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- PDB-1f46: THE BACTERIAL CELL-DIVISION PROTEIN ZIPA AND ITS INTERACTION WITH... -

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Basic information

Entry
Database: PDB / ID: 1f46
TitleTHE BACTERIAL CELL-DIVISION PROTEIN ZIPA AND ITS INTERACTION WITH AN FTSZ FRAGMENT REVEALED BY X-RAY CRYSTALLOGRAPHY
ComponentsCELL DIVISION PROTEIN ZIPA
KeywordsCELL CYCLE / cell division protein ZIPA / cell division / transmembrane / inner membrane
Function / homology
Function and homology information


divisome complex / division septum assembly / FtsZ-dependent cytokinesis / cell division site / cell division / protein homodimerization activity / plasma membrane
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) / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Cell division protein ZipA
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.5 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 1.3Feb 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)31,3242
Polymers31,3242
Non-polymers00
Water7,602422
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.890, 41.740, 71.160
Angle α, β, γ (deg.)90.00, 98.26, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein CELL DIVISION PROTEIN ZIPA


Mass: 15661.905 Da / Num. of mol.: 2
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 422 / 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: 2.34 Å3/Da / Density % sol: 47.43 %
Crystal grow
*PLUS
Temperature: 18 ℃ / pH: 6 / Method: vapor diffusion, hanging drop
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: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1.2
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 12, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2 Å / Relative weight: 1
ReflectionResolution: 1.5→20 Å / Num. all: 46702 / Num. obs: 46702 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.81 % / Biso Wilson estimate: 30 Å2 / Rmerge(I) obs: 0.063 / Net I/σ(I): 19.8
Reflection shellResolution: 1.5→1.55 Å / Redundancy: 3 % / Rmerge(I) obs: 0.042 / % possible all: 97.8
Reflection
*PLUS
Num. measured all: 93040
Reflection shell
*PLUS
% possible obs: 97.8 % / Rmerge(I) obs: 0.199 / Mean I/σ(I) obs: 4.2

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Processing

Software
NameClassification
SHARPphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 1.5→20 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.217 2335 random
Rwork0.198 --
all0.198 46702 -
obs0.198 46702 -
Refinement stepCycle: LAST / Resolution: 1.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2185 0 0 422 2607
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.34
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.5 Å / σ(F): 0 / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS

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