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- PDB-1pzm: Crystal structure of HGPRT-ase from Leishmania tarentolae in comp... -

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Basic information

Entry
Database: PDB / ID: 1pzm
TitleCrystal structure of HGPRT-ase from Leishmania tarentolae in complex with GMP
Componentshypoxanthine-guanine phosphoribosyltransferase
KeywordsTRANSFERASE
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
GUANOSINE-5'-MONOPHOSPHATE / Hypoxanthine phosphoribosyltransferase
Similarity search - Component
Biological speciesLeishmania tarentolae (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsMonzani, P.S. / Trapani, S. / Oliva, G. / Thiemann, O.H.
Citation
Journal: Bmc Struct.Biol. / Year: 2007
Title: Crystal structure of Leishmania tarentolae hypoxanthine-guanine phosphoribosyltransferase.
Authors: Monzani, P.S. / Trapani, S. / Thiemann, O.H. / Oliva, G.
#1: Journal: BIOCHIM.BIOPHYS.ACTA / Year: 2002
Title: Cloning, characterization and preliminary crystallographic analysis of Leishmania hypoxanthine-guanine phosphoribosyltransferase
Authors: Monzani, P.S. / Alfonzo, J.D. / Simpson, L. / Oliva, G. / Thiemann, O.H.
History
DepositionJul 11, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 27, 2004Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Aug 16, 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

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Assembly

Deposited unit
A: hypoxanthine-guanine phosphoribosyltransferase
B: hypoxanthine-guanine phosphoribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,0474
Polymers47,3212
Non-polymers7262
Water4,378243
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3950 Å2
ΔGint-19 kcal/mol
Surface area14420 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)58.104, 85.443, 87.598
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe asymmetric unit content represents the biological assembly, which is a dimer.

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Components

#1: Protein hypoxanthine-guanine phosphoribosyltransferase / HGPRT


Mass: 23660.475 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leishmania tarentolae (eukaryote) / Gene: hgprt / Plasmid: pET29a(+) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q9NJI5, hypoxanthine phosphoribosyltransferase
#2: Chemical ChemComp-5GP / GUANOSINE-5'-MONOPHOSPHATE


Mass: 363.221 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N5O8P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 243 / 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: 2.3 Å3/Da / Density % sol: 46.45 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: PEG 4000, i-propanol, glycerol, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: D03B-MX1 / Wavelength: 1.537 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 16, 2001
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.537 Å / Relative weight: 1
ReflectionResolution: 2.1→48.4 Å / Num. all: 24801 / Num. obs: 24231 / % possible obs: 92.8 % / Observed criterion σ(F): 1
Reflection shellResolution: 2.1→2.16 Å / Redundancy: 5.5 % / % possible all: 96.8

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Processing

Software
NameVersionClassification
REFMAC5.1.09refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1TC1

1tc1


Resolution: 2.1→48.22 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.92 / SU B: 4.105 / SU ML: 0.109 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.189 / ESU R Free: 0.166 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21525 1276 5.1 %RANDOM
Rwork0.17336 ---
obs0.17549 24231 94.98 %-
all-24801 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 14.486 Å2
Baniso -1Baniso -2Baniso -3
1--3.84 Å20 Å20 Å2
2--1.78 Å20 Å2
3---2.06 Å2
Refinement stepCycle: LAST / Resolution: 2.1→48.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2633 0 48 243 2924
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0222756
X-RAY DIFFRACTIONr_angle_refined_deg2.0282.0053750
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3165
X-RAY DIFFRACTIONr_dihedral_angle_2_deg13.13615
X-RAY DIFFRACTIONr_chiral_restr0.1340.2447
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021987
X-RAY DIFFRACTIONr_nbd_refined0.2150.21228
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1740.2253
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1750.225
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1380.210
X-RAY DIFFRACTIONr_mcbond_it1.21.51695
X-RAY DIFFRACTIONr_mcangle_it2.01222739
X-RAY DIFFRACTIONr_scbond_it3.03531061
X-RAY DIFFRACTIONr_scangle_it4.4914.51011
LS refinement shellResolution: 2.1→2.155 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.242 102
Rwork0.195 1729
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.6888-0.24-0.07812.7784-0.32981.24480.0318-0.11590.11870.1973-0.0621-0.2914-0.20530.09050.03030.4934-0.0397-0.01040.00650.01430.05463.54148.76329.439
20.7328-0.30690.06091.3119-0.23340.60840.0387-0.0387-0.0186-0.0373-0.0202-0.06080.050.0153-0.01850.4402-0.0164-0.00570.00590.0060.0332-1.13725.71732.058
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA20 - 20220 - 202
2X-RAY DIFFRACTION1AC3011
3X-RAY DIFFRACTION2BB20 - 20120 - 201
4X-RAY DIFFRACTION2BD3021

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