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- PDB-1yr9: PAB0955 crystal structure : a GTPase in GDP and PO4 bound form fr... -

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Basic information

Entry
Database: PDB / ID: 1yr9
TitlePAB0955 crystal structure : a GTPase in GDP and PO4 bound form from Pyrococcus abyssi
ComponentsATP(GTP)binding protein
KeywordsHYDROLASE / GTP binding protein / GTPase / P-loop / Rossmann Fold / GDP
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
GUANOSINE-5'-DIPHOSPHATE / PHOSPHATE ION / : / GPN-loop GTPase PAB0955
Similarity search - Component
Biological speciesPyrococcus abyssi (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 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 1.5Oct 25, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.6Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ATP(GTP)binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,8733
Polymers30,3351
Non-polymers5382
Water43224
1
A: ATP(GTP)binding protein
hetero molecules

A: ATP(GTP)binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,7466
Polymers60,6702
Non-polymers1,0764
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Buried area6430 Å2
ΔGint-64 kcal/mol
Surface area19990 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)58.820, 84.051, 53.167
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Detailsthe biological assembly is a dimer generated by two fold axis : -x +1, -y, 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: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: 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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 24 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.17 Å3/Da / Density % sol: 43.29 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 8% PEG6000, 1M Lithium chloride, 50mM NaCl, 10% glycerol, 0.1M Citric Acid , 1mM GTP, 20mM DTT, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.979 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jun 18, 2004 / Details: mirror
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.8→100 Å / Num. all: 6880 / Num. obs: 6729 / % possible obs: 97.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.4 % / Biso Wilson estimate: 46.798 Å2 / Rmerge(I) obs: 0.093 / Rsym value: 0.093 / Net I/σ(I): 15.19
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 7.6 % / Rmerge(I) obs: 0.455 / Mean I/σ(I) obs: 4.6 / Num. unique all: 618 / Rsym value: 0.455 / % possible all: 93.8

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
ProDCdata collection
XDSdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1YR6

1yr6


Resolution: 2.8→15 Å / Cor.coef. Fo:Fc: 0.914 / SU B: 10.88 / SU ML: 0.23 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.346 663 -random
Rwork0.225 ---
all0.232 6794 --
obs0.232 6680 98.11 %-
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: 46.798 Å2
Baniso -1Baniso -2Baniso -3
1-1.29 Å20 Å20 Å2
2---1.37 Å20 Å2
3---0.08 Å2
Refinement stepCycle: LAST / Resolution: 2.8→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1999 0 33 24 2056
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0222080
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1752.0122822
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7365245
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.34224.08298
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.11715368
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.791513
X-RAY DIFFRACTIONr_chiral_restr0.0670.2312
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.021555
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2930.31172
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3470.51409
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2820.5148
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2950.379
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1970.56
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.66721247
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.19831996
X-RAY DIFFRACTIONr_scbond_it0.7163936
X-RAY DIFFRACTIONr_scangle_it1.0924826
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.803→2.897 Å / Total num. of bins used: 15
RfactorNum. reflection% reflection
Rfree0.35 61 -
Rwork0.26 599 -
obs-538 95.38 %

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