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- PDB-1o63: Crystal structure of an ATP phosphoribosyltransferase -

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Basic information

Entry
Database: PDB / ID: 1o63
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
ATP phosphoribosyltransferase
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Se-Met MAD phasing / Resolution: 2 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: 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_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ATP phosphoribosyltransferase
B: ATP phosphoribosyltransferase


Theoretical massNumber of molelcules
Total (without water)49,8272
Polymers49,8272
Non-polymers00
Water1,874104
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.257, 49.972, 76.403
Angle α, β, γ (deg.)90.00, 92.75, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein ATP phosphoribosyltransferase /


Mass: 24913.314 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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 104 / 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: 2.04 Å3/Da / Density % sol: 39.65 %
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: 0.9795 , 1.5418
DetectorType: MARRESEARCH / Detector: CCD
RadiationProtocol: MAD / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97951
21.54181
ReflectionResolution: 2→25.91 Å / Num. all: 27249 / Num. obs: 27249 / % possible obs: 99.5 % / Redundancy: 4.9 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 14.3
Reflection shellResolution: 2→2.11 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.178 / Mean I/σ(I) obs: 8.1 / % possible all: 99.5
Reflection
*PLUS
Rmerge(I) obs: 0.07
Reflection shell
*PLUS
% possible obs: 99.5 %

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Processing

Software
NameVersionClassification
REFMAC4refinement
MOSFLMdata reduction
CCP4(SCALAdata scaling
TRUNCATEdata scaling
RefinementMethod to determine structure: Se-Met MAD phasing / Resolution: 2→25.91 Å / σ(F): 0
RfactorNum. reflection
Rfree0.264 2672
Rwork0.219 -
obs-26811
Solvent computationSolvent model: Babinet bulk solvent correction / Bsol: 153.412 Å2 / ksol: 0.784 e/Å3
Displacement parametersBiso mean: 33.193 Å2
Baniso -1Baniso -2Baniso -3
1-0.358 Å20 Å2-1.294 Å2
2---1.047 Å20 Å2
3---0.565 Å2
Refine Biso Class: all / Treatment: isotropic
Refinement stepCycle: 1 / Resolution: 2→25.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3147 0 0 104 3251
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.011
X-RAY DIFFRACTIONp_angle_d1.843
X-RAY DIFFRACTIONp_planar_tor3.836
X-RAY DIFFRACTIONp_chiral_restr0.135
X-RAY DIFFRACTIONp_plane_restr0.012
X-RAY DIFFRACTIONp_mcbond_it1.814
X-RAY DIFFRACTIONp_mcangle_it3.07
X-RAY DIFFRACTIONp_scbond_it2.987
X-RAY DIFFRACTIONp_scangle_it4.557
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg1.8

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