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- PDB-2oxr: PAB0955 crystal structure : a GTPase in GDP and Mg bound form fro... -

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Basic information

Entry
Database: PDB / ID: 2oxr
TitlePAB0955 crystal structure : a GTPase in GDP and Mg bound form from Pyrococcus abyssi (after GTP hydrolysis)
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 / GPN-loop GTPase PAB0955
Similarity search - Component
Biological speciesPyrococcus abyssi (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsGras, S. / Carpentier, P. / Armengaud, J. / Housset, D.
CitationJournal: 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.
History
DepositionFeb 21, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 24, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Nov 12, 2014Group: Structure summary
Revision 1.4Aug 30, 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 / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)30,8023
Polymers30,3351
Non-polymers4682
Water1,00956
1
A: ATP(GTP)binding protein
hetero molecules

A: ATP(GTP)binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,6056
Polymers60,6702
Non-polymers9354
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556y,x,-z+11
Buried area6010 Å2
ΔGint-62 kcal/mol
Surface area20930 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)60.189, 60.189, 116.512
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein ATP(GTP)binding protein


Mass: 30334.795 Da / Num. of mol.: 1
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: UniProt: Q9UYR9
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#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.: 56 / 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: 2.19 Å3/Da / Density % sol: 38.7314 %
Crystal growTemperature: 293 K / pH: 5.6
Details: 0.1M tri-Na citrate pH 5.6, 15% PEG 4000, 0.2M ammonium acetate, 20mM DTT, 0.65mM GTP, 8mg/ml protein, VAPOR DIFFUSION, HANGING DROP, temperature 293K, pH 5.60

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.979
DetectorType: MAR CCD 130 mm / Detector: CCD / Date: Feb 26, 2004 / Details: MIRROR
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.4→100 Å / Num. obs: 9973 / % possible obs: 99 % / Observed criterion σ(I): 0 / Redundancy: 9.3 % / Rsym value: 0.067 / Net I/σ(I): 19.55
Reflection shellResolution: 2.4→2.45 Å / Redundancy: 9.5 % / Rmerge(I) obs: 0.404 / Mean I/σ(I) obs: 5.76 / Rsym value: 0.404 / % possible all: 98.8

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0005refinement
PDB_EXTRACT2data extraction
XDSdata reduction
XDSdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1YRB

1yrb


Resolution: 2.4→15 Å / Cor.coef. Fo:Fc: 0.9275 / Cor.coef. Fo:Fc free: 0.875 / Isotropic thermal model: isotropic / σ(F): 0 / ESU R: 0.617 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.324 981 9.9 %RANDOM
Rwork0.212 ---
obs0.221 9913 99.23 %-
all-10300 --
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: 50.15 Å2
Baniso -1Baniso -2Baniso -3
1-2.39 Å21.19 Å20 Å2
2--2.39 Å20 Å2
3----3.58 Å2
Refinement stepCycle: LAST / Resolution: 2.4→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2001 0 29 56 2086
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0222081
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.192.0122821
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4675245
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.45224.08298
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.69915373
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.1141513
X-RAY DIFFRACTIONr_chiral_restr0.0740.2312
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021555
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.270.3883
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3320.51356
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2920.5144
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3330.357
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3770.513
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9621227
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.68531996
X-RAY DIFFRACTIONr_scbond_it1.223854
X-RAY DIFFRACTIONr_scangle_it1.7444825
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.4→2.48 Å / Total num. of bins used: 15
RfactorNum. reflection% reflection
Rfree0.39 85 -
Rwork0.2 858 -
obs--98.85 %

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