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- PDB-1tc1: A 1.4 ANGSTROM CRYSTAL STRUCTURE FOR THE HYPOXANTHINE PHOSPHORIBO... -

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Basic information

Entry
Database: PDB / ID: 1tc1
TitleA 1.4 ANGSTROM CRYSTAL STRUCTURE FOR THE HYPOXANTHINE PHOSPHORIBOSYLTRANSFERASE OF TRYPANOSOMA CRUZI
ComponentsPROTEIN (HYPOXANTHINE PHOSPHORIBOSYLTRANSFERASE)
KeywordsTRANSFERASE / PHOSPHORIBOSYLTRANSFERASE / PURINE SALVAGE / NUCLEOTIDE METABOLISM
Function / homology
Function and homology information


hypoxanthine phosphoribosyltransferase / guanine phosphoribosyltransferase activity / hypoxanthine 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
FORMYCIN B / Hypoxanthine phosphoribosyltransferase / Hypoxanthine phosphoribosyltransferase
Similarity search - Component
Biological speciesTrypanosoma cruzi (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.41 Å
AuthorsFocia, P.J. / Craig III, S.P. / Nieves-Alicea, R. / Fletterick, R.J. / Eakin, A.E.
CitationJournal: Biochemistry / Year: 1998
Title: A 1.4 A crystal structure for the hypoxanthine phosphoribosyltransferase of Trypanosoma cruzi.
Authors: Focia, P.J. / Craig III, S.P. / Nieves-Alicea, R. / Fletterick, R.J. / Eakin, A.E.
History
DepositionSep 30, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Oct 7, 1999Provider: 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 1.5Aug 23, 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 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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: PROTEIN (HYPOXANTHINE PHOSPHORIBOSYLTRANSFERASE)
B: PROTEIN (HYPOXANTHINE PHOSPHORIBOSYLTRANSFERASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,8556
Polymers50,9282
Non-polymers9274
Water2,666148
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4460 Å2
ΔGint0 kcal/mol
Surface area15390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.500, 94.090, 52.120
Angle α, β, γ (deg.)90.00, 94.75, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.888793, -0.341844, 0.305271), (-0.338296, -0.938707, -0.066224), (0.309198, -0.044413, -0.94996)
Vector: -8.9489, 5.5439, 61.5864)

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Components

#1: Protein PROTEIN (HYPOXANTHINE PHOSPHORIBOSYLTRANSFERASE) / E.C.2.4.8 TRANSFERASE


Mass: 25464.209 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
#2: Chemical ChemComp-FMB / FORMYCIN B


Mass: 268.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H12N4O5
#3: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID / MES (buffer)


Mass: 195.237 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 148 / 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: 2.6 Å3/Da / Density % sol: 49 %
Crystal growpH: 5.75 / Details: pH 5.75
Crystal
*PLUS
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110-15 mg/mlenzyme1drop
25-10 mMFmB1reservoir
315-20 %PEG60001reservoir
40.1 MMES1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 1.41→6 Å / Num. obs: 71678 / % possible obs: 98 % / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Biso Wilson estimate: 14.6 Å2 / Rmerge(I) obs: 0.061 / Rsym value: 0.061 / Net I/σ(I): 21.3
Reflection shellResolution: 1.41→1.44 Å / Rmerge(I) obs: 0.196 / Mean I/σ(I) obs: 4.7 / Rsym value: 0.196 / % possible all: 81.9
Reflection shell
*PLUS
% possible obs: 81.9 %

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Processing

Software
NameVersionClassification
AMoREphasing
X-PLOR3.8refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1HGX

1hgx


Resolution: 1.41→6 Å / Cross valid method: THROUGHOUT / σ(F): 1
RfactorNum. reflection% reflectionSelection details
Rfree0.228 6791 10 %RANDOM
Rwork0.198 ---
obs0.193 71678 98 %-
Displacement parametersBiso mean: 15.6 Å2
Refine analyzeLuzzati d res low obs: 10 Å / Luzzati sigma a obs: 0.15 Å
Refinement stepCycle: LAST / Resolution: 1.41→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2869 0 44 148 3061
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
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_deg1.48
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d23.85
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.33
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 1.41→1.44 Å / Total num. of bins used: 15
RfactorNum. reflection% reflection
Rfree0.25 397 11.21 %
Rwork0.246 3143 -
obs--81.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM.WATTOPH.WAT
X-RAY DIFFRACTION3FMC.PARFMC.TOP
X-RAY DIFFRACTION4MES.PARMES.TOP
Software
*PLUS
Name: X-PLOR / Version: 3.8 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 6 Å / σ(F): 1 / % reflection Rfree: 10 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 15.6 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg23.85
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.33
LS refinement shell
*PLUS
Rfactor Rfree: 0.25 / Rfactor Rwork: 0.246

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