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- PDB-2xbu: Saccharomyces cerevisiae hypoxanthine-guanine phosphoribosyltrans... -

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Basic information

Entry
Database: PDB / ID: 2xbu
TitleSaccharomyces cerevisiae hypoxanthine-guanine phosphoribosyltransferase in complex with GMP (monoclinic crystal form)
ComponentsHYPOXANTHINE-GUANINE PHOSPHORIBOSYLTRANSFERASE
KeywordsTRANSFERASE / GLYCOSYLTRANSFERASE / PURINE SALVAGE / FLIP PEPTIDE-PLANE
Function / homology
Function and homology information


XMP salvage / hypoxanthine phosphoribosyltransferase / guanine phosphoribosyltransferase activity / hypoxanthine metabolic process / hypoxanthine phosphoribosyltransferase activity / GMP salvage / IMP salvage / purine ribonucleoside salvage / nucleotide binding / metal ion binding ...XMP salvage / hypoxanthine phosphoribosyltransferase / guanine phosphoribosyltransferase activity / hypoxanthine metabolic process / hypoxanthine phosphoribosyltransferase activity / GMP salvage / IMP salvage / purine ribonucleoside salvage / nucleotide binding / metal ion binding / nucleus / cytoplasm
Similarity search - Function
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 / ACETATE ION / Hypoxanthine-guanine phosphoribosyltransferase
Similarity search - Component
Biological speciesSACCHAROMYCES CEREVISIAE (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsMoynie, L. / Giraud, M.F. / Breton, A. / Boissier, F. / Daignan-Fornier, B. / Dautant, A.
Citation
Journal: Protein Sci. / Year: 2012
Title: Functional Significance of Four Successive Glycine Residues in the Pyrophosphate Binding Loop of Fungal 6-Oxopurine Phosphoribosyltransferases.
Authors: Moynie, L. / Giraud, M.F. / Breton, A. / Boissier, F. / Daignan-Fornier, B. / Dautant, A.
#1: Journal: Genetics / Year: 2008
Title: Lethal Accumulation of Guanylic Nucleotides in Saccharomyces Cerevisiae Hpt1-Deregulated Mutants.
Authors: Breton, A. / Pinson, B. / Coulpier, F. / Giraud, M. / Dautant, A. / Daignan-Fornier, B.
History
DepositionApr 15, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 4, 2011Provider: repository / Type: Initial release
Revision 1.1Sep 19, 2012Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Refinement description / Structure summary / Version format compliance
Revision 1.2Jan 30, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.method
Revision 1.3Feb 6, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.4Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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.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_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_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_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: HYPOXANTHINE-GUANINE PHOSPHORIBOSYLTRANSFERASE
B: HYPOXANTHINE-GUANINE PHOSPHORIBOSYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,3167
Polymers50,4472
Non-polymers8695
Water8,557475
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5020 Å2
ΔGint-19.5 kcal/mol
Surface area17960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.577, 77.521, 56.655
Angle α, β, γ (deg.)90.00, 95.13, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.9848, 0.01737, 0.173), (0.01829, -0.9998, -0.003695), (0.1729, 0.006802, -0.9849)
Vector: -2.286, -20.26, 28.42)

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Components

#1: Protein HYPOXANTHINE-GUANINE PHOSPHORIBOSYLTRANSFERASE / BYPASS OF REPRESSION BY ADENINE PROTEIN 6 / HGPRTASE / HGPRT


Mass: 25223.715 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Strain: Y1846 / Plasmid: PET-21 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q04178, hypoxanthine phosphoribosyltransferase
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-5GP / GUANOSINE-5'-MONOPHOSPHATE


Mass: 363.221 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N5O8P
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 475 / 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: 1.35 Å3/Da / Density % sol: 45.1 % / Description: NONE
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 0.2 M AMMONIUM ACETATE, 30% PEG 4000, 0.1 M TRI-SODIUM CITRATE, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K, pH 5.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.934
DetectorType: ADSC CCD / Detector: CCD / Date: Feb 27, 2008 / Details: MIRRORS
RadiationMonochromator: SI(111) SINGLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 1.8→28.21 Å / Num. obs: 39543 / % possible obs: 96.6 % / Observed criterion σ(I): 0 / Redundancy: 4.3 % / Biso Wilson estimate: 19.57 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 15.3
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 3 / % possible all: 98.4

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2JKY

2jky


Resolution: 1.8→28.214 Å / SU ML: 0.22 / σ(F): 1.36 / Phase error: 19.97 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2058 1994 5 %
Rwork0.1669 --
obs0.1689 39543 96.09 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 63.25 Å2 / ksol: 0.393 e/Å3
Displacement parametersBiso mean: 25.6 Å2
Baniso -1Baniso -2Baniso -3
1-0.3246 Å20 Å20.1616 Å2
2---0.0939 Å2-0 Å2
3----0.2307 Å2
Refinement stepCycle: LAST / Resolution: 1.8→28.214 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3208 0 57 475 3740
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043384
X-RAY DIFFRACTIONf_angle_d0.924608
X-RAY DIFFRACTIONf_dihedral_angle_d17.1011249
X-RAY DIFFRACTIONf_chiral_restr0.062513
X-RAY DIFFRACTIONf_plane_restr0.004590
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.801-1.8460.24661390.21992734X-RAY DIFFRACTION98
1.846-1.89590.28491510.22312712X-RAY DIFFRACTION98
1.8959-1.95170.25131320.21162732X-RAY DIFFRACTION98
1.9517-2.01470.21361490.18922711X-RAY DIFFRACTION98
2.0147-2.08670.22931490.17662723X-RAY DIFFRACTION98
2.0867-2.17020.22771430.16712710X-RAY DIFFRACTION97
2.1702-2.26890.18971680.16462667X-RAY DIFFRACTION97
2.2689-2.38850.19871350.15682686X-RAY DIFFRACTION97
2.3885-2.5380.20311630.15882655X-RAY DIFFRACTION96
2.538-2.73390.19931210.15822704X-RAY DIFFRACTION96
2.7339-3.00870.22581330.15892684X-RAY DIFFRACTION95
3.0087-3.44340.19471310.15152650X-RAY DIFFRACTION95
3.4434-4.33580.15371300.13412603X-RAY DIFFRACTION92
4.3358-28.21780.20391500.17092578X-RAY DIFFRACTION91
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)
10.3693-0.03520.07871.00980.05810.9970.0294-0.0936-0.02170.0065-0.05250.0518-0.0825-0.03860.00030.054-0.01-0.00910.08510.01440.0855-3.8477-0.702221.5939
20.521-0.0946-0.1771.2616-0.01530.96180.03640.07-0.025-0.2972-0.06460.04970.2274-0.0487-0.03070.20780.0293-0.00210.08490.00620.0747-2.4059-19.73236.5278
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESSEQ 1:217)
2X-RAY DIFFRACTION2CHAIN B AND (RESSEQ 1:217)

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