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- PDB-1i0i: ANALYSIS OF AN INVARIANT ASPARTIC ACID IN HPRTS-GLUTAMINE MUTANT -

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Basic information

Entry
Database: PDB / ID: 1i0i
TitleANALYSIS OF AN INVARIANT ASPARTIC ACID IN HPRTS-GLUTAMINE MUTANT
ComponentsHYPOXANTHINE-GUANINE PHOSPHORIBOSYLTRANSFERASE
KeywordsTRANSFERASE / PHOSPHORIBOSYLTRANSFERASE / NUCLEOTIDE METABOLISM / PURINE SALVAGE / TERNARY COMPLEX / CATALYTIC BASE
Function / homology
Function and homology information


hypoxanthine phosphoribosyltransferase / hypoxanthine phosphoribosyltransferase activity / guanine phosphoribosyltransferase activity / IMP salvage / purine ribonucleoside salvage / nucleotide binding / metal ion binding / cytoplasm
Similarity search - Function
Hypoxanthine phosphoribosyl transferase / Rossmann fold - #2020 / Phosphoribosyl transferase domain / Phosphoribosyltransferase-like / Phosphoribosyltransferase domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Hypoxanthine phosphoribosyltransferase / 7-HYDROXY-PYRAZOLO[4,3-D]PYRIMIDINE / Chem-PRP / Hypoxanthine phosphoribosyltransferase
Similarity search - Component
Biological speciesTrypanosoma cruzi (eukaryote)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.06 Å
AuthorsCanyuk, B. / Focia, P.J. / Eakin, A.E.
Citation
Journal: Biochemistry / Year: 2001
Title: The role for an invariant aspartic acid in hypoxanthine phosphoribosyltransferases is examined using saturation mutagenesis, functional analysis, and X-ray crystallography.
Authors: Canyuk, B. / Focia, P.J. / Eakin, A.E.
#1: Journal: Biochemistry / Year: 1998
Title: Approaching the Transition State in the Crystal Structure of a Phosphoribosyltransferase
Authors: Focia, P.J. / Craig, S.P. / Eakin, A.E.
History
DepositionJan 29, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 29, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.4Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5Oct 27, 2021Group: Database references / Structure summary / Category: chem_comp / database_2 / struct_ref_seq_dif
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Remark 999SEQUENCE THIS HPRT WAS CLONED FROM A DIFFERENT STRAIN OF TRYPANOSOMA CRUZI AND VARIES FROM A ...SEQUENCE THIS HPRT WAS CLONED FROM A DIFFERENT STRAIN OF TRYPANOSOMA CRUZI AND VARIES FROM A PREVIOUSLY REPORTED SEQUENCE AT LYS 23, CYS 66 AND LEU 86.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HYPOXANTHINE-GUANINE PHOSPHORIBOSYLTRANSFERASE
B: HYPOXANTHINE-GUANINE PHOSPHORIBOSYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,22410
Polymers51,0752
Non-polymers1,1508
Water3,495194
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5530 Å2
ΔGint-68 kcal/mol
Surface area15630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.38, 101.27, 51.67
Angle α, β, γ (deg.)90.00, 94.25, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein HYPOXANTHINE-GUANINE PHOSPHORIBOSYLTRANSFERASE /


Mass: 25537.367 Da / Num. of mol.: 2 / Mutation: M23K, S66C, V86L, D115Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma cruzi (eukaryote) / Production host: Escherichia coli (E. coli)
References: UniProt: Q27796, UniProt: Q4DRC4*PLUS, hypoxanthine phosphoribosyltransferase
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-7HP / 7-HYDROXY-PYRAZOLO[4,3-D]PYRIMIDINE


Mass: 136.111 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H4N4O
#4: Sugar ChemComp-PRP / 1-O-pyrophosphono-5-O-phosphono-alpha-D-ribofuranose / ALPHA-PHOSPHORIBOSYLPYROPHOSPHORIC ACID / 1-O-pyrophosphono-5-O-phosphono-alpha-D-ribose / 1-O-pyrophosphono-5-O-phosphono-D-ribose / 1-O-pyrophosphono-5-O-phosphono-ribose / Phosphoribosyl pyrophosphate


Type: D-saccharide / Mass: 390.070 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H13O14P3
IdentifierTypeProgram
a-D-Ribf1PO35PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 194 / 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: 2.01 Å3/Da / Density % sol: 38.84 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: PEG 6000, Sodium acetate, Ammonium acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Jul 25, 1998
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.06→30 Å / Num. obs: 22986 / % possible obs: 92.1 % / Observed criterion σ(I): -3 / Redundancy: 4.5 % / Rmerge(I) obs: 0.068 / Rsym value: 0.068 / Net I/σ(I): 17.3
Reflection shellResolution: 2.06→2.11 Å / Redundancy: 4 % / Rmerge(I) obs: 0.411 / % possible all: 56.2
Reflection
*PLUS
Num. obs: 21963
Reflection shell
*PLUS
% possible obs: 56.2 % / Mean I/σ(I) obs: 2.6

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Processing

Software
NameVersionClassification
AMoREphasing
X-PLOR3.851refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1tc2 with ligands, waters and loop II removed
Resolution: 2.06→6 Å / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 0 / Stereochemistry target values: Engh & Huber
Details: PATCH STATEMENTS WERE USED FOR CIS PEPTIDES AND METAL-OXYGEN BONDS
RfactorNum. reflection% reflectionSelection details
Rfree0.259 1363 7 %RANDOM
Rwork0.168 ---
obs0.25 20837 92.1 %-
Refinement stepCycle: LAST / Resolution: 2.06→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3011 0 78 184 3273
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.011
X-RAY DIFFRACTIONx_angle_deg1.62
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM11X.DNATOPH11.DNA
X-RAY DIFFRACTION3PRPP.PARPRPP.TOP
X-RAY DIFFRACTION4PARAM19.IONTOPH19.ION
X-RAY DIFFRACTION5PARAM11.WATTOPH11.WAT
Refinement
*PLUS
Rfactor all: 0.25 / Rfactor obs: 0.168
Solvent computation
*PLUS
Displacement parameters
*PLUS

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