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- PDB-6y1u: Mycobacterium tuberculosis FtsZ-GDP in complex with 4-hydroxycoumarin -

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Basic information

Entry
Database: PDB / ID: 6y1u
TitleMycobacterium tuberculosis FtsZ-GDP 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 / GUANOSINE-5'-DIPHOSPHATE / Cell division protein FtsZ
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.68 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: 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

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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)66,57526
Polymers64,1672
Non-polymers2,40824
Water7,134396
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8760 Å2
ΔGint56 kcal/mol
Surface area22740 Å2
Unit cell
Length a, b, c (Å)88.130, 88.130, 176.783
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

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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.: 21 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#3: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE / Guanosine diphosphate


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#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.: 2 / Source method: obtained synthetically / Formula: C9H6O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 396 / 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: 3.07 Å3/Da / Density % sol: 59.99 %
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: I04-1 / Wavelength: 0.9159 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 5, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9159 Å / Relative weight: 1
ReflectionResolution: 1.68→76.323 Å / Num. obs: 88000 / % possible obs: 100 % / Redundancy: 8 % / Biso Wilson estimate: 25.04 Å2 / CC1/2: 0.999 / Net I/σ(I): 17.5
Reflection shellResolution: 1.68→1.74 Å / Num. unique obs: 8733 / CC1/2: 0.479

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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: 1.68→76.32 Å / SU ML: 0.1855 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 20.2549
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1966 4365 4.96 %
Rwork0.1684 83632 -
obs0.1698 87997 99.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 33.9 Å2
Refinement stepCycle: LAST / Resolution: 1.68→76.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4262 0 108 396 4766
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01184533
X-RAY DIFFRACTIONf_angle_d1.21556161
X-RAY DIFFRACTIONf_chiral_restr0.0824742
X-RAY DIFFRACTIONf_plane_restr0.0067830
X-RAY DIFFRACTIONf_dihedral_angle_d5.92793595
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.68-1.70.34731620.29452770X-RAY DIFFRACTION99.42
1.7-1.720.29451690.292718X-RAY DIFFRACTION99.48
1.72-1.740.29781600.26892753X-RAY DIFFRACTION99.62
1.74-1.760.30241340.26472802X-RAY DIFFRACTION99.59
1.76-1.790.26711640.2452742X-RAY DIFFRACTION99.45
1.79-1.810.27431300.24142807X-RAY DIFFRACTION99.69
1.81-1.840.3061340.22562812X-RAY DIFFRACTION99.7
1.84-1.860.26121260.20882774X-RAY DIFFRACTION99.55
1.86-1.890.23451420.19812757X-RAY DIFFRACTION99.83
1.89-1.920.2271260.18952806X-RAY DIFFRACTION99.66
1.92-1.960.21621440.17682818X-RAY DIFFRACTION99.83
1.96-1.990.19381570.17452739X-RAY DIFFRACTION99.76
1.99-2.030.20771500.17282796X-RAY DIFFRACTION99.83
2.03-2.070.21741520.1682752X-RAY DIFFRACTION99.97
2.07-2.120.19351190.16812823X-RAY DIFFRACTION99.83
2.12-2.170.1791220.16072825X-RAY DIFFRACTION100
2.17-2.220.21871730.16592772X-RAY DIFFRACTION99.93
2.22-2.280.19711430.16242768X-RAY DIFFRACTION99.9
2.28-2.350.19281740.16042756X-RAY DIFFRACTION99.97
2.35-2.420.20271560.16432796X-RAY DIFFRACTION99.97
2.42-2.510.19851470.16242798X-RAY DIFFRACTION99.93
2.51-2.610.19591520.16672773X-RAY DIFFRACTION100
2.61-2.730.18961050.16372834X-RAY DIFFRACTION99.97
2.73-2.870.18171290.16962804X-RAY DIFFRACTION100
2.87-3.050.23131610.16682796X-RAY DIFFRACTION100
3.05-3.290.17851350.15852817X-RAY DIFFRACTION100
3.29-3.620.15741600.15172777X-RAY DIFFRACTION100
3.62-4.140.17671460.14942800X-RAY DIFFRACTION100
4.14-5.220.17661370.14332832X-RAY DIFFRACTION100
5.22-76.310.17871560.17422815X-RAY DIFFRACTION99.9
Refinement TLS params.Method: refined / Origin x: -48.9133743045 Å / Origin y: 21.1360341601 Å / Origin z: 10.9634906097 Å
111213212223313233
T0.190476504465 Å2-0.0169204251691 Å2-0.00931775028288 Å2-0.189940671138 Å2-0.000622427670158 Å2--0.180375925028 Å2
L1.08505341772 °2-0.314648668975 °20.00958400270555 °2-0.271768775866 °2-0.0559143925304 °2--0.239390798348 °2
S-0.0208348328476 Å °-0.121130937628 Å °0.0172149640803 Å °-0.0339552221321 Å °0.0549103540363 Å °-0.0132119972128 Å °-0.056208044336 Å °-0.0305409200113 Å °-0.036532563041 Å °
Refinement TLS groupSelection details: all

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