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- PDB-2rhh: Synthetic Gene Encoded Bacillus Subtilis FtsZ with Bound Sulfate Ion -

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Basic information

Entry
Database: PDB / ID: 2rhh
TitleSynthetic Gene Encoded Bacillus Subtilis FtsZ with Bound Sulfate Ion
ComponentsCell Division Protein ftsZ
KeywordsCELL CYCLE / CELL DIVISION PROTEIN / TUBULIN HOMOLOG / GTP-BINDING / POLYMERIZATION / GTPASE / Structural Genomics / PSI-2 / Protein Structure Initiative / Accelerated Technologies Center for Gene to 3D Structure / ATCG3D
Function / homology
Function and homology information


cell septum / FtsZ-dependent cytokinesis / division septum assembly / cell division site / protein polymerization / cell division / GTPase activity / GTP binding / identical protein binding / cytoplasm
Similarity search - Function
Tubulin-like protein FtsZ/CetZ / 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/FtsZ, C-terminal domain / Tubulin/FtsZ, GTPase domain / 60s Ribosomal Protein L30; Chain: A; ...Tubulin-like protein FtsZ/CetZ / 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/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
Cell division protein FtsZ
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.001 Å
AuthorsLovell, S. / Halloran, Z. / Hjerrild, K. / Sheridan, D. / Burgin, A. / Stewart, L. / Accelerated Technologies Center for Gene to 3D Structure (ATCG3D)
CitationJournal: BMC Biotechnol. / Year: 2009
Title: Combined protein construct and synthetic gene engineering for heterologous protein expression and crystallization using Gene Composer.
Authors: Raymond, A. / Lovell, S. / Lorimer, D. / Walchli, J. / Mixon, M. / Wallace, E. / Thompkins, K. / Archer, K. / Burgin, A. / Stewart, L.
History
DepositionOct 9, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 21, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)34,1482
Polymers34,0521
Non-polymers961
Water2,054114
1
A: Cell Division Protein ftsZ
hetero molecules

A: Cell Division Protein ftsZ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,2964
Polymers68,1032
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Buried area3040 Å2
ΔGint-45 kcal/mol
Surface area22720 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)66.370, 66.370, 152.089
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Cell Division Protein ftsZ /


Mass: 34051.707 Da / Num. of mol.: 1 / Fragment: residues 12-315
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: ftsZ / Plasmid: pET28c / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P17865
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 114 / 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: 2.46 Å3/Da / Density % sol: 49.99 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7
Details: 50% PEG 200, 0.1M Tris, 50mM lithium sulfate, pH 7.0, vapor diffusion, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97934 Å
DetectorType: CUSTOM-MADE / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 2.001→50 Å / Num. obs: 23413 / % possible obs: 98.3 % / Observed criterion σ(I): 0 / Redundancy: 11.4 % / Rmerge(I) obs: 0.087 / Χ2: 0.493 / Net I/σ(I): 19.8
Reflection shellResolution: 2.001→2.07 Å / Redundancy: 6 % / Rmerge(I) obs: 0.449 / Mean I/σ(I) obs: 1.4 / Num. unique all: 2052 / Χ2: 0.445 / % possible all: 88.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMAC5.2.0019refinement
PDB_EXTRACT3data extraction
SBC-Collectcollectdata collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.001→50 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.917 / SU B: 4.767 / SU ML: 0.133 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.184 / ESU R Free: 0.17 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.257 1194 5.1 %RANDOM
Rwork0.212 ---
all0.215 23347 --
obs0.215 23347 98.27 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 28.927 Å2
Baniso -1Baniso -2Baniso -3
1-1.52 Å20 Å20 Å2
2--1.52 Å20 Å2
3----3.04 Å2
Refinement stepCycle: LAST / Resolution: 2.001→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2191 0 5 114 2310
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0222210
X-RAY DIFFRACTIONr_bond_other_d0.0030.021434
X-RAY DIFFRACTIONr_angle_refined_deg1.581.9762986
X-RAY DIFFRACTIONr_angle_other_deg0.97433556
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5325303
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.30726.82485
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.16115391
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.718159
X-RAY DIFFRACTIONr_chiral_restr0.090.2362
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022506
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02375
X-RAY DIFFRACTIONr_nbd_refined0.2190.2488
X-RAY DIFFRACTIONr_nbd_other0.2020.21515
X-RAY DIFFRACTIONr_nbtor_refined0.1720.21102
X-RAY DIFFRACTIONr_nbtor_other0.0890.21196
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1740.2133
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0070.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.160.210
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2560.232
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3830.210
X-RAY DIFFRACTIONr_mcbond_it1.3221.51922
X-RAY DIFFRACTIONr_mcbond_other0.2481.5636
X-RAY DIFFRACTIONr_mcangle_it1.53422372
X-RAY DIFFRACTIONr_scbond_it3.0593784
X-RAY DIFFRACTIONr_scangle_it4.4924.5614
LS refinement shellResolution: 2.001→2.053 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.311 79 -
Rwork0.264 1403 -
all-1482 -
obs--87.18 %

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