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- PDB-5mn4: S. aureus FtsZ 12-316 F138A GDP Open form (1FOf) -

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Basic information

Entry
Database: PDB / ID: 5mn4
TitleS. aureus FtsZ 12-316 F138A GDP Open form (1FOf)
ComponentsCell division protein FtsZ
KeywordsHYDROLASE / bacterial cell division / bacterial cytoskeleton / filamentous / gtpase
Function / homology
Function and homology information


division septum assembly / FtsZ-dependent cytokinesis / cell division site / protein polymerization / GTPase activity / GTP binding / cytoplasm
Similarity search - Function
Cell division protein FtsZ / Cell division protein FtsZ, conserved site / Cell division protein FtsZ, C-terminal / FtsZ family, C-terminal domain / FtsZ protein signature 1. / FtsZ protein signature 2. / Tubulin-like protein FtsZ/CetZ / Tubulin/FtsZ, C-terminal domain / Tubulin/FtsZ, GTPase domain / 60s Ribosomal Protein L30; Chain: A; ...Cell division protein FtsZ / Cell division protein FtsZ, conserved site / Cell division protein FtsZ, C-terminal / FtsZ family, C-terminal domain / FtsZ protein signature 1. / FtsZ protein signature 2. / Tubulin-like protein FtsZ/CetZ / Tubulin/FtsZ, C-terminal domain / Tubulin/FtsZ, GTPase domain / 60s Ribosomal Protein L30; Chain: A; / Tubulin/FtsZ family, C-terminal domain / Tubulin/FtsZ-like, C-terminal domain / Tubulin/FtsZ, C-terminal / Tubulin/FtsZ, 2-layer sandwich domain / Tubulin/FtsZ family, GTPase domain / Tubulin/FtsZ family, GTPase domain / Tubulin/FtsZ, GTPase domain / Tubulin/FtsZ, GTPase domain superfamily / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / Cell division protein FtsZ
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsWagstaff, J.M. / Tsim, M. / Kureisaite-Ciziene, D. / Lowe, J.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom)U105184326 United Kingdom
Wellcome Trust095514/Z/11/Z United Kingdom
CitationJournal: MBio / Year: 2017
Title: A Polymerization-Associated Structural Switch in FtsZ That Enables Treadmilling of Model Filaments.
Authors: Wagstaff, J.M. / Tsim, M. / Oliva, M.A. / Garcia-Sanchez, A. / Kureisaite-Ciziene, D. / Andreu, J.M. / Lowe, J.
History
DepositionDec 12, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 21, 2016Provider: repository / Type: Initial release
Revision 1.1May 17, 2017Group: Database references
Revision 1.2Sep 13, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Jan 24, 2018Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name ..._entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain / _entity_src_gen.pdbx_host_org_variant
Revision 1.4Jan 17, 2024Group: 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 FtsZ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,0123
Polymers31,4511
Non-polymers5612
Water4,522251
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1130 Å2
ΔGint-18 kcal/mol
Surface area12890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.839, 51.116, 88.132
Angle α, β, γ (deg.)90.00, 110.97, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Cell division protein FtsZ


Mass: 31450.535 Da / Num. of mol.: 1 / Mutation: F138A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: ftsZ / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C41 / References: UniProt: P0A031
#2: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#3: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 251 / 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: 2.4 Å3/Da / Density % sol: 48.8 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 12.5 % w/v PEG 1k, 12.5 % w/v PEG 3350, 12.5 % v/v MPD, 0.1 M bicine/Tris pH 8.5, 0.03 M NaF, NaBr and NaI

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.93 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 15, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.93 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. obs: 45872 / % possible obs: 98.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Biso Wilson estimate: 20 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.045 / Net I/σ(I): 14.1
Reflection shellResolution: 1.5→1.58 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.652 / Mean I/σ(I) obs: 1.7 / CC1/2: 0.74 / % possible all: 97.9

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3VO8

3vo8


Resolution: 1.5→41.147 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.14 / Phase error: 22.33
RfactorNum. reflection% reflectionSelection details
Rfree0.2119 4352 4.9 %Random selection
Rwork0.1782 ---
obs0.1798 45872 94.77 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.5→41.147 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2187 0 36 251 2474
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092239
X-RAY DIFFRACTIONf_angle_d1.1583030
X-RAY DIFFRACTIONf_dihedral_angle_d10.9661358
X-RAY DIFFRACTIONf_chiral_restr0.067364
X-RAY DIFFRACTIONf_plane_restr0.006398
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.51710.28941440.30392858X-RAY DIFFRACTION95
1.5171-1.53490.32271270.29452734X-RAY DIFFRACTION94
1.5349-1.55360.3141370.29452776X-RAY DIFFRACTION93
1.5536-1.57330.32071150.29072904X-RAY DIFFRACTION94
1.5733-1.5940.36421390.26812751X-RAY DIFFRACTION94
1.594-1.61580.31241570.27262799X-RAY DIFFRACTION95
1.6158-1.63890.26681300.2622825X-RAY DIFFRACTION93
1.6389-1.66340.27561520.24272730X-RAY DIFFRACTION94
1.6634-1.68940.27411590.24522878X-RAY DIFFRACTION96
1.6894-1.71710.26311720.23832730X-RAY DIFFRACTION95
1.7171-1.74670.21672020.22462806X-RAY DIFFRACTION95
1.7467-1.77840.26851490.22032794X-RAY DIFFRACTION95
1.7784-1.81260.29351520.20922854X-RAY DIFFRACTION96
1.8126-1.84960.24311560.19792830X-RAY DIFFRACTION96
1.8496-1.88990.21681470.19652826X-RAY DIFFRACTION95
1.8899-1.93380.25181390.19212861X-RAY DIFFRACTION96
1.9338-1.98220.241240.18872753X-RAY DIFFRACTION91
1.9822-2.03580.22761460.1832819X-RAY DIFFRACTION96
2.0358-2.09570.21751290.18022901X-RAY DIFFRACTION96
2.0957-2.16330.16781300.16622841X-RAY DIFFRACTION96
2.1633-2.24060.22931560.17092872X-RAY DIFFRACTION96
2.2406-2.33030.22991550.16732919X-RAY DIFFRACTION97
2.3303-2.43640.20181400.17162882X-RAY DIFFRACTION97
2.4364-2.56480.20491240.16832787X-RAY DIFFRACTION93
2.5648-2.72550.20521340.15992860X-RAY DIFFRACTION97
2.7255-2.93590.19961600.16762855X-RAY DIFFRACTION96
2.9359-3.23120.17671330.15652855X-RAY DIFFRACTION96
3.2312-3.69850.16511780.15632714X-RAY DIFFRACTION92
3.6985-4.65870.16411460.1452749X-RAY DIFFRACTION93
4.6587-41.16210.24281200.16452769X-RAY DIFFRACTION92

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