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- PDB-5imj: Crystal structure of a Z-ring associated protein from Escherichia coli -

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Basic information

Entry
Database: PDB / ID: 5imj
TitleCrystal structure of a Z-ring associated protein from Escherichia coli
ComponentsCell division protein ZapD
KeywordsCELL CYCLE / ZapD / cytokinesis / cell division / FtsZ
Function / homology
Function and homology information


division septum assembly / FtsZ-dependent cytokinesis / cell division site / protein homodimerization activity / identical protein binding / cytosol
Similarity search - Function
YacF-like / YacF-like / YacF-like / YacF-like domains / Cell division protein ZapD / Z ring-associated protein D, C-terminal / ZapD domain superfamily / Cell division protein / Sandwich / Orthogonal Bundle ...YacF-like / YacF-like / YacF-like / YacF-like domains / Cell division protein ZapD / Z ring-associated protein D, C-terminal / ZapD domain superfamily / Cell division protein / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Cell division protein ZapD
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsChoi, H. / Yoon, H.J. / Lee, H.H.
CitationJournal: To Be Published
Title: Crystal structure of ZapD, a positive regulator of Z-ring formation during bacterial cytokinesis
Authors: Lee, H.H. / Choi, H. / Min, K.J. / Yoon, H.J. / Ha, J.M.
History
DepositionMar 6, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 8, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 8, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cell division protein ZapD
B: Cell division protein ZapD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,8657
Polymers56,3852
Non-polymers4805
Water73941
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4080 Å2
ΔGint-64 kcal/mol
Surface area25650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.490, 109.490, 106.659
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number172
Space group name H-MP64
Components on special symmetry positions
IDModelComponents
11A-408-

HOH

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Components

#1: Protein Cell division protein ZapD / Z ring-associated protein D


Mass: 28192.396 Da / Num. of mol.: 2 / Fragment: UNP residues 2-247
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: zapD, yacF, b0102, JW0099 / Production host: Escherichia coli (E. coli) / References: UniProt: P36680
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 41 / 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: 3.27 Å3/Da / Density % sol: 62.42 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: Lithium sulfate, HEPES pH 7.8, PEG400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.97952 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Jun 2, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97952 Å / Relative weight: 1
ReflectionResolution: 2.95→50 Å / Num. obs: 15284 / % possible obs: 99.3 % / Redundancy: 9.1 % / Rmerge(I) obs: 0.505 / Rsym value: 0.505 / Net I/σ(I): 33.4
Reflection shellResolution: 2.95→3 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2OEZ

2oez


Resolution: 3.1→35.43 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.902 / SU B: 21.347 / SU ML: 0.373 / Cross valid method: THROUGHOUT / ESU R Free: 0.109 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28263 879 6.7 %RANDOM
Rwork0.22253 ---
obs0.22662 12262 99.01 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 94.516 Å2
Baniso -1Baniso -2Baniso -3
1--0.23 Å20 Å20 Å2
2---0.23 Å20 Å2
3---0.46 Å2
Refinement stepCycle: 1 / Resolution: 3.1→35.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3968 0 25 41 4034
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0194066
X-RAY DIFFRACTIONr_bond_other_d0.0010.023970
X-RAY DIFFRACTIONr_angle_refined_deg1.2081.9725514
X-RAY DIFFRACTIONr_angle_other_deg0.80139080
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7665490
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.1423.725204
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.63515722
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1451540
X-RAY DIFFRACTIONr_chiral_restr0.0650.2627
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0214590
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02978
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.4939.4281966
X-RAY DIFFRACTIONr_mcbond_other4.4929.4271965
X-RAY DIFFRACTIONr_mcangle_it7.4614.132454
X-RAY DIFFRACTIONr_mcangle_other7.45914.132455
X-RAY DIFFRACTIONr_scbond_it3.849.62098
X-RAY DIFFRACTIONr_scbond_other3.8369.5712080
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.5414.2653031
X-RAY DIFFRACTIONr_long_range_B_refined11.52973.7684693
X-RAY DIFFRACTIONr_long_range_B_other11.51273.7564691
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.1→3.18 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.384 65 -
Rwork0.284 915 -
obs--99.59 %

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