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- PDB-1yr6: PAB0955 crystal structure : a GTPase in Apo form from Pyrococcus ... -

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Basic information

Entry
Database: PDB / ID: 1yr6
TitlePAB0955 crystal structure : a GTPase in Apo form from Pyrococcus abyssi
ComponentsATP(GTP)binding protein
KeywordsHYDROLASE / GTP binding protein / GTPase / P-loop / Rossmann Fold
Function / homology
Function and homology information


Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / GTPase activity / GTP binding
Similarity search - Function
GPN-loop GTPase 1 / GPN-loop GTPase / Conserved hypothetical ATP binding protein / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
: / GPN-loop GTPase PAB0955
Similarity search - Component
Biological speciesPyrococcus abyssi (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 2.15 Å
AuthorsGras, S. / Carpentier, P. / Armengaud, J. / Housset, D.
Citation
Journal: Embo Rep. / Year: 2007
Title: Structural insights into a new homodimeric self-activated GTPase family.
Authors: Gras, S. / Chaumont, V. / Fernandez, B. / Carpentier, P. / Charrier-Savournin, F. / Schmitt, S. / Pineau, C. / Flament, D. / Hecker, A. / Forterre, P. / Armengaud, J. / Housset, D.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2005
Title: Expression, purification, crystallization and preliminary crystallographic analysis of the PAB0955 gene product
Authors: Gras, S. / Fernandez, B. / Chaumont, V. / Carpentier, P. / Armengaud, J. / Housset, D.
History
DepositionFeb 3, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 14, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Nov 12, 2014Group: Structure summary
Revision 1.4Oct 11, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.5Mar 13, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ATP(GTP)binding protein


Theoretical massNumber of molelcules
Total (without water)30,3351
Polymers30,3351
Non-polymers00
Water1,08160
1
A: ATP(GTP)binding protein

A: ATP(GTP)binding protein


Theoretical massNumber of molelcules
Total (without water)60,6702
Polymers60,6702
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area4160 Å2
ΔGint-31 kcal/mol
Surface area21320 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)60.290, 60.290, 117.110
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
DetailsThe biological assembly is a dimer generated by the two fold axis : y, x, -z

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Components

#1: Protein ATP(GTP)binding protein / PAB0955 gene product


Mass: 30334.795 Da / Num. of mol.: 1 / Fragment: residues 1-248
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus abyssi (archaea) / Gene: PAB0955 / Plasmid: pCRT7/NT-topo / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3)pLys / References: GenBank: 5458856, UniProt: Q9UYR9*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 60 / 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: 2.03 Å3/Da / Density % sol: 39 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 15% PEG 4000, 3% dioxane, 0.1M tri-sodium citrate dihydrate, 20mM DTT, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: May 12, 2003
RadiationMonochromator: mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2.15→50 Å / Num. all: 13967 / Num. obs: 13737 / % possible obs: 98.34 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.1 % / Biso Wilson estimate: 40.1 Å2 / Rmerge(I) obs: 0.054 / Rsym value: 0.054 / Net I/σ(I): 22.46
Reflection shellResolution: 2.15→2.23 Å / Redundancy: 7.6 % / Rmerge(I) obs: 0.328 / Mean I/σ(I) obs: 5.31 / Num. unique all: 1338 / Rsym value: 0.328 / % possible all: 95

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
ProDCdata collection
XDSdata scaling
SOLVEphasing
RefinementMethod to determine structure: MIRAS / Resolution: 2.15→15 Å / Cor.coef. Fo:Fc: 0.942 / SU B: 5.358 / SU ML: 0.143 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.316 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.299 685 -RANDOM
Rwork0.231 ---
all0.23535 13967 --
obs0.23535 13681 98.35 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 53.557 Å2
Baniso -1Baniso -2Baniso -3
1-3.34 Å21.67 Å20 Å2
2--3.34 Å20 Å2
3----5 Å2
Refinement stepCycle: LAST / Resolution: 2.15→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2011 0 0 60 2071
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0222055
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2461.9942779
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0785247
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.14924.02197
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.03315371
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.7561513
X-RAY DIFFRACTIONr_chiral_restr0.0820.2308
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021547
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2710.3993
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3330.51409
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2630.5172
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3080.345
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.5360.58
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.17721266
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.00332007
X-RAY DIFFRACTIONr_scbond_it1.5443884
X-RAY DIFFRACTIONr_scangle_it2.1734772
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.15→2.224 Å / Total num. of bins used: 15
RfactorNum. reflection% reflection
Rfree0.33 58 -
Rwork0.251 1243 -
obs-1338 94.74 %

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