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- PDB-1fsz: CRYSTAL STRUCTURE OF THE CELL-DIVISION PROTEIN FTSZ AT 2.8A RESOLUTION -

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Basic information

Entry
Database: PDB / ID: 1fsz
TitleCRYSTAL STRUCTURE OF THE CELL-DIVISION PROTEIN FTSZ AT 2.8A RESOLUTION
ComponentsFTSZ
KeywordsCELL-DIVISION PROTEIN / FTSZ / CELL DIVISION PROTEIN / TUBULIN
Function / homology
Function and homology information


chloroplast fission / 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'-DIPHOSPHATE / Cell division protein FtsZ 1
Similarity search - Component
Biological speciesMethanocaldococcus jannaschii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 2.8 Å
AuthorsLowe, J. / Amos, L.A.
CitationJournal: Nature / Year: 1998
Title: Crystal structure of the bacterial cell-division protein FtsZ.
Authors: Lowe, J. / Amos, L.A.
History
DepositionJun 24, 1997Processing site: BNL
Revision 1.0Jun 24, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Assembly

Deposited unit
A: FTSZ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,3862
Polymers39,9431
Non-polymers4431
Water2,090116
1
A: FTSZ
hetero molecules

A: FTSZ
hetero molecules

A: FTSZ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,1596
Polymers119,8293
Non-polymers1,3303
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Unit cell
Length a, b, c (Å)159.140, 159.140, 159.140
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number199
Space group name H-MI213

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Components

#1: Protein FTSZ / SULB


Mass: 39943.121 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanocaldococcus jannaschii (archaea)
Description: DSM 2661 METHANOCOCCUS JANNASCHII / Cellular location: CYTOPLASM-MEMBRANE / Cellular location (production host): CYTOPLASM / Production host: Escherichia coli (E. coli) / Strain (production host): C41 / References: UniProt: Q57816
#2: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


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


Mass: 18.015 Da / Num. of mol.: 116 / Source method: isolated from a natural source / Formula: H2O

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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: 4.2 Å3/Da / Density % sol: 71 %
Crystal growpH: 6.62 / Details: pH 6.62
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlprotein1drop
217 %PEG4001reservoir
30.1 MMES1reservoir
46 %ethanol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 9, 1997 / Details: MIRRORS
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 2.8→37.8 Å / Num. obs: 17024 / % possible obs: 99 % / Redundancy: 3 % / Biso Wilson estimate: 65 Å2 / Rmerge(I) obs: 0.065 / Rsym value: 0.065 / Net I/σ(I): 9.9
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.336 / Mean I/σ(I) obs: 2.9 / Rsym value: 0.336 / % possible all: 99.7
Reflection shell
*PLUS
% possible obs: 99.7 % / Rmerge(I) obs: 0.31 / Mean I/σ(I) obs: 2.3

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Processing

Software
NameVersionClassification
MLPHAREphasing
SOLOMONphasing
X-PLOR3.8refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MIRAS / Resolution: 2.8→8 Å / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.0001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: USED REFMAC UP TO 3.5 ANGSTROMS RESOLUTION
RfactorNum. reflection% reflectionSelection details
Rfree0.282 -5 %RANDOM
Rwork0.199 ---
obs0.199 15823 99.5 %-
Displacement parametersBiso mean: 53 Å2
Refinement stepCycle: LAST / Resolution: 2.8→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2515 0 28 116 2659
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.012
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.77
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d30.1
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.77
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it2
X-RAY DIFFRACTIONx_mcangle_it2.5
X-RAY DIFFRACTIONx_scbond_it2.5
X-RAY DIFFRACTIONx_scangle_it3
LS refinement shellResolution: 2.8→2.92 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.384 -5 %
Rwork0.332 1851 -
obs--99.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM19.SOLTOPH19.SOL
X-RAY DIFFRACTION3GDP.PAR
Software
*PLUS
Name: X-PLOR / Version: 3.8 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg30.1
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.77
LS refinement shell
*PLUS
Rfactor obs: 0.332

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