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- PDB-1i13: ANALYSIS OF AN INVARIANT ASPARTIC ACID IN HPRTS-ALANINE MUTANT -

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Basic information

Entry
Database: PDB / ID: 1i13
TitleANALYSIS OF AN INVARIANT ASPARTIC ACID IN HPRTS-ALANINE MUTANT
ComponentsHYPOXANTHINE-GUANINE PHOSPHORIBOSYLTRANSFERASE
KeywordsTRANSFERASE / PHOSPHORIBOSYLTRANSFERASE / NUCLEOTIDE METABOLISM / PURINE SALVAGE / TERNARY COMPLEX / CATALYTIC BASE
Function / homology
Function and homology information


hypoxanthine phosphoribosyltransferase / guanine salvage / hypoxanthine metabolic process / hypoxanthine phosphoribosyltransferase activity / GMP salvage / IMP salvage / purine ribonucleoside salvage / nucleotide binding / magnesium ion binding / cytosol
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
7-HYDROXY-PYRAZOLO[4,3-D]PYRIMIDINE / FORMIC ACID / Chem-PRP / Hypoxanthine phosphoribosyltransferase / Hypoxanthine phosphoribosyltransferase
Similarity search - Component
Biological speciesTrypanosoma cruzi (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.84 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 30, 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 1.3Jul 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 1.4Oct 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
Revision 1.5Aug 9, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
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)52,15611
Polymers50,9612
Non-polymers1,1969
Water3,207178
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5740 Å2
ΔGint-70 kcal/mol
Surface area15060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.45, 102.25, 52.00
Angle α, β, γ (deg.)90.00, 94.11, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein / Sugars , 2 types, 4 molecules AB

#1: Protein HYPOXANTHINE-GUANINE PHOSPHORIBOSYLTRANSFERASE


Mass: 25480.316 Da / Num. of mol.: 2 / Mutation: M23K, S66C, V86L, D115A
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
#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


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

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Non-polymers , 4 types, 185 molecules

#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
#5: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 178 / 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: 2.05 Å3/Da / Density % sol: 40.06 %
Crystal growMethod: 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: SYNCHROTRON / Site: NSLS / Beamline: X12B / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 21, 1999
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.84→30 Å / Num. obs: 36405 / % possible obs: 95.8 % / Observed criterion σ(I): -3 / Redundancy: 2.3 % / Rmerge(I) obs: 0.056 / Net I/σ(I): 13.7
Reflection shellResolution: 1.8→1.84 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 2.3 / % possible all: 92.5
Reflection
*PLUS
Num. obs: 33269
Reflection shell
*PLUS
Highest resolution: 1.84 Å / Lowest resolution: 1.89 Å / % possible obs: 93.7 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 2.9

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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, water molecules and loop II removed

1tc2


Resolution: 1.84→6 Å / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
Details: PATCH STATEMENTS WERE USED FOR CIS PEPTIDES AND METAL-OXYGEN BONDS
RfactorNum. reflection% reflectionSelection details
Rfree0.252 2082 7.1 %random
Rwork0.192 ---
obs0.25 29126 95.8 %-
Refinement stepCycle: LAST / Resolution: 1.84→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2979 0 78 171 3228
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.011
X-RAY DIFFRACTIONx_angle_deg1.57
LS refinement shellResolution: 1.8→1.84 Å / Total num. of bins used: 15
RfactorNum. reflection% reflection
Rfree0.318 116 7.9 %
Rwork0.271 1340 -
obs--93.7 %
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: 0.192
Solvent computation
*PLUS
Displacement parameters
*PLUS
LS refinement shell
*PLUS
Rfactor obs: 0.271

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