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- PDB-4b46: CetZ1 from Haloferax volcanii - GDP bound monomer -

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Basic information

Entry
Database: PDB / ID: 4b46
TitleCetZ1 from Haloferax volcanii - GDP bound monomer
ComponentsCELL DIVISION PROTEIN FTSZ
KeywordsSTRUCTURAL PROTEIN / TUBULIN / ARCHAEA / CYTOSKELETON / CELL SHAPE
Function / homology
Function and homology information


cell division site / microtubule-based process / regulation of cell shape / microtubule / cell division / GTPase activity / GTP binding / cytoplasm
Similarity search - Function
: / Tubulin-like CetZ, C-terminal domain / Tubulin-like protein CetZ / Tubulin-like protein FtsZ/CetZ / Tubulin/FtsZ, C-terminal domain / Tubulin/FtsZ, GTPase domain / 60s Ribosomal Protein L30; Chain: A; / Tubulin, conserved site / Tubulin subunits alpha, beta, and gamma signature. / Tubulin/FtsZ-like, C-terminal domain ...: / Tubulin-like CetZ, C-terminal domain / Tubulin-like protein CetZ / Tubulin-like protein FtsZ/CetZ / Tubulin/FtsZ, C-terminal domain / Tubulin/FtsZ, GTPase domain / 60s Ribosomal Protein L30; Chain: A; / Tubulin, conserved site / Tubulin subunits alpha, beta, and gamma signature. / Tubulin/FtsZ-like, C-terminal 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 / Tubulin-like protein CetZ1
Similarity search - Component
Biological speciesHALOFERAX VOLCANII (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsAylett, C.H.S. / Duggin, I.G. / Lowe, J.
CitationJournal: Nature / Year: 2015
Title: Cetz Tubulin-Like Proteins Control Archaeal Cell Shape
Authors: Duggin, I.G. / Aylett, C.H.S. / Walsh, J.C. / Michie, K.A. / Wang, Q. / Turnbull, L. / Dawson, E.M. / Harry, E.J. / Whitchurch, C.B. / Amos, A. / Lowe, J.
History
DepositionJul 27, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 14, 2013Provider: repository / Type: Initial release
Revision 1.1Aug 21, 2013Group: Other / Structure summary
Revision 1.2Dec 17, 2014Group: Database references
Revision 1.3Jan 14, 2015Group: Database references
Revision 1.4Mar 25, 2015Group: Database references
Revision 1.5May 1, 2024Group: 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: CELL DIVISION PROTEIN FTSZ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,5502
Polymers42,1071
Non-polymers4431
Water3,549197
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)56.339, 62.214, 96.496
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein CELL DIVISION PROTEIN FTSZ / CETZ1


Mass: 42106.777 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HALOFERAX VOLCANII (archaea) / Plasmid: PHIS17 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): C41 / References: UniProt: D4GVD7
#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.: 197 / 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: 2.01 Å3/Da / Density % sol: 38.79 %
Description: POOR MODEL FROM SEMET IN LOW RESOLUTION CRYSTALS USED TO PROVIDE SEARCH MODEL FOR HIGHER RESOLUTION CRYSTAL FORM.
Crystal growpH: 4
Details: 20% W/V PEG 6K, 1 M LITHIUM CHLORIDE, 0.1 M NA CITRATE PH 4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9
DetectorType: ADSC QUANTUM CCD / Detector: CCD / Date: Sep 2, 2011
RadiationMonochromator: GRAPHITE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.9→48.65 Å / Num. obs: 27386 / % possible obs: 99.8 % / Observed criterion σ(I): 1.9 / Redundancy: 4.2 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 10
Reflection shellResolution: 1.9→2 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.58 / Mean I/σ(I) obs: 1.9 / % possible all: 99.4

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PARTIAL MODEL OF CETZ4

Resolution: 1.9→48.654 Å / SU ML: 0.19 / σ(F): 1.07 / Phase error: 21.45 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.2071 2534 5 %
Rwork0.1736 --
obs0.1753 27386 98.17 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 1 Å2 / ksol: 1 e/Å3
Refinement stepCycle: LAST / Resolution: 1.9→48.654 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2460 0 28 197 2685
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062522
X-RAY DIFFRACTIONf_angle_d1.0363414
X-RAY DIFFRACTIONf_dihedral_angle_d15.511928
X-RAY DIFFRACTIONf_chiral_restr0.064389
X-RAY DIFFRACTIONf_plane_restr0.004448
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.93660.33141440.30872425X-RAY DIFFRACTION89
1.9366-1.97610.30781210.2742528X-RAY DIFFRACTION94
1.9761-2.01910.31621550.26032662X-RAY DIFFRACTION97
2.0191-2.0660.28211370.23622669X-RAY DIFFRACTION97
2.066-2.11770.26071180.22772672X-RAY DIFFRACTION98
2.1177-2.1750.23321350.20342694X-RAY DIFFRACTION98
2.175-2.2390.22731620.18672673X-RAY DIFFRACTION99
2.239-2.31120.20761530.18162695X-RAY DIFFRACTION100
2.3112-2.39380.24161360.17752730X-RAY DIFFRACTION99
2.3938-2.48970.21751350.17542697X-RAY DIFFRACTION99
2.4897-2.6030.19461530.17382716X-RAY DIFFRACTION99
2.603-2.74020.21451340.17322698X-RAY DIFFRACTION100
2.7402-2.91190.21421380.15462743X-RAY DIFFRACTION100
2.9119-3.13670.17231550.15812730X-RAY DIFFRACTION100
3.1367-3.45220.16571270.14592722X-RAY DIFFRACTION100
3.4522-3.95160.1791250.13672720X-RAY DIFFRACTION99
3.9516-4.97780.15351410.13252714X-RAY DIFFRACTION100
4.9778-48.66950.19721650.16722683X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: -13.571 Å / Origin y: -17.1168 Å / Origin z: 16.5366 Å
111213212223313233
T0.131 Å20.0023 Å20.0061 Å2-0.1564 Å2-0.0051 Å2--0.099 Å2
L1.3989 °20.4073 °20.1402 °2-2.3091 °2-0.0456 °2--0.4575 °2
S-0.0354 Å °0.1042 Å °0.011 Å °-0.1415 Å °0.0186 Å °0.0299 Å °-0.0036 Å °0.0087 Å °0.0212 Å °
Refinement TLS groupSelection details: CHAIN A

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