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- PDB-3acc: Crystal structure of hypoxanthine-guanine phosphoribosyltransfera... -

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Basic information

Entry
Database: PDB / ID: 3acc
TitleCrystal structure of hypoxanthine-guanine phosphoribosyltransferase with GMP from Thermus thermophilus HB8
ComponentsHypoxanthine-guanine phosphoribosyltransferase
KeywordsTRANSFERASE / Rossmann fold / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
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
GUANOSINE-5'-MONOPHOSPHATE / 1,4-DIETHYLENE DIOXIDE / Hypoxanthine phosphoribosyltransferase
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.16 Å
AuthorsKanagawa, M. / Baba, S. / Hirotsu, K. / Kuramitsu, S. / Yokoyama, S. / Kawai, G. / Sampei, G. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2010
Title: Structures of hypoxanthine-guanine phosphoribosyltransferase (TTHA0220) from Thermus thermophilus HB8.
Authors: Kanagawa, M. / Baba, S. / Ebihara, A. / Shinkai, A. / Hirotsu, K. / Mega, R. / Kim, K. / Kuramitsu, S. / Sampei, G. / Kawai, G.
History
DepositionDec 30, 2009Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 9, 2010Provider: repository / Type: Initial release
SupersessionFeb 23, 2010ID: 2YWT
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,7334
Polymers20,1931
Non-polymers5393
Water1,928107
1
A: Hypoxanthine-guanine phosphoribosyltransferase
hetero molecules

A: Hypoxanthine-guanine phosphoribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,4658
Polymers40,3872
Non-polymers1,0796
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-y+1,-x+1,-z+1/61
Buried area2920 Å2
ΔGint-17 kcal/mol
Surface area14370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.139, 67.139, 152.543
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein Hypoxanthine-guanine phosphoribosyltransferase


Mass: 20193.264 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Gene: TTHA0220 / Plasmid: pET-11A / Production host: Escherichia coli (E. coli)
References: UniProt: Q5SLS3, hypoxanthine phosphoribosyltransferase
#2: Chemical ChemComp-5GP / GUANOSINE-5'-MONOPHOSPHATE


Mass: 363.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O8P
#3: Chemical ChemComp-DIO / 1,4-DIETHYLENE DIOXIDE


Mass: 88.105 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H8O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 107 / 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: 2.46 Å3/Da / Density % sol: 49.95 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 15% Glycerol, 28% Dioxane, 0.005M GMP, 0.01M Magnesium chloride, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 1 Å
DetectorType: RIGAKU RAXIS V / Detector: IMAGE PLATE / Date: Mar 18, 2007
RadiationMonochromator: Fixed exit Si double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.16→50 Å / Num. obs: 10796 / % possible obs: 93.4 % / Redundancy: 10.2 % / Biso Wilson estimate: 14.9 Å2 / Rmerge(I) obs: 0.086
Reflection shellResolution: 2.16→2.24 Å / Redundancy: 9 % / Rmerge(I) obs: 0.163 / Num. unique all: 952 / % possible all: 86.1

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ACB

3acb


Resolution: 2.16→46.24 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 484347.93 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.25 1110 10.3 %RANDOM
Rwork0.21 ---
obs0.21 10794 93.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 44.0057 Å2 / ksol: 0.341017 e/Å3
Displacement parametersBiso mean: 25 Å2
Baniso -1Baniso -2Baniso -3
1-1.78 Å21.72 Å20 Å2
2--1.78 Å20 Å2
3----3.57 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.28 Å0.23 Å
Luzzati d res low-5 Å
Luzzati sigma a0.22 Å0.13 Å
Refinement stepCycle: LAST / Resolution: 2.16→46.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1308 0 36 107 1451
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d22.8
X-RAY DIFFRACTIONc_improper_angle_d0.82
Refine LS restraints NCSNCS model details: NONE
LS refinement shellResolution: 2.16→2.3 Å / Rfactor Rfree error: 0.029 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.326 130 9.7 %
Rwork0.26 1208 -
obs--72.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater_rep.top
X-RAY DIFFRACTION35gp.param5gp.top
X-RAY DIFFRACTION4dio.paramdio.top
X-RAY DIFFRACTION5cis_peptide.param

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