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- PDB-4uy3: Cytoplasmic domain of bacterial cell division protein ezra -

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Basic information

Entry
Database: PDB / ID: 4uy3
TitleCytoplasmic domain of bacterial cell division protein ezra
ComponentsSEPTATION RING FORMATION REGULATOR EZRA
KeywordsSTRUCTURAL PROTEIN / 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 / plasma membrane / Septation ring formation regulator EzrA
Function and homology information
Biological speciesSTAPHYLOCOCCUS AUREUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 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 28, 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 1, 2024Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
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)23,1201
Polymers23,1201
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)96.135, 96.135, 97.128
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein SEPTATION RING FORMATION REGULATOR EZRA / EZRA


Mass: 23119.725 Da / Num. of mol.: 1
Fragment: CYTOPLASMIC DOMAIN, N-TERMINAL SPECTRIN-LIKE, REPEATS 1-2, UNP RESIDUES 24-214
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) STAPHYLOCOCCUS AUREUS (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA PLYSS / References: UniProt: A7X3E7

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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: 4.86 Å3/Da / Density % sol: 74.71 % / Description: NONE
Crystal growpH: 7.5 / Details: 0.1M TRIS PH 7.5, 34% MPD

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 10, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.6→48.56 Å / Num. obs: 14588 / % possible obs: 100 % / Observed criterion σ(I): -2 / Redundancy: 14.4 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 15.3
Reflection shellResolution: 2.6→2.72 Å / Redundancy: 14.8 % / Rmerge(I) obs: 0.97 / Mean I/σ(I) obs: 2.8 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: TO BE DEPOSITED

Resolution: 2.6→48.56 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.949 / SU B: 23.391 / SU ML: 0.205 / Cross valid method: THROUGHOUT / ESU R: 0.256 / ESU R Free: 0.224 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.24894 753 5.2 %RANDOM
Rwork0.2093 ---
obs0.21112 13770 99.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 87.02 Å2
Baniso -1Baniso -2Baniso -3
1-0.14 Å20 Å20 Å2
2--0.14 Å20 Å2
3----0.29 Å2
Refinement stepCycle: LAST / Resolution: 2.6→48.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1586 0 0 0 1586
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0191608
X-RAY DIFFRACTIONr_bond_other_d0.0010.021523
X-RAY DIFFRACTIONr_angle_refined_deg1.3171.962159
X-RAY DIFFRACTIONr_angle_other_deg0.78433512
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1565193
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.88726.08792
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.71515316
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.256158
X-RAY DIFFRACTIONr_chiral_restr0.0710.2231
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021851
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02363
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_it3.6676.454775
X-RAY DIFFRACTIONr_mcbond_other3.6596.453774
X-RAY DIFFRACTIONr_mcangle_it5.3269.692967
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it5.6287.149833
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it8.80610.4471193
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.6→2.668 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.478 64 -
Rwork0.43 982 -
obs--99.71 %
Refinement TLS params.Method: refined / Origin x: 10.1167 Å / Origin y: -18.345 Å / Origin z: -11.6054 Å
111213212223313233
T0.0949 Å20.0164 Å2-0.0068 Å2-0.014 Å20.0336 Å2--0.1184 Å2
L1.7834 °2-2.8155 °2-0.6032 °2-6.269 °21.3615 °2--0.975 °2
S-0.0707 Å °-0.095 Å °-0.1846 Å °-0.2165 Å °0.1047 Å °0.3917 Å °-0.1881 Å °-0.0255 Å °-0.034 Å °

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