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- PDB-2q1y: Crystal Structure of cell division protein FtsZ from Mycobacteriu... -

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Basic information

Entry
Database: PDB / ID: 2q1y
TitleCrystal Structure of cell division protein FtsZ from Mycobacterium tuberculosis in complex with GTP-gamma-S
ComponentsCell division protein ftsZ
KeywordsCell Cycle / Signaling Protein / FtsZ / Cell Division / Protein / tuberculosis / GTP / GTP-gamma-S
Function / homology
Function and homology information


septin ring assembly / FtsZ-dependent cytokinesis / division septum assembly / cell division site / protein polymerization / positive regulation of cell cycle / cell division / GTPase activity / GTP binding / magnesium ion binding ...septin ring assembly / FtsZ-dependent cytokinesis / division septum assembly / 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
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
5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE / Cell division protein FtsZ / Cell division protein FtsZ
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.3 Å
AuthorsTruglio, J.J.
CitationJournal: To be Published
Title: Identification of FtsZ Polymerization Regulatory Elements Using a Mycobacterium tuberculosis FtsZ Temperature Sensitive Mutant
Authors: Respicio, L. / Nair, P.A. / Huang, Q. / Anil, B. / Tracz, S. / Truglio, J.J. / Kisker, C. / Raleigh, D.P. / Ojima, I. / Knudson, D.L.
History
DepositionMay 25, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 6, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Oct 18, 2017Group: Refinement description / Category: software
Revision 1.3Aug 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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)78,1213
Polymers77,5812
Non-polymers5391
Water2,972165
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)88.698, 88.698, 178.629
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65
DetailsThe asymmetric unit contains two biological units.

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Components

#1: Protein Cell division protein ftsZ /


Mass: 38790.730 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: ftsZ / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) pLysS / References: UniProt: P64170, UniProt: P9WN95*PLUS
#2: Chemical ChemComp-GSP / 5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE


Mass: 539.246 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3S
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 165 / 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: 2.61 Å3/Da / Density % sol: 52.94 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 0.1M sodium citrate pH 5.6, 30% PEG 4000, 0.3M ammonium acetate, 40% acetonitrile, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X26C / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 18, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionRedundancy: 7.4 % / Av σ(I) over netI: 8 / Number: 262207 / Rmerge(I) obs: 0.118 / Χ2: 1.14 / D res high: 2.3 Å / D res low: 40 Å / Num. obs: 35297 / % possible obs: 100
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
4.954099.910.0571.1117.3
3.934.9510010.0691.3287.4
3.443.9310010.0871.3257.4
3.123.4410010.121.2377.5
2.93.1210010.1681.1327.5
2.732.910010.2191.0817.5
2.592.7310010.2911.0747.5
2.482.5910010.3621.0567.5
2.382.4810010.4451.057.4
2.32.3810010.5451.057.5
ReflectionResolution: 2.3→40 Å / Num. obs: 35297 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 7.4 % / Rmerge(I) obs: 0.118 / Χ2: 1.144 / Net I/σ(I): 8
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.545 / Mean I/σ(I) obs: 4 / Num. unique all: 3506 / Χ2: 1.05 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT2data extraction
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB entry 2Q1X

2q1x


Resolution: 2.3→40 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.938 / SU B: 10.655 / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.216 / ESU R Free: 0.18 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21 1769 5 %RANDOM
Rwork0.172 ---
obs0.174 35256 100 %-
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: 32.016 Å2
Baniso -1Baniso -2Baniso -3
1--0.4 Å2-0.2 Å20 Å2
2---0.4 Å20 Å2
3---0.6 Å2
Refinement stepCycle: LAST / Resolution: 2.3→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4268 0 32 165 4465
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0224333
X-RAY DIFFRACTIONr_bond_other_d0.0010.024136
X-RAY DIFFRACTIONr_angle_refined_deg1.2381.995861
X-RAY DIFFRACTIONr_angle_other_deg0.75139563
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0385594
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.83125.417168
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.55515722
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.831528
X-RAY DIFFRACTIONr_chiral_restr0.0690.2704
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.024946
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02790
X-RAY DIFFRACTIONr_nbd_refined0.1980.2857
X-RAY DIFFRACTIONr_nbd_other0.1710.23887
X-RAY DIFFRACTIONr_nbtor_refined0.1590.22165
X-RAY DIFFRACTIONr_nbtor_other0.0820.22594
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1360.2191
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2250.214
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1570.254
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1820.29
X-RAY DIFFRACTIONr_mcbond_it1.67923801
X-RAY DIFFRACTIONr_mcbond_other0.21921268
X-RAY DIFFRACTIONr_mcangle_it1.9734618
X-RAY DIFFRACTIONr_scbond_it1.31821541
X-RAY DIFFRACTIONr_scangle_it2.13731243
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.267 127 -
Rwork0.205 2469 -
obs-2596 100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.62430.11620.42020.58970.33471.0271-0.02210.0607-0.09080.05930.0382-0.0239-0.04350.0185-0.0161-0.05690.0176-0.0231-0.0278-0.0046-0.0158-2.299635.14951.3129
20.4536-0.24040.35520.8836-0.65950.9409-0.07420.03430.02760.110.0462-0.0445-0.0976-0.01830.0280.0049-0.0031-0.0044-0.06950.0092-0.0347-10.685772.3666-1.2884
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA8 - 3128 - 312
2X-RAY DIFFRACTION1AC4011
3X-RAY DIFFRACTION2BB6 - 3126 - 312

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