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- PDB-1rq7: MYCOBACTERIUM TUBERCULOSIS FTSZ IN COMPLEX WITH GDP -

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Basic information

Entry
Database: PDB / ID: 1rq7
TitleMYCOBACTERIUM TUBERCULOSIS FTSZ IN COMPLEX WITH GDP
ComponentsCell division protein ftsZ
KeywordsCELL CYCLE / SIGNALING PROTEIN / TUBULIN / GTPASE
Function / homology
Function and homology information


septin ring assembly / division septum assembly / FtsZ-dependent cytokinesis / cell division site / protein polymerization / positive regulation of cell cycle / cell division / GTPase activity / GTP binding / magnesium ion binding ...septin ring assembly / division septum assembly / FtsZ-dependent cytokinesis / cell division site / protein polymerization / positive regulation of cell cycle / cell division / GTPase activity / GTP binding / magnesium ion binding / plasma membrane / 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 / Cell division protein FtsZ
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsLeung, A.K.W. / White, E.L. / Ross, L.J. / Reynolds, R.C. / DeVito, J.A. / Borhani, D.W.
Citation
Journal: J.Mol.Biol. / Year: 2004
Title: Structure of Mycobacterium tuberculosis FtsZ reveals unexpected, G protein-like conformational switches.
Authors: Leung, A.K. / Lucile White, E. / Ross, L.J. / Reynolds, R.C. / DeVito, J.A. / Borhani, D.W.
#1: Journal: To be Published
Title: Polymerization of C-Terminally Truncated Mycobacterium tuberculosis FtsZ Is Unlikely to be Physiologically Relevant
Authors: Borhani, D.W. / White, E.L.
#2: Journal: Acta Crystallogr.,Sect.D / Year: 2000
Title: Crystallization of the Mycobacterium tuberculosis cell-division protein FtsZ
Authors: Leung, A.K.W. / White, E.L. / Ross, L.J. / Borhani, D.W.
#3: Journal: J.Bacteriol. / Year: 2000
Title: Slow polymerization of Mycobacterium tuberculosis FtsZ
Authors: White, E.L. / Ross, L.J. / Reynolds, R.C. / Seitz, L.E. / Moore, G.D. / Borhani, D.W.
#4: Journal: J.ANTIMICROB.CHEMOTHER. / Year: 2002
Title: 2-Alkoxycarbonylaminopyridines: inhibitors of Mycobacterium tuberculosis FtsZ
Authors: White, E.L. / Suling, W.J. / Ross, L.J. / Seitz, L.E. / Reynolds, R.C.
History
DepositionDec 4, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 31, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Jul 24, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
Revision 1.5Aug 23, 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 / 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)78,5893
Polymers78,1462
Non-polymers4431
Water3,279182
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)88.619, 88.619, 179.196
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein Cell division protein ftsZ


Mass: 39073.004 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: FTSZ, RV2150C, MT2209, MTCY270.18, MB2174C / Plasmid: pJD168 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-pLysS / References: UniProt: P64170, UniProt: P9WN95*PLUS
#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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 182 / 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: 2.58 Å3/Da / Density % sol: 53 %
Description: GDP INTRODUCED BY SOAKING CRYSTAL, GROWN UNDER FTSZ/CITRATE COMPLEX CONDITIONS (PDB ENTRY 1RQ2), WITH 2MM GDP AND 10MM MGCL2 OVERNIGHT.
Crystal growTemperature: 293 K / pH: 5.6
Details: 30% PEG 4000, 0.1M SODIUM CITRATE, 0.2M AMMONIUM ACETATE, 2MM SRI-7614, ETHYL (6-AMINO-2,3-DIHYDRO-4-PHENYL-1H-PYRIDO[4,3-B][1,4]DIAZEPIN-8-YL)-CARBAMATE, WAS INCLUDED AS WELL, BUT WAS NOT ...Details: 30% PEG 4000, 0.1M SODIUM CITRATE, 0.2M AMMONIUM ACETATE, 2MM SRI-7614, ETHYL (6-AMINO-2,3-DIHYDRO-4-PHENYL-1H-PYRIDO[4,3-B][1,4]DIAZEPIN-8-YL)-CARBAMATE, WAS INCLUDED AS WELL, BUT WAS NOT LOCATED IN THE FINAL STRUCTURE, VAPOR DIFFUSION, SITTING DROP, temperature 293K, pH 5.60

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: SIEMENS / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 29, 2000 / Details: DUAL OSMIC MULTILAYER MIRRORS
RadiationMonochromator: DUAL OSMIC MULTILAYER MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.6→15 Å / Num. obs: 23644 / % possible obs: 96.6 % / Observed criterion σ(I): 0 / Redundancy: 2.6 % / Biso Wilson estimate: 29 Å2 / Rmerge(I) obs: 0.119 / Rsym value: 0.119 / Net I/σ(I): 6.7
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.476 / Mean I/σ(I) obs: 1.7 / Rsym value: 0.476 / % possible all: 77.3

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Processing

Software
NameVersionClassification
REFMAC5.1.27refinement
SCALAdata scaling
TRUNCATEdata reduction
X-PLORmodel building
X-PLORrefinement
CCP4(SCALAdata scaling
TRUNCATEdata scaling
X-PLORphasing
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PARTIALLY REFINED MODEL OF THE MYCOBACTERIUM TUBERCULOSIS FTSZ/CITRATE COMPLEX, PDB ENTRY 1RQ2.

1rq2


Resolution: 2.6→14.99 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.897 / SU B: 10.206 / SU ML: 0.214 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / ESU R: 0.475 / ESU R Free: 0.287 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: X-PLOR-GENERATED BULK SOLVENT PARTIAL STRUCTURE FACTORS WERE USED IN REFMAC AS PARTIAL STRUCTURE FACTORS (FPART/PHIPART), EXCEPT IN LAST ROUND, WHERE REFMAC BABINET MODEL WITH MASK WAS USED.
RfactorNum. reflection% reflectionSelection details
Rfree0.2417 1217 5.2 %RANDOM
Rwork0.18365 ---
obs0.18672 22385 97.06 %-
all-23604 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 38.108 Å2
Baniso -1Baniso -2Baniso -3
1--0.25 Å2-0.13 Å20 Å2
2---0.25 Å20 Å2
3---0.38 Å2
Refinement stepCycle: LAST / Resolution: 2.6→14.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4207 0 28 182 4417
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0214267
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6191.9845777
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3435590
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0960.2699
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023166
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2150.21903
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1370.2204
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1910.248
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1570.27
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it1.091.52902
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.03624585
X-RAY DIFFRACTIONr_scbond_it2.7131365
X-RAY DIFFRACTIONr_scangle_it4.74.51192
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.6→2.666 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.38 76
Rwork0.249 1190

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