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- PDB-4uxv: Cytoplasmic domain of bacterial cell division protein EzrA -

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Basic information

Entry
Database: PDB / ID: 4uxv
TitleCytoplasmic domain of bacterial cell division protein EzrA
ComponentsSEPTATION RING FORMATION REGULATOR EZRA
KeywordsCELL CYCLE / DIVISOME / FTSZ / CELL WALL / TUBULIN / SPECTRIN / Z-RING
Function / homologySeptation ring formation regulator EzrA / Septation ring formation regulator, EzrA / septin ring assembly / septin ring / division septum assembly / positive regulation of cell division / membrane raft / plasma membrane / Septation ring formation regulator EzrA
Function and homology information
Biological speciesBACILLUS SUBTILIS SUBSP. SUBTILIS STR. 168 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.961 Å
AuthorsCleverley, R.M. / Barrett, J.R. / Basle, A. / Khai-Bui, N. / Hewitt, L. / Solovyova, A. / Xu, Z. / Daniela, R.A. / Dixon, N.E. / Harry, E.J. ...Cleverley, R.M. / Barrett, J.R. / Basle, A. / Khai-Bui, N. / Hewitt, L. / Solovyova, A. / Xu, Z. / Daniela, R.A. / Dixon, N.E. / Harry, E.J. / Oakley, A.J. / Vollmer, W. / Lewis, R.J.
CitationJournal: Nat.Commun. / Year: 2014
Title: Structure and Function of a Spectrin-Like Regulator of Bacterial Cytokinesis.
Authors: Cleverley, R.M. / Barrett, J.R. / Basle, A. / Bui, N.K. / Hewitt, L. / Solovyova, A. / Xu, Z. / Daniel, R.A. / Dixon, N.E. / Harry, E.J. / Oakley, A.J. / Vollmer, W. / Lewis, R.J.
History
DepositionAug 27, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 22, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 3, 2014Group: Database references
Revision 1.2May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SEPTATION RING FORMATION REGULATOR EZRA


Theoretical massNumber of molelcules
Total (without water)63,1711
Polymers63,1711
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)222.703, 222.703, 184.115
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

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Components

#1: Protein SEPTATION RING FORMATION REGULATOR EZRA / EZRA


Mass: 63171.113 Da / Num. of mol.: 1 / Fragment: CYTOPLASMIC DOMAIN, RESIDUES 22-562
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BACILLUS SUBTILIS SUBSP. SUBTILIS STR. 168 (bacteria)
Production host: ESCHERICHIA COLI B (bacteria) / Strain (production host): B834(DE3) / References: UniProt: O34894

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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: 6.91 Å3/Da / Density % sol: 82.2 % / Description: NONE
Crystal growpH: 6.7
Details: 50 MM MES PH 6.7, 1 M SODIUM CITRATE, 0.2M NDSB-201, 0.1M AMMONIUM SULPHATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9173
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Oct 16, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9173 Å / Relative weight: 1
ReflectionResolution: 3.95→29.17 Å / Num. obs: 15330 / % possible obs: 99.6 % / Observed criterion σ(I): 0 / Redundancy: 22.4 % / Biso Wilson estimate: 130.78 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 20.8
Reflection shellResolution: 3.95→4.16 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 3.5 / % possible all: 99.2

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 3.961→29.044 Å / SU ML: 0.64 / σ(F): 1.63 / Phase error: 43.53 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.3483 1540 10.16 %
Rwork0.3169 --
obs0.3199 15307 99.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 155.6 Å2
Refinement stepCycle: LAST / Resolution: 3.961→29.044 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4264 0 0 0 4264
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034320
X-RAY DIFFRACTIONf_angle_d0.7855806
X-RAY DIFFRACTIONf_dihedral_angle_d14.0621694
X-RAY DIFFRACTIONf_chiral_restr0.056649
X-RAY DIFFRACTIONf_plane_restr0.004754
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.961-4.08850.46661240.4561209X-RAY DIFFRACTION98
4.0885-4.23420.40571450.38491235X-RAY DIFFRACTION100
4.2342-4.40320.36951260.35961253X-RAY DIFFRACTION100
4.4032-4.60280.32541650.34761226X-RAY DIFFRACTION100
4.6028-4.84440.34381550.31111212X-RAY DIFFRACTION100
4.8444-5.14640.33151430.28311249X-RAY DIFFRACTION100
5.1464-5.54120.45391450.36441243X-RAY DIFFRACTION100
5.5412-6.09420.45751400.39731249X-RAY DIFFRACTION100
6.0942-6.96540.43851380.37311272X-RAY DIFFRACTION100
6.9654-8.73590.27631240.30971290X-RAY DIFFRACTION100
8.7359-29.04440.27731350.24091329X-RAY DIFFRACTION100

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