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- PDB-5dko: The structure of Escherichia coli ZapD -

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Basic information

Entry
Database: PDB / ID: 5dko
TitleThe structure of Escherichia coli ZapD
ComponentsCell division protein ZapD
KeywordsREPLICATION / cell division / FtsZ ring
Function / homology
Function and homology information


FtsZ-dependent cytokinesis / division septum assembly / 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: 2.4 Å
AuthorsWroblewski, C. / Kimber, M.S.
Funding support Canada, 1items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada) Canada
CitationJournal: J.Bacteriol. / Year: 2016
Title: Structure and Mutational Analyses of Escherichia coli ZapD Reveal Charged Residues Involved in FtsZ Filament Bundling.
Authors: Roach, E.J. / Wroblewski, C. / Seidel, L. / Berezuk, A.M. / Brewer, D. / Kimber, M.S. / Khursigara, C.M.
History
DepositionSep 3, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 13, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 1, 2016Group: Database references
Revision 1.2Sep 6, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 27, 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

Downloads & links

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Assembly

Deposited unit
A: Cell division protein ZapD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,2904
Polymers30,0011
Non-polymers2883
Water18010
1
A: Cell division protein ZapD
hetero molecules

A: Cell division protein ZapD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,5798
Polymers60,0032
Non-polymers5766
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_555-x+y,y,-z1
Buried area4650 Å2
ΔGint-80 kcal/mol
Surface area24700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.900, 108.900, 106.970
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number181
Space group name H-MP6422
SymmetryPoint symmetry: (Schoenflies symbol: C2 (2 fold cyclic)) / Helical symmetry: (Circular symmetry: 2 )
Components on special symmetry positions
IDModelComponents
11A-303-

SO4

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Components

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


Mass: 30001.416 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: zapD, yacF, b0102, JW0099 / Plasmid: pBAD24 / Production host: Escherichia coli (E. coli) / Strain (production host): (DE3) pLysS / References: UniProt: P36680
#2: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.05 Å3/Da / Density % sol: 59.69 % / Description: hexagonal prisms
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 15 mg/ml ZapD with 1.2 M ammonium sulfate, 100 mM HEPES, pH 7.5, 10 % PEG 600

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97888 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Dec 12, 2014
RadiationMonochromator: Accel/Bruker double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97888 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. all: 26464 / Num. obs: 26464 / % possible obs: 95.2 % / Redundancy: 7.9 % / Biso Wilson estimate: 54.8 Å2 / Rsym value: 0.078 / Net I/σ(I): 13.7
Reflection shellResolution: 2.4→2.46 Å / Rmerge(I) obs: 0.76 / Mean I/σ(I) obs: 2.3 / % possible all: 96.1

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2OEZ

2oez


Resolution: 2.4→48.525 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 38.62 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2881 2628 9.93 %random
Rwork0.2468 ---
obs0.2511 26453 95.22 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 74.3 Å2
Baniso -1Baniso -2Baniso -3
1-43.69 Å20 Å20 Å2
2--43.69 Å20 Å2
3---100.27 Å2
Refinement stepCycle: LAST / Resolution: 2.4→48.525 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1976 0 15 10 2001
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032031
X-RAY DIFFRACTIONf_angle_d0.6652744
X-RAY DIFFRACTIONf_dihedral_angle_d15.094763
X-RAY DIFFRACTIONf_chiral_restr0.025310
X-RAY DIFFRACTIONf_plane_restr0.004358
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.44380.40611400.35141264X-RAY DIFFRACTION96
2.4438-2.49080.37181350.32781256X-RAY DIFFRACTION94
2.4908-2.54160.43521430.34511262X-RAY DIFFRACTION96
2.5416-2.59690.37451370.33061208X-RAY DIFFRACTION93
2.5969-2.65730.4461370.35911246X-RAY DIFFRACTION94
2.6573-2.72370.39281340.33891231X-RAY DIFFRACTION93
2.7237-2.79740.43271300.36831197X-RAY DIFFRACTION92
2.7974-2.87970.42031320.34481237X-RAY DIFFRACTION93
2.8797-2.97260.36491330.34121215X-RAY DIFFRACTION93
2.9726-3.07880.38641350.32851231X-RAY DIFFRACTION94
3.0788-3.20210.29581390.33741259X-RAY DIFFRACTION94
3.2021-3.34780.41191350.31111220X-RAY DIFFRACTION94
3.3478-3.52420.30671370.26781240X-RAY DIFFRACTION95
3.5242-3.7450.28661370.2521265X-RAY DIFFRACTION95
3.745-4.0340.20191440.22761262X-RAY DIFFRACTION96
4.034-4.43970.27031440.2061280X-RAY DIFFRACTION98
4.4397-5.08150.25981450.17651307X-RAY DIFFRACTION99
5.0815-6.39990.23861460.21961326X-RAY DIFFRACTION100
6.3999-48.53510.20471450.1751319X-RAY DIFFRACTION100
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)
12.5293-0.75741.96124.75691.49872.5054-0.05010.85040.6043-0.24320.07850.0014-0.24160.49580.01040.4248-0.01240.09560.79530.23140.769624.5361-36.452216.5144
20.4621-0.01881.10330.2445-0.14432.9547-0.1198-0.06130.07060.071-0.14420.06550.1297-0.25330.22150.4626-0.00340.17820.6653-0.06410.719-4.3286-34.754616.1257
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND ( RESID 3:12 OR RESID 179:247 ) )A3 - 12
2X-RAY DIFFRACTION1( CHAIN A AND ( RESID 3:12 OR RESID 179:247 ) )A179 - 247
3X-RAY DIFFRACTION2( CHAIN A AND RESID 13:178 )A13 - 178

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