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- PDB-6y1v: Mycobacterium tuberculosis FtsZ-GTP-gamma-S in complex with 4-hyd... -

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Basic information

Entry
Database: PDB / ID: 6y1v
TitleMycobacterium tuberculosis FtsZ-GTP-gamma-S in complex with 4-hydroxycoumarin
ComponentsCell division protein FtsZ
KeywordsANTIBIOTIC / Cell division Protein
Function / homology
Function and homology information


chloroplast fission / FtsZ-dependent cytokinesis / division septum assembly / cell division site / protein polymerization / 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 family, C-terminal domain / Tubulin/FtsZ-like, C-terminal domain / Tubulin/FtsZ, C-terminal ...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 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
Similarity search - Domain/homology
4-HYDROXY-2H-CHROMEN-2-ONE / 5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE / Cell division protein FtsZ
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsAlnami, A.T. / Norton, R.S. / Pena, H.P. / Haider, M. / kozielski, F.
CitationJournal: J.Mol.Biol. / Year: 2021
Title: Conformational Flexibility of A Highly Conserved Helix Controls Cryptic Pocket Formation in FtsZ.
Authors: Alnami, A. / Norton, R.S. / Pena, H.P. / Haider, S. / Kozielski, F.
History
DepositionFeb 13, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 9, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 16, 2021Group: Database references / Structure summary / Category: citation / citation_author / struct
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.identifier_ORCID / _citation_author.name / _struct.title
Revision 1.2Jan 24, 2024Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)65,80616
Polymers64,1672
Non-polymers1,63914
Water4,197233
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6120 Å2
ΔGint32 kcal/mol
Surface area23390 Å2
Unit cell
Length a, b, c (Å)88.539, 88.539, 180.297
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65
Space group name HallP65
Symmetry operation#1: x,y,z
#2: x-y,x,z+5/6
#3: y,-x+y,z+1/6
#4: -y,x-y,z+2/3
#5: -x+y,-x,z+1/3
#6: -x,-y,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LEULEULEULEU(chain 'A' and ((resid 8 through 9 and (name N...AA8 - 478 - 47
12SERSERVALVAL(chain 'A' and ((resid 8 through 9 and (name N...AA50 - 5850 - 58
13ALAALAARGARG(chain 'A' and ((resid 8 through 9 and (name N...AA70 - 13970 - 139
14ASNASNASNASN(chain 'A' and ((resid 8 through 9 and (name N...AA142 - 163142 - 163
15LEULEUGLNGLN(chain 'A' and ((resid 8 through 9 and (name N...AA166 - 168166 - 168
16VALVALASPASP(chain 'A' and ((resid 8 through 9 and (name N...AA174 - 184174 - 184
17LEULEUALAALA(chain 'A' and ((resid 8 through 9 and (name N...AA187 - 218187 - 218
18ALAALALEULEU(chain 'A' and ((resid 8 through 9 and (name N...AA221 - 269221 - 269
19ILEILEGLYGLY(chain 'A' and ((resid 8 through 9 and (name N...AA272 - 311272 - 311
210LEULEULEULEU(chain 'B' and (resid 8 through 48 or resid 50...BB8 - 478 - 47
211SERSERVALVAL(chain 'B' and (resid 8 through 48 or resid 50...BB50 - 5850 - 58
212ALAALAARGARG(chain 'B' and (resid 8 through 48 or resid 50...BB70 - 13970 - 139
213ASNASNASNASN(chain 'B' and (resid 8 through 48 or resid 50...BB142 - 163142 - 163
214LEULEUGLNGLN(chain 'B' and (resid 8 through 48 or resid 50...BB166 - 168166 - 168
215VALVALASPASP(chain 'B' and (resid 8 through 48 or resid 50...BB174 - 184174 - 184
216LEULEUALAALA(chain 'B' and (resid 8 through 48 or resid 50...BB187 - 218187 - 218
217ALAALALEULEU(chain 'B' and (resid 8 through 48 or resid 50...BB221 - 269221 - 269
218ILEILEGLYGLY(chain 'B' and (resid 8 through 48 or resid 50...BB272 - 311272 - 311

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Components

#1: Protein Cell division protein FtsZ /


Mass: 32083.266 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain CDC 1551 / Oshkosh) (bacteria)
Strain: CDC 1551 / Oshkosh / Gene: ftsZ, MT2209 / Production host: Escherichia coli (E. coli) / References: UniProt: P9WN94
#2: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE / Dimethyl sulfoxide


Mass: 78.133 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#3: Chemical ChemComp-GSP / 5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE


Mass: 539.246 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3S
#4: Chemical ChemComp-4HC / 4-HYDROXY-2H-CHROMEN-2-ONE / 4-HYDROXY-1-BENZOPYRAN-2-ONE / 4-HYDROXYCOUMARIN / 4-Hydroxycoumarin


Mass: 162.142 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H6O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 233 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 3.17 Å3/Da / Density % sol: 61.23 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 27.5% PEG4000, 0.4 M ammonium acetate and 0.1 M Na citrate soaked with 37.5 mM of inhibitor

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Data collection

DiffractionMean temperature: 298.15 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 20, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.4→180.3 Å / Num. obs: 31240 / % possible obs: 100 % / Redundancy: 4.3 % / Biso Wilson estimate: 39.88 Å2 / CC1/2: 0.992 / Net I/σ(I): 6.8
Reflection shellResolution: 2.4→2.53 Å / Num. unique obs: 4542 / CC1/2: 0.52

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1rq7

1rq7


Resolution: 2.4→76.68 Å / SU ML: 0.366 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.1739
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2299 1632 5.24 %
Rwork0.1722 29537 -
obs0.1752 31169 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 42.91 Å2
Refinement stepCycle: LAST / Resolution: 2.4→76.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4251 0 80 233 4564
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01294391
X-RAY DIFFRACTIONf_angle_d1.39955945
X-RAY DIFFRACTIONf_chiral_restr0.0739713
X-RAY DIFFRACTIONf_plane_restr0.009798
X-RAY DIFFRACTIONf_dihedral_angle_d9.60733495
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.470.35891550.29282426X-RAY DIFFRACTION99.69
2.47-2.550.31591230.25962452X-RAY DIFFRACTION99.69
2.55-2.640.33411360.23792461X-RAY DIFFRACTION99.88
2.64-2.750.26321290.22112464X-RAY DIFFRACTION99.92
2.75-2.870.28811410.20692455X-RAY DIFFRACTION99.96
2.87-3.020.25151490.19722432X-RAY DIFFRACTION99.88
3.02-3.210.26391330.18432466X-RAY DIFFRACTION99.92
3.21-3.460.25621500.16672446X-RAY DIFFRACTION99.92
3.46-3.810.24161310.15282463X-RAY DIFFRACTION100
3.81-4.360.19551250.13992490X-RAY DIFFRACTION99.89
4.36-5.490.18411340.14042485X-RAY DIFFRACTION100
5.49-76.680.1531260.15212497X-RAY DIFFRACTION99.81

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