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- PDB-1yr7: PAB0955 crystal structure : a GTPase in GTP-gamma-S bound form fr... -

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Basic information

Entry
Database: PDB / ID: 1yr7
TitlePAB0955 crystal structure : a GTPase in GTP-gamma-S bound form from Pyrococcus abyssi
ComponentsATP(GTP)binding protein
KeywordsHYDROLASE / GTP binding protein / GTPase / P-loop / Rossmann Fold / GTP analog
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
5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE / : / GPN-loop GTPase PAB0955
Similarity search - Component
Biological speciesPyrococcus abyssi (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.08 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_conn / 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_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.6Dec 25, 2024Group: Advisory / Derived calculations / Structure summary
Category: pdbx_entry_details / pdbx_validate_close_contact / struct_conn

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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)30,8742
Polymers30,3351
Non-polymers5391
Water1,54986
1
A: ATP(GTP)binding protein
hetero molecules

A: ATP(GTP)binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,7484
Polymers60,6702
Non-polymers1,0782
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556y,x,-z+11
Buried area5180 Å2
ΔGint-36 kcal/mol
Surface area20900 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)60.170, 60.170, 115.890
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: Chemical ChemComp-GSP / 5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE


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


Mass: 18.015 Da / Num. of mol.: 86 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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 Å3/Da / Density % sol: 38.5 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 13% PEG 4000, 0.2M ammonium acetate, 0.1M tri-sodium citrate dihydrate, 20mM DTT, 0.65mM GTP-gamma-S, 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: 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: 2.08→50 Å / Num. all: 15141 / Num. obs: 15034 / % possible obs: 94.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.5 % / Biso Wilson estimate: 45 Å2 / Rmerge(I) obs: 0.069 / Rsym value: 0.069 / Net I/σ(I): 17.75
Reflection shellResolution: 2.08→2.15 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.232 / Mean I/σ(I) obs: 6.36 / Num. unique all: 893 / Rsym value: 0.232 / % possible all: 64.2

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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: 2.08→15 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.899 / SU B: 7.122 / SU ML: 0.193 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.426 / ESU R Free: 0.295 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.29463 1587 9.8 %RANDOM
Rwork0.20835 ---
all0.21691 13196 --
obs0.21691 12488 83.18 %-
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: 45.443 Å2
Baniso -1Baniso -2Baniso -3
1-1.8 Å20.9 Å20 Å2
2--1.8 Å20 Å2
3----2.7 Å2
Refinement stepCycle: LAST / Resolution: 2.08→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1981 0 32 86 2099
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0222094
X-RAY DIFFRACTIONr_angle_refined_deg1.2962.0162844
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5955242
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.06924.314102
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.18915380
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.6611513
X-RAY DIFFRACTIONr_chiral_restr0.0860.2318
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021559
X-RAY DIFFRACTIONr_nbd_refined0.2610.31106
X-RAY DIFFRACTIONr_nbtor_refined0.3310.51429
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.3240.5193
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.360.360
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.4110.514
X-RAY DIFFRACTIONr_mcbond_it1.08421244
X-RAY DIFFRACTIONr_mcangle_it1.80931994
X-RAY DIFFRACTIONr_scbond_it1.4293956
X-RAY DIFFRACTIONr_scangle_it1.9214850
LS refinement shellResolution: 2.087→2.159 Å / Total num. of bins used: 15
RfactorNum. reflection% reflection
Rfree0.351 89 -
Rwork0.267 950 -
obs-893 64.2 %

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