ / Cell division protein ZipA
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / Resolution: 1.95 Å
AuthorsMosyak, L. / Zhang, Y. / Glasfeld, E. / Stahl, M. / Somers, W.S.
CitationJournal: EMBO J. / Year: 2000
Title: The bacterial cell-division protein ZipA and its interaction with an FtsZ fragment revealed by X-ray crystallography.
Authors: Mosyak, L. / Zhang, Y. / Glasfeld, E. / Haney, S. / Stahl, M. / Seehra, J. / Somers, W.S.
History
DepositionJun 7, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 13, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow
Item: _exptl_crystal_grow.pdbx_details / _exptl_crystal_grow.temp
Revision 1.4Feb 7, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: CELL DIVISION PROTEIN ZIPA
A: CELL DIVISION PROTEIN FTSZ


Theoretical massNumber of molelcules
Total (without water)18,1572
Polymers18,1572
Non-polymers00
Water3,657203
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1130 Å2
ΔGint-12 kcal/mol
Surface area9180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.526, 38.901, 54.541
Angle α, β, γ (deg.)90.00, 104.11, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein CELL DIVISION PROTEIN ZIPA


Mass: 16134.484 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: UniProt: P77173
#2: Protein/peptide CELL DIVISION PROTEIN FTSZ


Mass: 2022.281 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: UniProt: P0A9A6
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 203 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.07 Å3/Da / Density % sol: 40.57 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 30% PEG 6000, 100 mM Bicine, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 18K
Crystal grow
*PLUS
pH: 6
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
125 mg/mlprotein1drop
225 %PEG60001reservoir
3100 mMMES1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Dec 12, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.95→25 Å / Num. all: 10556 / Num. obs: 10556 / % possible obs: 95.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.92 % / Biso Wilson estimate: 30 Å2 / Rmerge(I) obs: 0.055 / Net I/σ(I): 26.9
Reflection shellResolution: 1.95→2.02 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.146 / % possible all: 88.6
Reflection
*PLUS
Reflection shell
*PLUS
% possible obs: 88.6 % / Mean I/σ(I) obs: 8.6

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
RefinementResolution: 1.95→25 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.251 527 random
Rwork0.205 --
all0.205 10556 -
obs0.205 10556 -
Refinement stepCycle: LAST / Resolution: 1.95→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1264 0 0 203 1467
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.42
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Lowest resolution: 25 Å / σ(F): 0 / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS

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