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- PDB-1o64: Crystal structure of an ATP phosphoribosyltransferase -

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Basic information

Entry
Database: PDB / ID: 1o64
TitleCrystal structure of an ATP phosphoribosyltransferase
ComponentsATP phosphoribosyltransferase
KeywordsTRANSFERASE / structural genomics
Function / homology
Function and homology information


ATP phosphoribosyltransferase / ATP phosphoribosyltransferase activity / histidine biosynthetic process / ATP binding / cytoplasm
Similarity search - Function
ATP phosphoribosyltransferase HisG, short form / ATP phosphoribosyltransferase HisG / ATP phosphoribosyltransferase, catalytic domain / ATP phosphoribosyltransferase, conserved site / ATP phosphoribosyltransferase / ATP phosphoribosyltransferase signature. / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / ATP phosphoribosyltransferase
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsStructural GenomiX
CitationJournal: Proteins / Year: 2005
Title: Structural analysis of a set of proteins resulting from a bacterial genomics project
Authors: Badger, J. / Sauder, J.M. / Adams, J.M. / Antonysamy, S. / Bain, K. / Bergseid, M.G. / Buchanan, S.G. / Buchanan, M.D. / Batiyenko, Y. / Christopher, J.A. / Emtage, S. / Eroshkina, A. / ...Authors: Badger, J. / Sauder, J.M. / Adams, J.M. / Antonysamy, S. / Bain, K. / Bergseid, M.G. / Buchanan, S.G. / Buchanan, M.D. / Batiyenko, Y. / Christopher, J.A. / Emtage, S. / Eroshkina, A. / Feil, I. / Furlong, E.B. / Gajiwala, K.S. / Gao, X. / He, D. / Hendle, J. / Huber, A. / Hoda, K. / Kearins, P. / Kissinger, C. / Laubert, B. / Lewis, H.A. / Lin, J. / Loomis, K. / Lorimer, D. / Louie, G. / Maletic, M. / Marsh, C.D. / Miller, I. / Molinari, J. / Muller-Dieckmann, H.J. / Newman, J.M. / Noland, B.W. / Pagarigan, B. / Park, F. / Peat, T.S. / Post, K.W. / Radojicic, S. / Ramos, A. / Romero, R. / Rutter, M.E. / Sanderson, W.E. / Schwinn, K.D. / Tresser, J. / Winhoven, J. / Wright, T.A. / Wu, L. / Xu, J. / Harris, T.J.
History
DepositionOct 23, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 11, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

Downloads & links

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Assembly

Deposited unit
A: ATP phosphoribosyltransferase
B: ATP phosphoribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,7354
Polymers49,5452
Non-polymers1902
Water1,76598
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2670 Å2
ΔGint-35 kcal/mol
Surface area18610 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)54.183, 50.398, 76.794
Angle α, β, γ (deg.)90.00, 94.60, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein ATP phosphoribosyltransferase /


Mass: 24772.631 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: HISG, TM1042 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9X0D2, ATP phosphoribosyltransferase
#2: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 98 / 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: 2.11 Å3/Da / Density % sol: 41.69 %
Crystal growTemperature: 293 K / Method: hanging drop vapor diffusion / pH: 7.5
Components of the solutions
IDConc.NameCrystal-IDSol-ID
121.6mg/ml protein11
220mM Tris12
3150mM NaClSodium chloride12
41mM beta-mercaptoethanol2-Mercaptoethanol12
510mM methionine12
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
110 mMHEPES1droppH7.5
2150 mM1dropNaCl
310 mMmethionine1drop
410 %glycerol1drop
55 mMdithiothreitol1drop
610 mg/mlprotein1drop

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 32-ID / Wavelength: 0.9794 Å
DetectorType: MARRESEARCH / Detector: CCD
RadiationScattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.11→32.44 Å / Num. all: 24260 / Num. obs: 24260 / % possible obs: 99.6 % / Redundancy: 7.5 % / Rmerge(I) obs: 0.033 / Net I/σ(I): 41.4
Reflection shellResolution: 2.1→2.21 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.088 / Mean I/σ(I) obs: 23.8 / % possible all: 99.6
Reflection
*PLUS
Highest resolution: 2.1 Å
Reflection shell
*PLUS
% possible obs: 99.6 %

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Processing

Software
NameVersionClassification
REFMAC4refinement
MOSFLMdata reduction
CCP4(SCALAdata scaling
TRUNCATEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→32.44 Å / σ(F): 0
RfactorNum. reflection
Rfree0.269 2387
Rwork0.227 -
obs-24152
Solvent computationSolvent model: Babinet bulk solvent correction / Bsol: 150.09 Å2 / ksol: 0.895 e/Å3
Displacement parametersBiso mean: 37.733 Å2
Baniso -1Baniso -2Baniso -3
1--0.571 Å20 Å2-1.862 Å2
2---0.134 Å20 Å2
3---0.406 Å2
Refine Biso Class: all / Treatment: isotropic
Refinement stepCycle: LAST / Resolution: 2.1→32.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3108 0 10 98 3216
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.01
X-RAY DIFFRACTIONp_angle_d1.967
X-RAY DIFFRACTIONp_planar_tor2.865
X-RAY DIFFRACTIONp_chiral_restr0.135
X-RAY DIFFRACTIONp_plane_restr0.011
X-RAY DIFFRACTIONp_mcbond_it1.565
X-RAY DIFFRACTIONp_mcangle_it2.753
X-RAY DIFFRACTIONp_scbond_it2.445
X-RAY DIFFRACTIONp_scangle_it3.791
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg2

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