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- PDB-5v68: Crystal structure of cell division protein FtsZ from Mycobacteriu... -

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Basic information

Entry
Database: PDB / ID: 5v68
TitleCrystal structure of cell division protein FtsZ from Mycobacterium tuberculosis bounded via the T9 loop
ComponentsCell division protein FtsZ
KeywordsCELL CYCLE / T9 loop / MtbFtsZ / phosphate / GDP / Z-ring
Function / homology
Function and homology information


FtsZ-dependent cytokinesis / division septum assembly / cell division site / protein polymerization / GTPase activity / GTP binding / 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/FtsZ, C-terminal domain / Tubulin/FtsZ, GTPase domain / 60s Ribosomal Protein L30; Chain: A; / Tubulin/FtsZ family, C-terminal domain ...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 / PHOSPHATE ION / Cell division protein FtsZ
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.46 Å
AuthorsLazo, E.O. / Ojima, I. / Chowdhury, S.R. / Awasthi, D. / Jakoncic, J.
Funding support United States, 7items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AIO78251 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AIO82164 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM-0080 United States
Department of Energy (DOE, United States)DE-AC02-98CH10886 United States
Office of Basic Energy SciencesDE-AC02-98CH10886 United States
National Institutes of Health/National Center for Research Resources (NIH/NCRR)P41RR012408 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P41GM103473 United States
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2019
Title: Novel T9 loop conformation of filamenting temperature-sensitive mutant Z from Mycobacterium tuberculosis.
Authors: Lazo, E.O. / Jakoncic, J. / RoyChowdhury, S. / Awasthi, D. / Ojima, I.
History
DepositionMar 16, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 29, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2May 15, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.3Jul 17, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
Revision 1.4Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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
C: Cell division protein FtsZ
D: Cell division protein FtsZ
E: Cell division protein FtsZ
F: Cell division protein FtsZ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)233,82110
Polymers232,7446
Non-polymers1,0764
Water0
1
A: Cell division protein FtsZ
B: Cell division protein FtsZ
C: Cell division protein FtsZ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,9105
Polymers116,3723
Non-polymers5382
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4380 Å2
ΔGint-32 kcal/mol
Surface area36700 Å2
MethodPISA
2
D: Cell division protein FtsZ
E: Cell division protein FtsZ
F: Cell division protein FtsZ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,9105
Polymers116,3723
Non-polymers5382
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4350 Å2
ΔGint-35 kcal/mol
Surface area34510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.110, 180.850, 220.160
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Cell division protein FtsZ /


Mass: 38790.730 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25177 / H37Ra) (bacteria)
Strain: ATCC 25177 / H37Ra / Gene: ftsZ, MRA_2165 / Production host: Escherichia coli (E. coli) / References: UniProt: A5U4H7
#2: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE / Guanosine diphosphate


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#3: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4

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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: 3.13 Å3/Da / Density % sol: 60.68 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 0.1M sodium citrate pH 5.6, 0.3M ammonium acetate, 15% PEG 4000. Protein concentration 3mg/ml. Incubated with 5mM SB-P17-A20
Temp details: room temperature

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.0781 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 1, 2013
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0781 Å / Relative weight: 1
ReflectionResolution: 3.46→55.05 Å / Num. obs: 37287 / % possible obs: 96.4 % / Redundancy: 3.3 % / CC1/2: 0.997 / Rmerge(I) obs: 0.089 / Rpim(I) all: 0.053 / Net I/σ(I): 9.3
Reflection shellResolution: 3.46→3.55 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.614 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 2754 / CC1/2: 0.735 / Rpim(I) all: 0.366 / % possible all: 97.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0151refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
PHENIXmodel building
PHENIXrefinement
xia2data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2Q1Y

2q1y


Resolution: 3.46→55.05 Å / Cor.coef. Fo:Fc: 0.914 / Cor.coef. Fo:Fc free: 0.886 / SU B: 36.59 / SU ML: 0.558 / Cross valid method: THROUGHOUT / ESU R Free: 0.641 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.3086 1881 5 %RANDOM
Rwork0.24295 ---
obs0.24636 35388 95.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 119.98 Å2
Baniso -1Baniso -2Baniso -3
1--2.08 Å20 Å2-0 Å2
2--3.73 Å20 Å2
3----1.66 Å2
Refinement stepCycle: 1 / Resolution: 3.46→55.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11874 0 66 0 11940
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.01912018
X-RAY DIFFRACTIONr_bond_other_d0.0030.0211824
X-RAY DIFFRACTIONr_angle_refined_deg1.471.98616241
X-RAY DIFFRACTIONr_angle_other_deg1.031327105
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.13551650
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.13725.375467
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.634151982
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.2931580
X-RAY DIFFRACTIONr_chiral_restr0.0740.21958
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0213935
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022419
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it7.42411.946663
X-RAY DIFFRACTIONr_mcbond_other7.42411.9396662
X-RAY DIFFRACTIONr_mcangle_it12.0617.8648292
X-RAY DIFFRACTIONr_mcangle_other12.05917.8648293
X-RAY DIFFRACTIONr_scbond_it6.4312.3095355
X-RAY DIFFRACTIONr_scbond_other6.4212.315343
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other10.91118.2967931
X-RAY DIFFRACTIONr_long_range_B_refined16.86213098
X-RAY DIFFRACTIONr_long_range_B_other16.8613097
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.46→3.55 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.37 143 -
Rwork0.348 2597 -
obs--96.65 %

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