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- PDB-1a98: XPRTASE FROM E. COLI COMPLEXED WITH GMP -

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Basic information

Entry
Database: PDB / ID: 1a98
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 / GMP salvage / guanine phosphoribosyltransferase activity / hypoxanthine phosphoribosyltransferase activity / IMP salvage / purine ribonucleoside salvage / guanosine tetraphosphate binding / Transferases; Glycosyltransferases; Pentosyltransferases ...xanthine phosphoribosyltransferase / XMP salvage / xanthine phosphoribosyltransferase activity / GMP salvage / guanine phosphoribosyltransferase activity / hypoxanthine phosphoribosyltransferase activity / 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
Xanthine-guanine phosphoribosyltransferase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT MOLECULAR REPLACEMENT / Resolution: 2.25 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 1.0Jun 17, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Other
Category: database_2 / pdbx_database_status / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_ref_seq_dif.details
Revision 1.4Aug 2, 2023Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: XANTHINE-GUANINE PHOSPHORIBOSYLTRANSFERASE
B: XANTHINE-GUANINE PHOSPHORIBOSYLTRANSFERASE


Theoretical massNumber of molelcules
Total (without water)33,9192
Polymers33,9192
Non-polymers00
Water1,18966
1
A: XANTHINE-GUANINE PHOSPHORIBOSYLTRANSFERASE
B: XANTHINE-GUANINE PHOSPHORIBOSYLTRANSFERASE

A: XANTHINE-GUANINE PHOSPHORIBOSYLTRANSFERASE
B: XANTHINE-GUANINE PHOSPHORIBOSYLTRANSFERASE


Theoretical massNumber of molelcules
Total (without water)67,8384
Polymers67,8384
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area9690 Å2
ΔGint-50 kcal/mol
Surface area20190 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)84.166, 70.927, 54.051
Angle α, β, γ (deg.)90.00, 113.40, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein XANTHINE-GUANINE PHOSPHORIBOSYLTRANSFERASE / XPRT


Mass: 16959.502 Da / Num. of mol.: 2 / 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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 66 / 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: 8
Details: XPRT WAS CRYSTALLIZED FROM 20% PEG4000 IN 0.1 M TRIS-HCL, pH 8.0
Crystal grow
*PLUS
pH: 7.6 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
120 %PEG40001reservoir
20.1 MTris-HCl1reservoirpH8.0
320 mg/mlprotein1drop
450 mMTris-HCl1droppH7.6
510 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: Mar 29, 1994 / Details: MIRRORS
RadiationMonochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.25→60 Å / Num. obs: 11089 / % possible obs: 79.5 % / Observed criterion σ(I): 0 / Redundancy: 1.5 % / Biso Wilson estimate: 24 Å2 / Rmerge(I) obs: 0.037 / Rsym value: 0.037 / Net I/σ(I): 11.8
Reflection shellResolution: 2.25→2.33 Å / Redundancy: 1.4 % / Rmerge(I) obs: 0.172 / Mean I/σ(I) obs: 3.4 / Rsym value: 0.172 / % possible all: 66.9
Reflection
*PLUS
Lowest resolution: 50 Å / Num. measured all: 16902 / Rmerge(I) obs: 0.037
Reflection shell
*PLUS
% possible obs: 66.9 % / Rmerge(I) obs: 0.172

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Processing

Software
NameVersionClassification
X-PLOR3.851model building
X-PLOR3.851refinement
PROCESS(HIGASHI)data reduction
PROCESS(HIGASHI)data scaling
X-PLOR3.851phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1NUL

1nul


Resolution: 2.25→50 Å / Rfactor Rfree error: 0.009 / 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
Rfree0.224 573 5.2 %RANDOM
Rwork0.21 ---
obs0.21 11083 79.4 %-
Displacement parametersBiso mean: 36.1 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.32 Å0.28 Å
Luzzati d res low-5 Å
Luzzati sigma a0.38 Å0.35 Å
Refinement stepCycle: LAST / Resolution: 2.25→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1900 0 0 66 1966
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_d23.7
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.02
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.441.5
X-RAY DIFFRACTIONx_mcangle_it2.532
X-RAY DIFFRACTIONx_scbond_it1.842
X-RAY DIFFRACTIONx_scangle_it2.852.5
LS refinement shellResolution: 2.25→2.39 Å / Rfactor Rfree error: 0.038 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.326 73 4.6 %
Rwork0.308 1520 -
obs--68 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM19.SOLTOPH19.SOL
X-RAY DIFFRACTION3CIS_PEP.PARCIS_PEP.TOP
Refinement
*PLUS
% reflection Rfree: 10 % / Rfactor obs: 0.21 / Rfactor Rfree: 0.224 / Rfactor Rwork: 0.21
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_deg1.075
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg23.7
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.02
LS refinement shell
*PLUS
Rfactor Rfree: 0.326 / Rfactor Rwork: 0.308

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