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- PDB-2r75: Aquifex aeolicus FtsZ with 8-morpholino-GTP -

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Basic information

Entry
Database: PDB / ID: 2r75
TitleAquifex aeolicus FtsZ with 8-morpholino-GTP
ComponentsCell division protein ftsZ
KeywordsCELL CYCLE / GTPase / tubulin-like / inhibitor
Function / homology
Function and homology information


FtsZ-dependent cytokinesis / division septum assembly / cell division site / protein polymerization / cell division / GTPase activity / GTP 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
Chem-01G / Cell division protein FtsZ
Similarity search - Component
Biological speciesAquifex aeolicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.402 Å
AuthorsLappchen, T. / Pinas, V.A. / Hartog, A.F. / Koomen, G.J. / Schaffner-Barbero, C. / Andreu, J.M. / Trambaiolo, D. / Lowe, J. / Juhem, A. / Popov, A.V. / den Blaauwen, T.
CitationJournal: Chem.Biol. / Year: 2008
Title: Probing FtsZ and tubulin with C8-substituted GTP analogs reveals differences in their nucleotide binding sites
Authors: Lappchen, T. / Pinas, V.A. / Hartog, A.F. / Koomen, G.J. / Schaffner-Barbero, C. / Andreu, J.M. / Trambaiolo, D. / Lowe, J. / Juhem, A. / Popov, A.V. / den Blaauwen, T.
History
DepositionSep 7, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 22, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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
1: Cell division protein ftsZ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,4623
Polymers36,8291
Non-polymers6332
Water5,098283
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)43.846, 74.177, 44.197
Angle α, β, γ (deg.)90.00, 95.08, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Cell division protein ftsZ /


Mass: 36829.219 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus (bacteria) / Strain: VF5
Description: Gene cloned into NdeI/HindIII restriction sites
Gene: ftsZ / Plasmid: pHis17 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(AI) / References: UniProt: O66809
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-01G / 8-morpholin-4-ylguanosine 5'-(tetrahydrogen triphosphate)


Mass: 608.285 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H23N6O15P3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 283 / 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: 1.94 Å3/Da / Density % sol: 36.72 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 15 g/L FtsZ, 0.1 M Na citrate pH 5.5, 0.1 M NaCl, 0.06 M MgCl2, 25% PEG400, VAPOR DIFFUSION, SITTING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9792 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Mar 20, 2007
RadiationMonochromator: Silicon (1 1 1) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.4→30 Å / Num. all: 55046 / Num. obs: 51744 / % possible obs: 94.1 % / Observed criterion σ(I): 2 / Redundancy: 2 % / Biso Wilson estimate: 12.3 Å2 / Rmerge(I) obs: 0.051 / Rsym value: 0.051 / Net I/σ(I): 13.4
Reflection shellResolution: 1.4→1.48 Å / Redundancy: 2 % / Rmerge(I) obs: 0.153 / Mean I/σ(I) obs: 4.7 / Num. unique all: 7899 / Rsym value: 0.153 / % possible all: 98.1

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
REFMAC5.2refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2R6R

2r6r


Resolution: 1.402→16.85 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.943 / SU B: 1.752 / SU ML: 0.033 / Cross valid method: THROUGHOUT / ESU R: 0.068 / ESU R Free: 0.064 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18441 2606 5 %RANDOM
Rwork0.13694 ---
obs0.13936 49114 93.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 11.772 Å2
Baniso -1Baniso -2Baniso -3
1--0.27 Å20 Å20.08 Å2
2--0.55 Å20 Å2
3----0.26 Å2
Refinement stepCycle: LAST / Resolution: 1.402→16.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2461 0 39 283 2783
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0222532
X-RAY DIFFRACTIONr_bond_other_d0.0010.021719
X-RAY DIFFRACTIONr_angle_refined_deg1.842.0073425
X-RAY DIFFRACTIONr_angle_other_deg1.0433.0014224
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9675322
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.98225.5100
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.58115473
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.8121513
X-RAY DIFFRACTIONr_chiral_restr0.1330.2408
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022755
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02443
X-RAY DIFFRACTIONr_nbd_refined0.2270.2514
X-RAY DIFFRACTIONr_nbd_other0.1910.21808
X-RAY DIFFRACTIONr_nbtor_refined0.1760.21278
X-RAY DIFFRACTIONr_nbtor_other0.0860.21326
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1820.2186
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2380.28
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2670.246
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.190.236
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.4011.52081
X-RAY DIFFRACTIONr_mcbond_other0.7941.5666
X-RAY DIFFRACTIONr_mcangle_it2.78422585
X-RAY DIFFRACTIONr_scbond_it4.30931051
X-RAY DIFFRACTIONr_scangle_it5.9194.5840
X-RAY DIFFRACTIONr_rigid_bond_restr2.06835055
X-RAY DIFFRACTIONr_sphericity_free8.7753284
X-RAY DIFFRACTIONr_sphericity_bonded4.27434218
LS refinement shellResolution: 1.402→1.438 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.234 196 -
Rwork0.135 3727 -
obs--96.32 %

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