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- PDB-1a95: XPRTASE FROM E. COLI COMPLEXED WITH MG:CPRPP AND GUANINE -

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Basic information

Entry
Database: PDB / ID: 1a95
TitleXPRTASE FROM E. COLI COMPLEXED WITH MG:CPRPP AND GUANINE
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
BORIC ACID / GUANINE / Chem-PCP / Xanthine-guanine phosphoribosyltransferase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 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 1.3Aug 2, 2023Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Refinement description
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_asym_id / _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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4May 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)69,21712
Polymers67,9664
Non-polymers1,2518
Water2,450136
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13490 Å2
ΔGint-86 kcal/mol
Surface area23190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.200, 94.200, 165.900
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
XANTHINE-GUANINE PHOSPHORIBOSYLTRANSFERASE / XPRT


Mass: 16991.568 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Cell line: HB101 / Cellular location: CYTOPLASM / Gene: GPT / Plasmid: PT7-7 / Cellular location (production host): CYTOPLASM / Gene (production host): GPT / Production host: Escherichia coli (E. coli) / Strain (production host): SPHI606
References: UniProt: P0A9M5, xanthine phosphoribosyltransferase

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Non-polymers , 5 types, 144 molecules

#2: Chemical ChemComp-BO3 / BORIC ACID


Mass: 61.833 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: BH3O3
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-PCP / 1-ALPHA-PYROPHOSPHORYL-2-ALPHA,3-ALPHA-DIHYDROXY-4-BETA-CYCLOPENTANE-METHANOL-5-PHOSPHATE / CARBOXYLIC PRPP / CPRPP


Mass: 388.097 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H15O13P3
#5: Chemical ChemComp-GUN / GUANINE


Mass: 151.126 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H5N5O
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 136 / 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% PEG4000, 0.1 M BORATE PH 9.0, 0.1 M AMMONIUM PHOSPHATE
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: Jul 11, 1997 / Details: MIRRORS
RadiationMonochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→100 Å / Num. obs: 40863 / % possible obs: 79.9 % / Observed criterion σ(I): 0 / Redundancy: 2.3 % / Biso Wilson estimate: 12 Å2 / Rmerge(I) obs: 0.065 / Rsym value: 0.065 / Net I/σ(I): 12
Reflection shellResolution: 2→2.07 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.226 / Mean I/σ(I) obs: 2.3 / % possible all: 61.8
Reflection
*PLUS
Lowest resolution: 100 Å / Num. measured all: 92728
Reflection shell
*PLUS
% possible obs: 61.8 %

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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→50 Å / Rfactor Rfree error: 0.004 / 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 AN UNFAVORABLE INTERACTION BETWEEN ARG D119 N AND PRO D120 CD ATOM COULD NOT BE CORRECTED.
RfactorNum. reflection% reflectionSelection details
Rfree0.232 4099 10.1 %RANDOM R VALUE (WORKING + TEST SET) : NULL
Rwork0.207 ---
obs0.207 40785 80 %-
Displacement parametersBiso mean: 26.7 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.27 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.3 Å0.29 Å
Refinement stepCycle: LAST / Resolution: 2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4500 0 76 136 4712
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.005
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_deg1.1
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24.4
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.95
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.351.5
X-RAY DIFFRACTIONx_mcangle_it2.312
X-RAY DIFFRACTIONx_scbond_it1.932
X-RAY DIFFRACTIONx_scangle_it3.152.5
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.295 563 10.5 %
Rwork0.293 4783 -
obs--64.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM19.SOLTOPH19.SOL
X-RAY DIFFRACTION3PARAM11.DNALIGANDS.TOP
X-RAY DIFFRACTION4LIGANDS.PARCIS_PEP.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_deg24.4
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.95

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