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- PDB-1tc2: TERNARY SUBSTRATE COMPLEX OF THE HYPOXANTHINE PHOSPHORIBOSYLTRANS... -

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Basic information

Entry
Database: PDB / ID: 1tc2
TitleTERNARY SUBSTRATE COMPLEX OF THE HYPOXANTHINE PHOSPHORIBOSYLTRANSFERASE FROM TRYPANOSOMA CRUZI
ComponentsPROTEIN (HYPOXANTHINE PHOSPHORIBOSYLTRANSFERASE)
KeywordsTRANSFERASE / GLYCOSYLTRANSFERASE / PHOSPHORIBOSYLTRANSFERASE / NUCLEOTIDE METABOLISM / PURINE SALVAGE / TERNARY COMPLEX / NEAR TRANSITION STATE
Function / homology
Function and homology information


hypoxanthine phosphoribosyltransferase / guanine salvage / hypoxanthine metabolic process / guanine phosphoribosyltransferase activity / 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 / : / Chem-PRP / Hypoxanthine phosphoribosyltransferase / Hypoxanthine phosphoribosyltransferase
Similarity search - Component
Biological speciesTrypanosoma cruzi (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.81 Å
AuthorsFocia, P.J. / Craig III, S.P. / Eakin, A.E.
CitationJournal: Biochemistry / Year: 1998
Title: Approaching the transition state in the crystal structure of a phosphoribosyltransferase.
Authors: Focia, P.J. / Craig III, S.P. / Eakin, A.E.
History
DepositionNov 4, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Mar 8, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.4Jan 31, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.5Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / 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_ref_seq_dif / 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_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_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.6Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROTEIN (HYPOXANTHINE PHOSPHORIBOSYLTRANSFERASE)
B: PROTEIN (HYPOXANTHINE PHOSPHORIBOSYLTRANSFERASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,37110
Polymers51,1912
Non-polymers1,1808
Water3,477193
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5710 Å2
ΔGint-66 kcal/mol
Surface area15650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.42, 101.76, 51.92
Angle α, β, γ (deg.)90.00, 94.23, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.865547, 0.408421, 0.289862), (0.410351, -0.91014, 0.05707), (0.287123, 0.069549, -0.955365)
Vector: -27.3294, 78.4611, 65.1382)

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Components

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Protein / Sugars , 2 types, 4 molecules AB

#1: Protein PROTEIN (HYPOXANTHINE PHOSPHORIBOSYLTRANSFERASE)


Mass: 25595.404 Da / Num. of mol.: 2
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, 199 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / 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-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 193 / 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: 2.03 Å3/Da / Density % sol: 39.35 %
Crystal growpH: 4.6 / Details: pH 4.6
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 6.8 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
15 mg/mlprotein1drop
25 mMPRPP1drop
35 mMHPP1drop
420 mMbis-tris1drop
56 mM1dropMgCl2
60.1 Msodium acetate1reservoir
70.2 Mammonium acetate1reservoir
830 %PEG40001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 4, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 1.81→20.6 Å / Num. obs: 33026 / % possible obs: 88.8 % / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Rsym value: 0.051 / Net I/σ(I): 20.8
Reflection shellResolution: 1.81→1.85 Å / Mean I/σ(I) obs: 3.8 / Rsym value: 0.32 / % possible all: 80.1
Reflection
*PLUS
Rmerge(I) obs: 0.051
Reflection shell
*PLUS
% possible obs: 80.1 % / Rmerge(I) obs: 0.32

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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 1TC1

1tc1


Resolution: 1.81→6 Å / Cross valid method: THROUGHOUT / σ(F): 1
Details: PATCH STATEMENTS WERE USED FOR CIS PEPTIDES AND METAL-OXYGEN BONDS SER 88 IS POORLY ORDERED IN SUBUNIT A THE ENERGIES FOR METAL-OXYGEN BOND LENGTHS AND ANGLES WERE SET ARTIFICIALLY LOW ...Details: PATCH STATEMENTS WERE USED FOR CIS PEPTIDES AND METAL-OXYGEN BONDS SER 88 IS POORLY ORDERED IN SUBUNIT A THE ENERGIES FOR METAL-OXYGEN BOND LENGTHS AND ANGLES WERE SET ARTIFICIALLY LOW DURING REFINEMENT IN ORDER TO ALLOW THESE ATOMS MORE FREEDOM TO ADJUST
RfactorNum. reflection% reflectionSelection details
Rfree0.232 1756 5.9 %RANDOM
Rwork0.1834 ---
obs0.191 29719 --
Refinement stepCycle: LAST / Resolution: 1.81→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3039 0 78 183 3300
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_angle_deg1.56
X-RAY DIFFRACTIONx_dihedral_angle_d24.48
X-RAY DIFFRACTIONx_improper_angle_d1.36
LS refinement shellResolution: 1.81→1.85 Å / Total num. of bins used: 15
RfactorNum. reflection% reflection
Rfree0.302 82 4.16 %
Rwork0.259 1403 -
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM11X.DNA (MODIFIED FOR 7HP)TOPH11.DNA (MODIFIED FOR 7HP)
X-RAY DIFFRACTION3PRPP.PARPRPP.TOP
X-RAY DIFFRACTION4PARAM19.ION (MODIFIED)TOPH19.ION (MODIFIED)
X-RAY DIFFRACTION5PARAM11.WATTOPH11.WAT
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24.48
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.36

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