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- PDB-4zfn: Hypoxanthine-guanine-xanthine phosphoribosyltransferase (HGXPRT) ... -

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Basic information

Entry
Database: PDB / ID: 4zfn
TitleHypoxanthine-guanine-xanthine phosphoribosyltransferase (HGXPRT) from Sulfolobus solfataricus containing GMP complexed in two different ways together with one or two MG2+
ComponentsPurine phosphoribosyltransferase (GpT-2)
KeywordsTRANSFERASE / HGXPRT / HGPRT / purine phosphoribosyltransferase
Function / homology
Function and homology information


glycosyltransferase activity / Transferases; Glycosyltransferases; Pentosyltransferases
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 / Purine phosphoribosyltransferase (GpT-2)
Similarity search - Component
Biological speciesSulfolobus solfataricus P2 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.901 Å
AuthorsChristoffersen, S.
CitationJournal: to be published
Title: Sulfolobus solfataricus P2
Authors: Christoffersen, S. / Hansen, M.R. / Jensen, K.S. / Larsen, S. / Jensen, K.F.
History
DepositionApr 21, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Apr 29, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: 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 / diffrn_radiation_wavelength / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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.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.value / _struct_conn.pdbx_dist_value / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Purine phosphoribosyltransferase (GpT-2)
B: Purine phosphoribosyltransferase (GpT-2)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,3569
Polymers41,3642
Non-polymers9917
Water7,692427
1
A: Purine phosphoribosyltransferase (GpT-2)
B: Purine phosphoribosyltransferase (GpT-2)
hetero molecules

A: Purine phosphoribosyltransferase (GpT-2)
B: Purine phosphoribosyltransferase (GpT-2)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,71118
Polymers82,7284
Non-polymers1,98314
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z+1/21
Buried area15960 Å2
ΔGint-198 kcal/mol
Surface area28320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.467, 74.467, 143.527
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Purine phosphoribosyltransferase (GpT-2)


Mass: 20682.057 Da / Num. of mol.: 2 / Fragment: hgxprt
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus solfataricus P2 (archaea) / Gene: gpT-2, SSO2424 / Plasmid: pKU1 / Production host: Escherichia coli (E. coli) / Strain (production host): NF1830
References: UniProt: Q97W22, Transferases; Glycosyltransferases; Pentosyltransferases
#2: Chemical ChemComp-5GP / GUANOSINE-5'-MONOPHOSPHATE


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


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 427 / 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: 2.41 Å3/Da / Density % sol: 48.86 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 2.0 M ammonium sulfate, 0.1 M BIS-TRIS hydrochloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 1.03688 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 20, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03688 Å / Relative weight: 1
ReflectionResolution: 1.9→47.842 Å / Num. all: 32611 / Num. obs: 32529 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 7.55 % / Biso Wilson estimate: 27.72 Å2 / Rmerge F obs: 0.999 / Rmerge(I) obs: 0.07 / Rrim(I) all: 0.075 / Rsym value: 0.075 / Χ2: 0.944 / Net I/σ(I): 19.85 / Num. measured all: 245734
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Highest resolution (Å)Redundancy (%)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
1.9-2.027.610.8580.7173.1439180517651470.76899.4
2.02-2.150.9410.4135.4937264484248370.44399.9
2.15-2.330.9760.2428.9534951454845460.259100
2.33-2.550.9920.14613.932123417941770.157100
2.55-2.850.9970.09220.3729344383938390.099100
2.85-3.280.9980.05630.6625776340234020.06100
3.28-4.020.9990.03844.0921478289928970.0499.9
4.02-5.650.9990.03152.4516430232023140.03399.7
5.650.9990.02853.079188140613700.0397.4

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation4.73 Å40.32 Å
Translation4.73 Å40.32 Å

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHASER2.5.0phasing
PHENIX1.9refinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1VDM

1vdm


Resolution: 1.901→40.251 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 22.92 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2361 1627 5 %Random selection
Rwork0.1805 30899 --
obs0.1833 32526 99.75 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 99.55 Å2 / Biso mean: 32.4168 Å2 / Biso min: 14.59 Å2
Refinement stepCycle: final / Resolution: 1.901→40.251 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2858 0 61 427 3346
Biso mean--37.63 41.37 -
Num. residues----350
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082985
X-RAY DIFFRACTIONf_angle_d1.0964068
X-RAY DIFFRACTIONf_chiral_restr0.046466
X-RAY DIFFRACTIONf_plane_restr0.005490
X-RAY DIFFRACTIONf_dihedral_angle_d14.6791106
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9005-1.95650.27281330.25172518265199
1.9565-2.01960.2961320.222925122644100
2.0196-2.09180.26751330.221925222655100
2.0918-2.17550.25611330.203525382671100
2.1755-2.27460.23731340.195925392673100
2.2746-2.39450.26851350.198625572692100
2.3945-2.54450.23741330.190225402673100
2.5445-2.74090.26731360.193325822718100
2.7409-3.01660.23341360.187325872723100
3.0166-3.45290.22221370.174825962733100
3.4529-4.34950.21271390.148826432782100
4.3495-40.26020.22341460.16752765291199

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