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- PDB-1a97: XPRTASE FROM E. COLI COMPLEXED WITH GMP -

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Basic information

Entry
Database: PDB / ID: 1a97
TitleXPRTASE FROM E. COLI COMPLEXED WITH GMP
ComponentsXANTHINE-GUANINE PHOSPHORIBOSYLTRANSFERASE
KeywordsPHOSPHORIBOSYLTRANSFERASE / TRANSFERASE / PURINE SALVAGE ENZYME / GLYCOSYLTRANSFERASE
Function / homology
Function and homology information


xanthine phosphoribosyltransferase / XMP salvage / xanthine phosphoribosyltransferase activity / guanine phosphoribosyltransferase activity / hypoxanthine phosphoribosyltransferase activity / GMP salvage / IMP salvage / purine ribonucleoside salvage / guanosine tetraphosphate binding / Transferases; Glycosyltransferases; Pentosyltransferases ...xanthine phosphoribosyltransferase / XMP salvage / xanthine phosphoribosyltransferase activity / guanine phosphoribosyltransferase activity / hypoxanthine phosphoribosyltransferase activity / GMP salvage / IMP salvage / purine ribonucleoside salvage / guanosine tetraphosphate binding / Transferases; Glycosyltransferases; Pentosyltransferases / protein homotetramerization / magnesium ion binding / protein-containing complex / identical protein binding / plasma membrane / cytosol
Similarity search - Function
Xanthine-guanine phosphoribosyltransferase / Purine/pyrimidine phosphoribosyl transferases signature. / Rossmann fold - #2020 / Phosphoribosyl transferase domain / Phosphoribosyltransferase-like / Phosphoribosyltransferase domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-MONOPHOSPHATE / BORIC ACID / Xanthine-guanine phosphoribosyltransferase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsVos, S. / Parry, R.J. / Burns, M.R. / De Jersey, J. / Martin, J.L.
CitationJournal: J.Mol.Biol. / Year: 1998
Title: Structures of free and complexed forms of Escherichia coli xanthine-guanine phosphoribosyltransferase.
Authors: Vos, S. / Parry, R.J. / Burns, M.R. / de Jersey, J. / Martin, J.L.
History
DepositionApr 16, 1998Processing site: BNL
Revision 1.0Nov 11, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 14, 2018Group: Database references / Other / Category: pdbx_database_status / struct_ref_seq_dif
Item: _pdbx_database_status.process_site / _struct_ref_seq_dif.details
Revision 1.4Aug 2, 2023Group: Database references / Derived calculations / Refinement description
Category: database_2 / pdbx_initial_refinement_model ...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 1.5May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: XANTHINE-GUANINE PHOSPHORIBOSYLTRANSFERASE
B: XANTHINE-GUANINE PHOSPHORIBOSYLTRANSFERASE
C: XANTHINE-GUANINE PHOSPHORIBOSYLTRANSFERASE
D: XANTHINE-GUANINE PHOSPHORIBOSYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,08210
Polymers66,1084
Non-polymers9746
Water86548
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12170 Å2
ΔGint-69 kcal/mol
Surface area22660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.042, 94.042, 166.914
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein
XANTHINE-GUANINE PHOSPHORIBOSYLTRANSFERASE / XPRT


Mass: 16526.982 Da / Num. of mol.: 4 / Mutation: C59A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: HB101 / Cellular location: CYTOPLASM / Gene: GPT / Plasmid: PT7-7 / Cellular location (production host): CYTOPLASM / Culture collection (production host): ATCC 87050 / Gene (production host): GPT / Production host: Escherichia coli (E. coli) / Strain (production host): SPHI606
References: UniProt: P0A9M5, xanthine phosphoribosyltransferase
#2: Chemical
ChemComp-BO3 / BORIC ACID


Mass: 61.833 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: BH3O3
#3: Chemical ChemComp-5GP / GUANOSINE-5'-MONOPHOSPHATE


Mass: 363.221 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N5O8P
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 48 / 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: 2.15 Å3/Da / Density % sol: 43 %
Crystal growpH: 9
Details: XPRT WAS CRYSTALLISED FROM 15 - 20% PEG 4000, 0.1 M AMMONIUM PHOSPHATE IN 0.1 M BORATE, PH 9., pH 9.0
Crystal
*PLUS
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop / pH: 7.6
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
115-20 %(w/v)PEG40001reservoir
20.1 Mborate1reservoir
30.2 Mammonium phosphate1reservoir
420 mg/mlprotein1drop
550 mMTris-HCl1droppH7.6
610 mM1dropMgCl2

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Data collection

DiffractionMean temperature: 289 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Apr 11, 1996 / Details: MIRRORS
RadiationMonochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.6→100 Å / Num. obs: 23936 / % possible obs: 89.5 % / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Biso Wilson estimate: 11.5 Å2 / Rmerge(I) obs: 0.073 / Rsym value: 0.073 / Net I/σ(I): 11.1
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.282 / Mean I/σ(I) obs: 2.6 / Rsym value: 0.282 / % possible all: 81.1
Reflection
*PLUS
Num. measured all: 76094
Reflection shell
*PLUS
% possible obs: 81.1 %

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Processing

Software
NameVersionClassification
X-PLOR3.851model building
X-PLOR3.851refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.851phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1NUL

1nul


Resolution: 2.6→50 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 100000 / Data cutoff low absF: 1 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.263 2132 9.9 %RANDOM R VALUE (WORKING + TEST SET) : NULL
Rwork0.233 ---
obs0.233 21557 90.7 %-
Displacement parametersBiso mean: 27.1 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.38 Å0.32 Å
Luzzati d res low-5 Å
Luzzati sigma a0.55 Å0.44 Å
Refinement stepCycle: LAST / Resolution: 2.6→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4309 0 64 48 4421
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.004
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24.9
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.92
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.481.5
X-RAY DIFFRACTIONx_mcangle_it2.572
X-RAY DIFFRACTIONx_scbond_it2.112
X-RAY DIFFRACTIONx_scangle_it3.22.5
LS refinement shellResolution: 2.6→2.76 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.358 331 9.7 %
Rwork0.316 3093 -
obs--88.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM19.SOLTOPH19.SOL
X-RAY DIFFRACTION35GP.PAR5GP.TOP
X-RAY DIFFRACTION4BO3.PARBO3.TOP
Software
*PLUS
Name: X-PLOR(ONLINE) / Version: 3.851 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24.9
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.92

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