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- PDB-1w5e: FtsZ W319Y mutant, P1 (M. jannaschii) -

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Basic information

Entry
Database: PDB / ID: 1w5e
TitleFtsZ W319Y mutant, P1 (M. jannaschii)
ComponentsFTSZ
KeywordsCELL DIVISION / CELL-DIVISION PROTEIN / GTP-BINDING / MULTIGENE FAMILY / SEPTATION / TUBULIN / FTSZ / FILAMENT / Z-RING / GTPASE
Function / homology
Function and homology information


FtsZ-dependent cytokinesis / division septum assembly / cell division site / protein polymerization / cell division / 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, 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
GUANOSINE-5'-TRIPHOSPHATE / Cell division protein FtsZ 1
Similarity search - Component
Biological speciesMETHANOCALDOCOCCUS JANNASCHII (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsOliva, M.A. / Cordell, S.C. / Lowe, J.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2004
Title: Structural Insights Into Ftsz Protofilament Formation
Authors: Oliva, M.A. / Cordell, S.C. / Lowe, J.
History
DepositionAug 6, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 1, 2004Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 24, 2018Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name ..._entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain / _entity_src_gen.pdbx_host_org_variant
Revision 1.4Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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 / _pdbx_database_status.status_code_sf / _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: FTSZ
B: FTSZ
C: FTSZ
D: FTSZ
E: FTSZ
F: FTSZ
G: FTSZ
H: FTSZ
I: FTSZ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)355,23218
Polymers350,5249
Non-polymers4,7099
Water12,178676
1
A: FTSZ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,4702
Polymers38,9471
Non-polymers5231
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: FTSZ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,4702
Polymers38,9471
Non-polymers5231
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
C: FTSZ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,4702
Polymers38,9471
Non-polymers5231
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
4
D: FTSZ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,4702
Polymers38,9471
Non-polymers5231
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
5
E: FTSZ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,4702
Polymers38,9471
Non-polymers5231
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
6
F: FTSZ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,4702
Polymers38,9471
Non-polymers5231
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
7
G: FTSZ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,4702
Polymers38,9471
Non-polymers5231
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
8
H: FTSZ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,4702
Polymers38,9471
Non-polymers5231
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
9
I: FTSZ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,4702
Polymers38,9471
Non-polymers5231
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)113.951, 114.332, 115.135
Angle α, β, γ (deg.)90.07, 90.19, 119.86
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
FTSZ /


Mass: 38947.086 Da / Num. of mol.: 9 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) METHANOCALDOCOCCUS JANNASCHII (archaea)
Plasmid: PHIS17 / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / Variant (production host): C41 / References: UniProt: Q57816
#2: Chemical
ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE / Guanosine triphosphate


Mass: 523.180 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 676 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHIS PROTEIN IS ESSENTIAL TO THE CELL-DIVISION PROCESS. IT SEEMS TO ASSEMBLE INTO A DYNAMIC RING ON ...THIS PROTEIN IS ESSENTIAL TO THE CELL-DIVISION PROCESS. IT SEEMS TO ASSEMBLE INTO A DYNAMIC RING ON THE INNER SURFACE OF THE CYTOPLASMIC MEMBRANE AT THE PLACE WHERE DIVISION WILL OCCUR. ENGINEERED MUTATION TRP 310 TYR

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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: 3.71 Å3/Da / Density % sol: 68 %

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.93
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.93 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 85869 / % possible obs: 94.7 % / Observed criterion σ(I): 0 / Redundancy: 1.9 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 6.6
Reflection shellResolution: 3→3.16 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 1.9 / % possible all: 94.7

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Processing

Software
NameVersionClassification
CNS1.1refinement
MOSFLMdata reduction
SCALAdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1FSZ

1fsz


Resolution: 3→50 Å / Data cutoff high absF: 10000 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MLF
RfactorNum. reflection% reflectionSelection details
Rfree0.2985 4818 4.8 %RANDOM
Rwork0.2638 ---
obs0.2638 95481 94.7 %-
Solvent computationBsol: 32.5513 Å2 / ksol: 0.273406 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--6.903 Å2-13.233 Å2-0.568 Å2
2---5.788 Å2-1.564 Å2
3---12.691 Å2
Refinement stepCycle: LAST / Resolution: 3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22167 0 288 676 23131
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.258
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 3→3.02 Å / Total num. of bins used: 50 /
Rfactor% reflection
Rfree0.518 5 %
Rwork0.492 -
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1PROTEIN_REP.PARAM
X-RAY DIFFRACTION2ION.PARAM
X-RAY DIFFRACTION3WATER.PARAM
X-RAY DIFFRACTION4GTP.PAR

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