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- PDB-6ym9: Mycobacterium tuberculosis FtsZ in complex with GTP-gamma-S -

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Basic information

Entry
Database: PDB / ID: 6ym9
TitleMycobacterium tuberculosis FtsZ in complex with GTP-gamma-S
ComponentsCell division protein FtsZ
KeywordsCELL CYCLE / Cell division Protein
Function / homology
Function and homology information


division septum assembly / FtsZ-dependent cytokinesis / 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-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
5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE / Cell division protein FtsZ
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.03 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
DepositionApr 8, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 21, 2021Provider: repository / Type: Initial release
Revision 2.0Jun 9, 2021Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Other / Polymer sequence / Source and taxonomy / Structure summary
Category: atom_site / cell ...atom_site / cell / entity / entity_poly / entity_poly_seq / entity_src_gen / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_assembly / pdbx_struct_assembly_prop / pdbx_unobs_or_zero_occ_residues / struct_asym / struct_ref / struct_ref_seq
Item: _atom_site.label_entity_id / _cell.Z_PDB ..._atom_site.label_entity_id / _cell.Z_PDB / _pdbx_entity_nonpoly.entity_id / _pdbx_nonpoly_scheme.entity_id / _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details / _struct_asym.entity_id / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_auth_seq_align_end / _struct_ref_seq.ref_id / _struct_ref_seq.seq_align_end
Revision 2.1Jun 16, 2021Group: 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.identifier_ORCID / _citation_author.name
Revision 2.2Jan 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

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)64,8803
Polymers64,3412
Non-polymers5391
Water6,089338
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)89.063, 89.063, 181.327
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: 32170.344 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-GSP / 5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE


Mass: 539.246 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3S / Feature type: SUBJECT OF INVESTIGATION / References: UniProt: P9WN94*PLUS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 338 / 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: 3.15 Å3/Da / Density % sol: 60.96 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion / pH: 5.6
Details: 27.5% PEG4000, 0.4 M ammonium acetate and 0.1 M Na citrate, soaked with 10 mM GPS for 4 hr.

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Data collection

DiffractionMean temperature: 86 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER2 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: 2.03→181.33 Å / Num. obs: 51881 / % possible obs: 99 % / Redundancy: 5.7 % / Biso Wilson estimate: 37 Å2 / CC1/2: 0.998 / Net I/σ(I): 9.3
Reflection shellResolution: 2.03→2.14 Å / Num. unique obs: 7482 / CC1/2: 0.565

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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: 2.03→77.13 Å / SU ML: 0.2512 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.9447
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2107 2743 5.3 %
Rwork0.1678 49060 -
obs0.17 51803 98.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 44.49 Å2
Refinement stepCycle: LAST / Resolution: 2.03→77.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4298 0 32 338 4668
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0124455
X-RAY DIFFRACTIONf_angle_d1.14266062
X-RAY DIFFRACTIONf_chiral_restr0.0715734
X-RAY DIFFRACTIONf_plane_restr0.006807
X-RAY DIFFRACTIONf_dihedral_angle_d7.61273584
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.03-2.060.32521610.28482373X-RAY DIFFRACTION97.99
2.06-2.10.28821170.24832436X-RAY DIFFRACTION98.34
2.1-2.140.24231210.23692468X-RAY DIFFRACTION98.33
2.14-2.190.30121350.22492426X-RAY DIFFRACTION98.39
2.19-2.230.24721760.21592414X-RAY DIFFRACTION98.63
2.23-2.290.2511540.21142424X-RAY DIFFRACTION98.62
2.29-2.340.25141350.19532448X-RAY DIFFRACTION98.59
2.34-2.410.25911380.19832450X-RAY DIFFRACTION98.85
2.41-2.480.26121350.1912440X-RAY DIFFRACTION98.7
2.48-2.560.26151220.18422424X-RAY DIFFRACTION98.07
2.56-2.650.21011270.17622460X-RAY DIFFRACTION98.97
2.65-2.760.21681140.18442480X-RAY DIFFRACTION99.12
2.76-2.880.2381390.18392469X-RAY DIFFRACTION99.16
2.88-3.030.26411160.18392473X-RAY DIFFRACTION99.31
3.03-3.220.19541430.17972470X-RAY DIFFRACTION99.58
3.22-3.470.21621530.1632448X-RAY DIFFRACTION99.46
3.47-3.820.18921690.1482459X-RAY DIFFRACTION99.7
3.82-4.370.15881420.12862476X-RAY DIFFRACTION99.73
4.37-5.510.15831390.13242501X-RAY DIFFRACTION99.92
5.51-77.130.21981070.15882521X-RAY DIFFRACTION99.06
Refinement TLS params.Method: refined / Origin x: -49.623813722 Å / Origin y: 20.8060315026 Å / Origin z: 12.0076174702 Å
111213212223313233
T0.283370066145 Å2-0.013715908587 Å2-0.0137750183758 Å2-0.265065219057 Å2-0.0163400090389 Å2--0.253882209589 Å2
L1.61722383653 °2-0.199767415188 °20.22116304008 °2-0.410681653477 °2-0.0975910016312 °2--0.358865108643 °2
S-0.0669688293719 Å °-0.165394896555 Å °0.0589490853581 Å °-0.0289699880001 Å °0.0633582636649 Å °-0.00723320849851 Å °-0.0795661862623 Å °-0.0599212960797 Å °0.00369000249969 Å °
Refinement TLS groupSelection details: all

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