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- PDB-1z7g: Free human HGPRT -

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Basic information

Entry
Database: PDB / ID: 1z7g
TitleFree human HGPRT
ComponentsHypoxanthine-guanine phosphoribosyltransferase
KeywordsTRANSFERASE / flexibility / trans cis peptide bond isomerization / nucleotide binding
Function / homology
Function and homology information


adenine metabolic process / Defective HPRT1 disrupts guanine and hypoxanthine salvage / GMP catabolic process / guanine salvage / hypoxanthine metabolic process / hypoxanthine salvage / cerebral cortex neuron differentiation / positive regulation of dopamine metabolic process / lymphocyte proliferation / hypoxanthine phosphoribosyltransferase ...adenine metabolic process / Defective HPRT1 disrupts guanine and hypoxanthine salvage / GMP catabolic process / guanine salvage / hypoxanthine metabolic process / hypoxanthine salvage / cerebral cortex neuron differentiation / positive regulation of dopamine metabolic process / lymphocyte proliferation / hypoxanthine phosphoribosyltransferase / IMP metabolic process / GMP salvage / guanine phosphoribosyltransferase activity / hypoxanthine phosphoribosyltransferase activity / grooming behavior / IMP salvage / Purine salvage / striatum development / AMP salvage / dopaminergic neuron differentiation / purine nucleotide biosynthetic process / Azathioprine ADME / purine ribonucleoside salvage / dendrite morphogenesis / dopamine metabolic process / central nervous system neuron development / response to amphetamine / locomotory behavior / T cell mediated cytotoxicity / protein homotetramerization / nucleotide binding / magnesium ion binding / extracellular exosome / identical protein binding / cytosol / cytoplasm
Similarity search - Function
Hypoxanthine phosphoribosyl transferase / Purine/pyrimidine phosphoribosyl transferases signature. / Rossmann fold - #2020 / Phosphoribosyl transferase domain / Phosphoribosyltransferase-like / Phosphoribosyltransferase domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Hypoxanthine-guanine phosphoribosyltransferase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsKeough, D.T. / Brereton, I.M. / de Jersey, J. / Guddat, L.W.
CitationJournal: J.Mol.Biol. / Year: 2005
Title: The Crystal Structure of Free Human Hypoxanthine-guanine Phosphoribosyltransferase Reveals Extensive Conformational Plasticity Throughout the Catalytic Cycle
Authors: Keough, D.T. / Brereton, I.M. / de Jersey, J. / Guddat, L.W.
History
DepositionMar 24, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 2, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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
C: Hypoxanthine-guanine phosphoribosyltransferase
D: Hypoxanthine-guanine phosphoribosyltransferase


Theoretical massNumber of molelcules
Total (without water)97,9254
Polymers97,9254
Non-polymers00
Water9,080504
1
A: Hypoxanthine-guanine phosphoribosyltransferase
B: Hypoxanthine-guanine phosphoribosyltransferase

A: Hypoxanthine-guanine phosphoribosyltransferase
B: Hypoxanthine-guanine phosphoribosyltransferase


Theoretical massNumber of molelcules
Total (without water)97,9254
Polymers97,9254
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1,y,-z1
2
C: Hypoxanthine-guanine phosphoribosyltransferase
D: Hypoxanthine-guanine phosphoribosyltransferase

C: Hypoxanthine-guanine phosphoribosyltransferase
D: Hypoxanthine-guanine phosphoribosyltransferase


Theoretical massNumber of molelcules
Total (without water)97,9254
Polymers97,9254
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Unit cell
Length a, b, c (Å)149.570, 51.800, 117.520
Angle α, β, γ (deg.)90.00, 105.80, 90.00
Int Tables number5
Space group name H-MC121
DetailsThe biological unit is a tetramer. The asymmetric unit consists of two seperate dimers. Tetramers are generated by crystallographic two fold axes of symmetry.

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Components

#1: Protein
Hypoxanthine-guanine phosphoribosyltransferase / / HGPRT / HGPRTase


Mass: 24481.217 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HPRT1, HPRT
Plasmid details: recombinant plasmid pHTM was obtained by site directed mutagenesis of pRG1 which in turn is derived from pT7-7
Plasmid: pHTM / Production host: Escherichia coli (E. coli) / Strain (production host): S 606
References: UniProt: P00492, hypoxanthine phosphoribosyltransferase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 504 / 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: 2.1 Å3/Da / Density % sol: 39.1 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 0.2 M ammonium acetate, 0.1 M sodium acetate, 30% PEG4000, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jun 3, 2003 / Details: Osmic
RadiationMonochromator: Single wavelength / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→46.3 Å / Num. all: 66957 / Num. obs: 66957 / % possible obs: 95.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.5 % / Rmerge(I) obs: 0.062 / Rsym value: 0.062 / Net I/σ(I): 12.3
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.288 / Mean I/σ(I) obs: 2.2 / Num. unique all: 5419 / Rsym value: 0.288 / % possible all: 79.3

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Processing

Software
NameVersionClassification
CRYSTALCLEAR 1.35data collection
CRYSTALCLEAR 1.35data reduction
CNSrefinement
CrystalClearV. 1.35 (MSC/RIGAKU)data reduction
CrystalClearV. 1.35 (MSC/RIGAKU)data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1HMP

1hmp


Resolution: 1.9→46.3 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 1 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.254 6505 -RANDOM
Rwork0.213 ---
all0.225 65782 --
obs0.219 64112 95.3 %-
Displacement parametersBiso mean: 59.11 Å2
Refinement stepCycle: LAST / Resolution: 1.9→46.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6273 0 0 504 6777
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d1.56
X-RAY DIFFRACTIONc_angle_d2.23
X-RAY DIFFRACTIONc_mcangle_it2.5
LS refinement shellResolution: 1.9→1.97 Å / Rfactor Rfree error: 0.034
RfactorNum. reflection% reflection
Rfree0.328 517 -
Rwork0.294 --
obs-4461 72.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top
X-RAY DIFFRACTION4carbohydrate.paramcarbohydrate.top

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