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- PDB-4b45: CetZ2 from Haloferax volcanii - GTPgS bound protofilament -

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Basic information

Entry
Database: PDB / ID: 4b45
TitleCetZ2 from Haloferax volcanii - GTPgS bound protofilament
Components(CELL DIVISION PROTEIN FTSZ) x 2
KeywordsSTRUCTURAL PROTEIN / TUBULIN / ARCHAEA / CYTOSKELETON / CELL SHAPE
Function / homology
Function and homology information


regulation of cell shape / GTPase activity / GTP binding / cytoplasm
Similarity search - Function
Tubulin-like protein CetZ / Tubulin/FtsZ, C-terminal domain / Tubulin/FtsZ, GTPase domain / 60s Ribosomal Protein L30; Chain: A; / 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 ...Tubulin-like protein CetZ / Tubulin/FtsZ, C-terminal domain / Tubulin/FtsZ, GTPase domain / 60s Ribosomal Protein L30; Chain: A; / 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
5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE / Tubulin-like protein CetZ2
Similarity search - Component
Biological speciesHALOFERAX VOLCANII (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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 1.3Dec 24, 2014Group: Derived calculations
Revision 1.4Jan 14, 2015Group: Database references / Derived calculations
Revision 1.5Mar 25, 2015Group: Database references
Revision 1.6May 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

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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)38,6723
Polymers38,1322
Non-polymers5391
Water1,78399
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2040 Å2
ΔGint-15.2 kcal/mol
Surface area14590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.427, 43.224, 48.450
Angle α, β, γ (deg.)68.87, 75.34, 86.90
Int Tables number1
Space group name H-MP1

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Components

#1: Protein CELL DIVISION PROTEIN FTSZ / CETZ2


Mass: 35798.789 Da / Num. of mol.: 1 / Fragment: RESIDUES 1-349
Source method: isolated from a genetically manipulated source
Details: CHAIN A AND B REPRESENT FRAGMENTS OF A SINGLE MOLECULE
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: D4GTC1
#2: Protein/peptide CELL DIVISION PROTEIN FTSZ / CETZ2


Mass: 2333.481 Da / Num. of mol.: 1 / Fragment: RESIDUES 350-360
Source method: isolated from a genetically manipulated source
Details: CHAIN A AND B REPRESENT FRAGMENTS OF A SINGLE MOLECULE
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: D4GTC1
#3: Chemical ChemComp-GSP / 5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE


Mass: 539.246 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 99 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsCHAIN B REPRESENTS PART OF THE C-TERMINAL TAIL OF THE SAME MOLECULE AS CHAIN A BUT HAS BEEN MAPPED ...CHAIN B REPRESENTS PART OF THE C-TERMINAL TAIL OF THE SAME MOLECULE AS CHAIN A BUT HAS BEEN MAPPED SEPARATELY AS IT CANNOT CLEARLY DETERMINED WHERE IT ORIGINATES FROM.

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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: 2.16 Å3/Da / Density % sol: 43.01 % / Description: NONE
Crystal growpH: 5 / Details: 3.15 M AMMONIUM SULFATE, 0.1 M NA CITRATE PH 5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9795
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 14, 2012
RadiationMonochromator: GRAPHITE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2→40.28 Å / Num. obs: 20523 / % possible obs: 97.9 % / Observed criterion σ(I): 1.5 / Redundancy: 3.5 % / Biso Wilson estimate: 24.65 Å2 / Rmerge(I) obs: 0.13 / Net I/σ(I): 8.1
Reflection shellResolution: 2→2.11 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.94 / Mean I/σ(I) obs: 1.5 / % possible all: 96.9

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Processing

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

Resolution: 2.1→40.284 Å / SU ML: 0.2 / σ(F): 1.24 / Phase error: 25.94 / Stereochemistry target values: MLHL
Details: CHAIN B REPRESENTS PART OF THE C-TERMINAL TAIL OF ANOTHER CETZ3 SUBUNIT, BUT HAS BEEN MODELED AS A SEPARATE CHAIN AS WE CANNOT BE CERTAIN FROM WHICH IT ORIGINATES FROM.
RfactorNum. reflection% reflection
Rfree0.228 1738 5.1 %
Rwork0.1771 --
obs0.1798 20523 94.65 %
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: 2.1→40.284 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2502 0 32 99 2633
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072559
X-RAY DIFFRACTIONf_angle_d1.0913474
X-RAY DIFFRACTIONf_dihedral_angle_d13.777924
X-RAY DIFFRACTIONf_chiral_restr0.069409
X-RAY DIFFRACTIONf_plane_restr0.004460
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.16180.37471370.28732688X-RAY DIFFRACTION94
2.1618-2.23160.33661580.24822654X-RAY DIFFRACTION94
2.2316-2.31130.26391450.24872662X-RAY DIFFRACTION94
2.3113-2.40390.30291580.21742724X-RAY DIFFRACTION94
2.4039-2.51320.2591260.20812713X-RAY DIFFRACTION95
2.5132-2.64570.25611700.20092714X-RAY DIFFRACTION95
2.6457-2.81140.25061300.18522751X-RAY DIFFRACTION95
2.8114-3.02840.26031450.17832763X-RAY DIFFRACTION96
3.0284-3.33310.22611310.15952709X-RAY DIFFRACTION96
3.3331-3.81510.18211550.13572712X-RAY DIFFRACTION95
3.8151-4.80530.13671280.13372751X-RAY DIFFRACTION94
4.8053-40.29140.21091550.16682679X-RAY DIFFRACTION94
Refinement TLS params.Method: refined / Origin x: 1.5484 Å / Origin y: -21.3657 Å / Origin z: -14.9165 Å
111213212223313233
T0.3346 Å20.0151 Å2-0.0003 Å2-0.3602 Å20.0113 Å2--0.3538 Å2
L1.0809 °20.6614 °2-0.034 °2-2.5708 °2-0.0511 °2--0.307 °2
S0.0386 Å °-0.034 Å °-0.0289 Å °-0.0298 Å °-0.0326 Å °-0.0247 Å °0.0061 Å °-0.0349 Å °0.0035 Å °
Refinement TLS groupSelection details: CHAIN A OR CHAIN B

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