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- PDB-2rho: Synthetic Gene Encoded Bacillus Subtilis FtsZ NCS Dimer with Boun... -

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Basic information

Entry
Database: PDB / ID: 2rho
TitleSynthetic Gene Encoded Bacillus Subtilis FtsZ NCS Dimer with Bound GDP and GTP-gamma-S
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
GUANOSINE-5'-DIPHOSPHATE / 5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE / Cell division protein FtsZ
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.45 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

Downloads & links

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Assembly

Deposited unit
A: Cell Division Protein ftsZ
B: Cell Division Protein ftsZ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,0864
Polymers68,1032
Non-polymers9822
Water1,78399
1
A: Cell Division Protein ftsZ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,5912
Polymers34,0521
Non-polymers5391
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Cell Division Protein ftsZ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,4952
Polymers34,0521
Non-polymers4431
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)82.295, 97.164, 134.719
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Cell Division Protein ftsZ /


Mass: 34051.707 Da / Num. of mol.: 2 / 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-GSP / 5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE


Mass: 539.246 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3S
#3: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE / Guanosine diphosphate


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 99 / 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: 3.95 Å3/Da / Density % sol: 68.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6
Details: 30% PEG 200, 0.1M MES, 5% PEG 3000, pH 6.0, 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: 2.45→50 Å / Num. obs: 40114 / % possible obs: 98.1 % / Observed criterion σ(I): 0 / Redundancy: 5.7 % / Rmerge(I) obs: 0.05 / Χ2: 0.656 / Net I/σ(I): 24.7
Reflection shellResolution: 2.45→2.54 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.568 / Mean I/σ(I) obs: 2 / Num. unique all: 3789 / Χ2: 0.542 / % possible all: 94.9

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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
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.45→50 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.911 / SU B: 7.287 / SU ML: 0.165 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.274 / ESU R Free: 0.235 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27 2005 5.1 %RANDOM
Rwork0.227 ---
all0.229 39678 --
obs0.229 39678 98.16 %-
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: 43.999 Å2
Baniso -1Baniso -2Baniso -3
1-4.04 Å20 Å20 Å2
2--1.11 Å20 Å2
3----5.15 Å2
Refinement stepCycle: LAST / Resolution: 2.45→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4377 0 60 99 4536
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0224470
X-RAY DIFFRACTIONr_bond_other_d0.0010.022878
X-RAY DIFFRACTIONr_angle_refined_deg1.5081.9926053
X-RAY DIFFRACTIONr_angle_other_deg0.93837137
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.875604
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.71426.824170
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.92715780
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.6681518
X-RAY DIFFRACTIONr_chiral_restr0.0780.2733
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.025024
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02754
X-RAY DIFFRACTIONr_nbd_refined0.2260.2998
X-RAY DIFFRACTIONr_nbd_other0.1920.22982
X-RAY DIFFRACTIONr_nbtor_refined0.1730.22231
X-RAY DIFFRACTIONr_nbtor_other0.0870.22465
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.160.2175
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1890.213
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2710.229
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1570.28
X-RAY DIFFRACTIONr_mcbond_it1.0911.53854
X-RAY DIFFRACTIONr_mcbond_other0.1351.51269
X-RAY DIFFRACTIONr_mcangle_it1.24824736
X-RAY DIFFRACTIONr_scbond_it1.99831642
X-RAY DIFFRACTIONr_scangle_it3.0794.51317
LS refinement shellResolution: 2.45→2.514 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.367 149 -
Rwork0.301 2649 -
all-2798 -
obs--94.98 %

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