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- PDB-1grv: Hypoxanthine Phosphoribosyltransferase from E. coli -

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Basic information

Entry
Database: PDB / ID: 1grv
TitleHypoxanthine Phosphoribosyltransferase from E. coli
ComponentsHYPOXANTHINE PHOSPHORIBOSYLTRANSFERASEHypoxanthine-guanine phosphoribosyltransferase
KeywordsTRANSFERASE / RIBOSYLTRANSFERASE / GLYCOSYLTRANSFERASE
Function / homology
Function and homology information


adenine salvage / guanine salvage / hypoxanthine metabolic process / hypoxanthine phosphoribosyltransferase / GMP salvage / guanine phosphoribosyltransferase activity / hypoxanthine phosphoribosyltransferase activity / IMP salvage / purine ribonucleoside salvage / guanosine tetraphosphate binding ...adenine salvage / guanine salvage / hypoxanthine metabolic process / hypoxanthine phosphoribosyltransferase / GMP salvage / guanine phosphoribosyltransferase activity / hypoxanthine phosphoribosyltransferase activity / IMP salvage / purine ribonucleoside salvage / guanosine tetraphosphate binding / protein homotetramerization / magnesium ion binding / protein-containing complex / identical protein binding / cytosol
Similarity search - Function
Hypoxanthine phosphoribosyl transferase / 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
Hypoxanthine phosphoribosyltransferase / Hypoxanthine phosphoribosyltransferase
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsGuddat, L.W. / Vos, S. / Martin, J.L. / Keough, D.T. / De Jersey, J.
CitationJournal: Protein Sci. / Year: 2002
Title: Crystal Structures of Free, Imp-, and Gmp- Bound Escherichia Coli Hypoxanthine Phosphoribosyltransferase
Authors: Guddat, L.W. / Vos, S. / Martin, J.L. / Keough, D.T. / De Jersey, J.
History
DepositionDec 17, 2001Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 13, 2002Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_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.ptnr1_label_seq_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.ptnr3_label_seq_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.ptnr1_label_seq_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_conn.ptnr2_label_seq_id / _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: HYPOXANTHINE PHOSPHORIBOSYLTRANSFERASE
B: HYPOXANTHINE PHOSPHORIBOSYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,3644
Polymers41,3162
Non-polymers492
Water1,33374
1
A: HYPOXANTHINE PHOSPHORIBOSYLTRANSFERASE
B: HYPOXANTHINE PHOSPHORIBOSYLTRANSFERASE
hetero molecules

A: HYPOXANTHINE PHOSPHORIBOSYLTRANSFERASE
B: HYPOXANTHINE PHOSPHORIBOSYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,7298
Polymers82,6324
Non-polymers974
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_675x-y+1,-y+2,-z+2/31
MethodPQS
Unit cell
Length a, b, c (Å)83.900, 83.900, 169.400
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein HYPOXANTHINE PHOSPHORIBOSYLTRANSFERASE / Hypoxanthine-guanine phosphoribosyltransferase / HPRT


Mass: 20657.887 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Production host: ESCHERICHIA COLI (E. coli)
References: UniProt: P36766, UniProt: P0A9M2*PLUS, hypoxanthine phosphoribosyltransferase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 74 / Source method: isolated from a natural source / Formula: H2O
Compound detailsCATALYTIC ACTIVITY IS IMP + DIPHOSPHATE = HYPOXANTHINE + 5-PHOSPHO-ALPHA-D-RIBOSE 1-DIPHOSPHATE. ...CATALYTIC ACTIVITY IS IMP + DIPHOSPHATE = HYPOXANTHINE + 5-PHOSPHO-ALPHA-D-RIBOSE 1-DIPHOSPHATE. THIS ENZYME ACTS EXCLUSIVELY ON HYPOXANTHINE AND NOT ON GUANINE. MEMBER OF THE PURINE/PYRIMIDINE PHOSPHORIBOSYLTRANSFERASE FAMILY

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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: 4.1 Å3/Da / Density % sol: 70 %
Description: DATA WERE COLLECTED USING THE OSCILLATION METHOD
Crystal growpH: 7.4 / Details: 0.1 M HEPES PH 7.5, 0.1 M SODIUM CITRATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-D / Wavelength: 1
DetectorType: ADSC CCD / Detector: CCD / Date: Dec 12, 2000 / Details: CARS DESIGN CYLINDRICAL FOCUSING MIRROE
RadiationMonochromator: CARS-DESIGN SI(III) MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. obs: 46525 / % possible obs: 92 % / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Rmerge(I) obs: 0.103 / Net I/σ(I): 7.2
Reflection shellResolution: 2.9→3 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.293 / Mean I/σ(I) obs: 2.8 / % possible all: 56

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Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1G9S

1g9s


Resolution: 2.9→50 Å / Data cutoff high absF: 10000000 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Details: THERE WAS INSUFFICIENT DENSITY TO MODEL THE POLYPEPTIDE CHAIN FOR RESIDUES 1-4, 73-81, 182 IN CHAIN A AND 1-4, 74-81 AND 182 IN CHAIN B
RfactorNum. reflection% reflectionSelection details
Rfree0.238 1429 9 %RANDOM
Rwork0.214 ---
obs0.214 14653 92 %-
Solvent computationSolvent model: SHELL MODEL / Bsol: 41 Å2 / ksol: 0.219 e/Å3
Displacement parametersBiso mean: 30.8 Å2
Baniso -1Baniso -2Baniso -3
1--4.753 Å2-7.427 Å20 Å2
2---4.753 Å20 Å2
3---9.506 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.41 Å0.35 Å
Luzzati d res low-5 Å
Luzzati sigma a0.47 Å0.43 Å
Refinement stepCycle: LAST / Resolution: 2.9→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2666 0 2 74 2742
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.4
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.74
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.1291.5
X-RAY DIFFRACTIONc_mcangle_it1.9762
X-RAY DIFFRACTIONc_scbond_it1.8372
X-RAY DIFFRACTIONc_scangle_it2.922.5
LS refinement shellResolution: 2.9→3 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.353 75 10 %
Rwork0.306 681 -
obs--56 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP

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