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- PDB-6igs: Crystal structure of HPRT from F. tularensis with Zinc -

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Basic information

Entry
Database: PDB / ID: 6igs
TitleCrystal structure of HPRT from F. tularensis with Zinc
ComponentsHypoxanthine phosphoribosyltransferase
KeywordsTRANSFERASE / hypoxanthine phosphoribosyltransferase / zinc / salvage pathway
Function / homology
Function and homology information


guanine salvage / hypoxanthine metabolic process / hypoxanthine phosphoribosyltransferase / guanine phosphoribosyltransferase activity / GMP salvage / hypoxanthine phosphoribosyltransferase activity / 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
Hypoxanthine phosphoribosyltransferase / Hypoxanthine phosphoribosyltransferase
Similarity search - Component
Biological speciesFrancisella tularensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.16 Å
AuthorsPavithra, G.C. / Kundapura, S.V. / Ramagopal, U.A.
CitationJournal: To be published
Title: Crystal structure of hypoxanthine phosphoribosyltransferase from Francisella tularensis
Authors: Pavithra, G.C. / Ramagopal, U.A.
History
DepositionSep 25, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 2, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 22, 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 / 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_asym_id / _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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_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_asym_id / _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_asym_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_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hypoxanthine phosphoribosyltransferase
B: Hypoxanthine phosphoribosyltransferase
C: Hypoxanthine phosphoribosyltransferase
D: Hypoxanthine phosphoribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,53319
Polymers81,3374
Non-polymers1,19615
Water2,954164
1
A: Hypoxanthine phosphoribosyltransferase
B: Hypoxanthine phosphoribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,2189
Polymers40,6682
Non-polymers5507
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3990 Å2
ΔGint-195 kcal/mol
Surface area14180 Å2
MethodPISA
2
C: Hypoxanthine phosphoribosyltransferase
D: Hypoxanthine phosphoribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,31410
Polymers40,6682
Non-polymers6468
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3870 Å2
ΔGint-203 kcal/mol
Surface area14290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.764, 90.193, 113.707
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Hypoxanthine phosphoribosyltransferase


Mass: 20334.238 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Francisella tularensis (bacteria) / Gene: hpt / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: A0A0E2ZT88, UniProt: Q5NI77*PLUS, hypoxanthine phosphoribosyltransferase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 164 / 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: 2.48 Å3/Da / Density % sol: 50.46 % / Mosaicity: 0.845 °
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 25% PEG 3350, 0.2M lithium sulphate pH 7.0, 5mM ZnCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.98011 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Nov 16, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98011 Å / Relative weight: 1
ReflectionResolution: 2.15→50 Å / Num. obs: 44059 / % possible obs: 99.6 % / Redundancy: 5.8 % / Rmerge(I) obs: 0.091 / Rpim(I) all: 0.042 / Rrim(I) all: 0.101 / Χ2: 0.902 / Net I/σ(I): 10.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.15-2.195.21.0372.2521830.6710.5131.160.77100
2.19-2.234.70.7721540.6430.4050.8750.8999.1
2.23-2.274.40.58921140.6360.310.6691.65698.3
2.27-2.325.20.8122080.7040.4020.9080.81299.8
2.32-2.3750.48521730.8260.2430.5450.78899.8
2.37-2.425.30.42421640.8610.2050.4720.7999.7
2.42-2.4860.36321810.930.1640.3990.77899.9
2.48-2.556.40.34121850.9570.1470.3720.78100
2.55-2.626.50.29521950.950.1270.3220.793100
2.62-2.716.50.24221930.9690.1030.2630.803100
2.71-2.816.50.20121950.9720.0860.2190.812100
2.81-2.926.50.1521970.9830.0640.1630.846100
2.92-3.056.50.11522030.9890.0490.1250.955100
3.05-3.216.40.09622060.9910.0410.1040.99100
3.21-3.416.40.08122170.9910.0350.0891.05100
3.41-3.6850.06721660.9870.0320.0741.20698.1
3.68-4.055.10.05222070.9950.0250.0571.01998.5
4.05-4.6350.04322390.9960.0210.0480.90299.6
4.63-5.836.70.04322790.9970.0180.0470.942100
5.83-37.246.60.0424000.9970.0170.0430.76499.6

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
REFMAC5.8.0230refinement
PDB_EXTRACT3.24data extraction
DENZOdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3OHP

3ohp


Resolution: 2.16→37.24 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.91 / SU B: 9.79 / SU ML: 0.131 / SU R Cruickshank DPI: 0.2322 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.232 / ESU R Free: 0.196
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2324 1965 4.8 %RANDOM
Rwork0.1826 ---
obs0.1849 39247 92.72 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 104.39 Å2 / Biso mean: 30.268 Å2 / Biso min: 7.5 Å2
Baniso -1Baniso -2Baniso -3
1-0.87 Å20 Å20 Å2
2--0.13 Å2-0 Å2
3----1 Å2
Refinement stepCycle: final / Resolution: 2.16→37.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5282 0 43 164 5489
Biso mean--39.17 27.74 -
Num. residues----650
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0145427
X-RAY DIFFRACTIONr_bond_other_d0.0010.0175015
X-RAY DIFFRACTIONr_angle_refined_deg1.861.6667337
X-RAY DIFFRACTIONr_angle_other_deg0.9511.63611700
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5775650
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.01823.141277
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.03215999
X-RAY DIFFRACTIONr_dihedral_angle_4_deg181527
X-RAY DIFFRACTIONr_chiral_restr0.0850.2738
X-RAY DIFFRACTIONr_gen_planes_refined0.010.025948
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021028
LS refinement shellResolution: 2.155→2.211 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.247 96 -
Rwork0.207 1980 -
all-2076 -
obs--64.03 %
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)
10.0876-0.27620.1462.2632-0.8850.37830.0295-0.0495-0.0462-0.3570.0280.15390.1228-0.0399-0.05750.08270.0104-0.02870.04170.03420.088741.128758.57269.7768
20.1411-0.0932-0.24471.2794-0.23640.56850.0141-0.0076-0.00720.0311-0.0621-0.002-0.03990.04170.0480.0049-0.0048-0.01030.04930.01960.07644.681377.276621.6264
30.64690.0837-0.51921.51080.31550.5723-0.06020.07920.01780.2713-0.02640.02360.1322-0.08860.08660.0681-0.01660.01670.0147-0.02120.143986.783982.0947.7995
40.85830.2180.79351.64220.09690.8082-0.07330.0603-0.0484-0.02970.0290.0895-0.03510.01820.04430.0232-0.02350.05010.0242-0.05360.140186.22969.243928.7417
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 177
2X-RAY DIFFRACTION2B2 - 177
3X-RAY DIFFRACTION3C2 - 177
4X-RAY DIFFRACTION4D2 - 177

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