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- PDB-4p1m: The structure of Escherichia coli ZapA -

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Basic information

Entry
Database: PDB / ID: 4p1m
TitleThe structure of Escherichia coli ZapA
ComponentsCell division protein ZapA
KeywordsCELL CYCLE / Cell division / FtsZ filament bundling / coiled-coil
Function / homology
Function and homology information


septin ring assembly / cell septum / FtsZ-dependent cytokinesis / division septum assembly / cell division site / cell division / identical protein binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Cell division protein ZapA, eubacteria / Cell division protein ZapA protomer, N-terminal domain / Cell division protein ZapA-like / Cell division protein ZapA-like superfamily / Cell division protein ZapA / Double Stranded RNA Binding Domain / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Cell division protein ZapA / Cell division protein ZapA
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsKimber, M.S. / Roach, E.J. / Khursigara, C.M.
Funding support Canada, 2items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada)327280 Canada
Natural Sciences and Engineering Research Council (NSERC, Canada)371639 Canada
CitationJournal: J.Biol.Chem. / Year: 2014
Title: Crystal Structure and Site-directed Mutational Analysis Reveals Key Residues Involved in Escherichia coli ZapA Function.
Authors: Roach, E.J. / Kimber, M.S. / Khursigara, C.M.
History
DepositionFeb 26, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 16, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 1, 2014Group: Database references
Revision 1.2Sep 20, 2017Group: Advisory / Author supporting evidence ...Advisory / Author supporting evidence / Database references / Derived calculations / Other / Source and taxonomy
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_audit_support / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list / pdbx_validate_close_contact
Item: _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag ..._citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _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 / refine_hist
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 ZapA
B: Cell division protein ZapA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,5473
Polymers28,5122
Non-polymers351
Water2,126118
1
A: Cell division protein ZapA
B: Cell division protein ZapA
hetero molecules

A: Cell division protein ZapA
B: Cell division protein ZapA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,0956
Polymers57,0244
Non-polymers712
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-y+1,-x+1,-z+5/61
Buried area16760 Å2
ΔGint-126 kcal/mol
Surface area21420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.100, 54.100, 328.070
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11B-321-

HOH

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Components

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


Mass: 14255.937 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: zapA / Plasmid: pBAD24 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q1JQN5, UniProt: P0ADS2*PLUS
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 118 / 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: 2.43 Å3/Da / Density % sol: 49.39 % / Description: Hexagonal bipyramid
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.6 / Details: ammonium sulfate, lithium sulfate, sodium citrate.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 12, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. obs: 22080 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 9.1 % / Biso Wilson estimate: 33.5 Å2 / Rsym value: 0.067 / Net I/σ(I): 19.4
Reflection shellResolution: 1.95→2 Å / Rmerge(I) obs: 0.84 / Mean I/σ(I) obs: 2.7 / % possible all: 99.9

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.8.2_1309) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1W2E

1w2e


Resolution: 1.95→46.381 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 27.06 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.27 1104 5 %random
Rwork0.2241 ---
obs0.2263 22067 99.88 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 51.8 Å2
Refinement stepCycle: LAST / Resolution: 1.95→46.381 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1726 0 1 118 1845
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061745
X-RAY DIFFRACTIONf_angle_d0.9962354
X-RAY DIFFRACTIONf_dihedral_angle_d17.978694
X-RAY DIFFRACTIONf_chiral_restr0.055268
X-RAY DIFFRACTIONf_plane_restr0.004323
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-2.03880.32881330.26982515X-RAY DIFFRACTION100
2.0388-2.14630.32411330.24122540X-RAY DIFFRACTION100
2.1463-2.28070.2981340.23082549X-RAY DIFFRACTION100
2.2807-2.45680.29641370.22292598X-RAY DIFFRACTION100
2.4568-2.7040.2731360.22292585X-RAY DIFFRACTION100
2.704-3.09520.27751370.22532596X-RAY DIFFRACTION100
3.0952-3.89940.22241410.21682695X-RAY DIFFRACTION100
3.8994-46.39450.27721530.22112885X-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)
11.5538-0.1928-0.23742.89050.07571.6331-0.0328-0.5944-0.081-0.36720.22010.1711-0.0243-0.23160.06710.1992-0.0788-0.01610.50440.06850.32221.024920.9437181.389
2-0.0359-0.05210.07420.01170.40570.8353-0.0532-0.0703-0.106-0.0041-0.1612-0.0582-0.41340.2193-0.00350.3172-0.00240.00980.38030.06490.308717.002323.8654146.7112
33.59630.58710.83613.4387-1.30322.0083-0.048-0.67570.1197-0.39470.1259-0.23040.2928-0.1545-0.1950.1855-0.0456-0.04590.39080.02070.256919.997719.8393181.645
4-0.0842-0.1306-0.32530.1815-0.36390.7204-0.1727-0.11580.0145-0.1066-0.1836-0.0367-0.0166-0.26080.00090.3038-0.02710.01540.37720.00440.29634.47624.2518146.2708
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and ((resseq 1:49))
2X-RAY DIFFRACTION2chain 'A' and (resseq 50:109)
3X-RAY DIFFRACTION3chain 'B' and (resseq 1:49)
4X-RAY DIFFRACTION4chain 'B' and (resseq 50:109)

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