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- PDB-5ipf: Crystal structure of Hypoxanthine-guanine phosphoribosyltransfera... -

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Basic information

Entry
Database: PDB / ID: 5ipf
TitleCrystal structure of Hypoxanthine-guanine phosphoribosyltransferase from Schistosoma mansoni in complex with IMP
ComponentsHypoxanthine-guanine phosphoribosyltransferase (HGPRT)
KeywordsTRANSFERASE / Hypoxanthine-guanine phosphoribosyltransferase / enzyme
Function / homology
Function and homology information


hypoxanthine phosphoribosyltransferase / guanine phosphoribosyltransferase activity / guanine salvage / hypoxanthine metabolic process / hypoxanthine phosphoribosyltransferase activity / GMP salvage / IMP salvage / purine ribonucleoside salvage / nucleotide binding / magnesium ion binding ...hypoxanthine phosphoribosyltransferase / guanine phosphoribosyltransferase activity / guanine salvage / hypoxanthine metabolic process / hypoxanthine phosphoribosyltransferase activity / GMP salvage / IMP salvage / purine ribonucleoside salvage / nucleotide binding / magnesium ion binding / metal ion 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
INOSINIC ACID / Hypoxanthine phosphoribosyltransferase / Hypoxanthine-guanine phosphoribosyltransferase
Similarity search - Component
Biological speciesSchistosoma mansoni (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.8 Å
AuthorsRomanello, L. / Torini, J.R.S. / Bird, L.E. / Nettleship, J.E. / Owens, R.J. / DeMarco, R. / Pereira, H.M. / Brandao-Neto, J.
Funding support Brazil, 2items
OrganizationGrant numberCountry
Sao Paulo Research Foundation (FAPESP)2012/14223-9 Brazil
Brazilian National Council for Scientific and Technological Development (CNPq)474402/2013-4 Brazil
CitationJournal: Mol. Biochem. Parasitol. / Year: 2019
Title: In vitro and in vivo characterization of the multiple isoforms of Schistosoma mansoni hypoxanthine-guanine phosphoribosyltransferases.
Authors: Romanello, L. / Zeraik, A.E. / de Freitas Fernandes, A. / Torini, J.R. / Bird, L.E. / Nettleship, J.E. / Rada, H. / Reddivari, Y. / Owens, R.J. / Serrao, V.H.B. / DeMarco, R. / Brandao-Neto, J. / Pereira, H.D.
History
DepositionMar 9, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 15, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2019Group: Data collection / Database references / Category: citation / citation_author / diffrn_source
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _diffrn_source.pdbx_synchrotron_site
Revision 2.0Apr 17, 2019Group: Author supporting evidence / Data collection / Polymer sequence
Category: entity_poly / pdbx_audit_support
Item: _entity_poly.pdbx_target_identifier / _pdbx_audit_support.funding_organization
Revision 2.1Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.2Sep 27, 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

Downloads & links

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Assembly

Deposited unit
A: Hypoxanthine-guanine phosphoribosyltransferase (HGPRT)
B: Hypoxanthine-guanine phosphoribosyltransferase (HGPRT)
C: Hypoxanthine-guanine phosphoribosyltransferase (HGPRT)
D: Hypoxanthine-guanine phosphoribosyltransferase (HGPRT)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,3358
Polymers112,9424
Non-polymers1,3934
Water2,216123
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11270 Å2
ΔGint-82 kcal/mol
Surface area29870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.953, 117.957, 139.366
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-guanine phosphoribosyltransferase (HGPRT) / HGPRTase


Mass: 28235.527 Da / Num. of mol.: 4 / Fragment: UNP residues 19-249
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schistosoma mansoni (invertebrata) / Gene: HGPRT, Smp_103560 / Plasmid: pOPINF / Production host: Escherichia coli (E. coli) / Strain (production host): BH
References: UniProt: G4LWQ2, UniProt: P09383*PLUS, hypoxanthine phosphoribosyltransferase
#2: Chemical
ChemComp-IMP / INOSINIC ACID


Mass: 348.206 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H13N4O8P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 123 / 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: 2.19 Å3/Da / Density % sol: 43.95 % / Description: small plates
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 12.5% PEG 1000, 12.5% PEG 3350, 12.5% MPD, 100mM MES/imidazole pH 6.5 30mM magnesium chloride, 30mM calcium chloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Apr 26, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 2.8→60 Å / Num. obs: 24452 / % possible obs: 98 % / Redundancy: 3.8 % / Biso Wilson estimate: 61.56 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.111 / Net I/σ(I): 8.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
2.8-2.953.80.9321.4199.2
8.85-603.70.03229.9196.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
xia2data scaling
PHENIX1.10.1_2155refinement
PHASERphasing
PDB_EXTRACT3.2data extraction
xia2data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1HMP

1hmp


Resolution: 2.8→59.996 Å / SU ML: 0.5 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.56
RfactorNum. reflection% reflectionSelection details
Rfree0.29 1167 4.78 %Random selection
Rwork0.2317 ---
obs0.2344 24416 97.39 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 155.19 Å2 / Biso mean: 69.7105 Å2 / Biso min: 24.06 Å2
Refinement stepCycle: final / Resolution: 2.8→59.996 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5604 0 92 123 5819
Biso mean--74.83 68.05 -
Num. residues----768
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0025803
X-RAY DIFFRACTIONf_angle_d0.5447911
X-RAY DIFFRACTIONf_chiral_restr0.046944
X-RAY DIFFRACTIONf_plane_restr0.0051001
X-RAY DIFFRACTIONf_dihedral_angle_d10.833422
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.8001-2.92750.39561640.33072857302199
2.9275-3.08180.40231460.30392848299497
3.0818-3.27490.34941590.27982894305399
3.2749-3.52770.3061580.25272902306098
3.5277-3.88270.28911380.222900303898
3.8827-4.44440.21421350.19282899303497
4.4444-5.59880.26941300.19942934306496
5.5988-60.00990.28261370.23253015315295
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)
14.1002-0.8712-1.10221.8304-0.12794.0747-0.12350.0128-0.09960.0447-0.0262-0.09660.31750.15440.13160.4092-0.06770.00260.2274-0.0710.4489-6.9256-0.5679-4.6828
22.3786-0.26990.5040.833-1.42062.41210.31310.54610.2401-0.0754-0.0651-0.2610.76090.8518-0.17180.84910.36290.09980.5982-0.05831.268711.6404-15.4437-3.135
33.10210.6375-1.35913.10660.36125.10690.2486-0.8457-0.59750.36480.0044-0.16530.69191.0645-0.15860.51970.0255-0.07110.5410.07430.4104-2.423-5.21036.4351
43.8776-0.90331.33674.5959-0.53821.8964-0.0995-0.9459-1.37130.65050.23091.03271.7153-0.6393-0.13640.8652-0.14430.19380.46980.13550.8768-20.3267-11.76513.9832
53.8733-0.29670.45741.4997-0.3813.1657-0.23330.45230.12690.03970.2021-0.0175-0.0426-0.37080.01270.3302-0.1152-0.00540.4151-0.01860.4956-26.61119.5519-13.1343
61.51621.8917-0.41262.61780.31442.9997-0.12360.06941.43670.0208-0.02930.5525-0.8053-0.51160.00590.52550.0329-0.0280.17760.01820.9593-28.319419.7077-9.0699
70.12360.1473-0.31420.1572-0.34680.7643-0.2880.3475-0.3879-0.45230.1212-0.25780.2640.33830.04921.1638-0.44480.43491.4776-0.67140.7583-6.3916-11.128-36.8021
81.4757-1.21490.76821.8384-0.27940.5388-0.18351.22120.0069-0.2674-0.1628-0.8544-0.01090.52630.26650.4346-0.25850.10011.1753-0.14490.6853.2117-1.8414-28.287
91.5729-0.11150.91070.0113-0.06160.5275-0.20710.5818-0.14480.02230.22190.59110.8688-0.4149-0.13140.8345-0.48190.25030.9576-0.37070.9277-18.8984-14.666-21.5794
105.107-0.86610.75020.1552-0.05252.42290.1432-0.2548-0.67760.06710.0595-0.01060.5024-0.2504-0.20030.7073-0.12150.09220.3544-0.17460.8387-15.3407-17.4698-11.2651
112.5431-1.2435-1.10973.71711.20133.2331-0.0937-0.0928-0.25240.37760.05910.22560.41920.04820.08070.9518-0.06390.28710.3182-0.26641.0855-7.7329-23.6284-19.0475
121.4060.17950.18510.0235-0.01091.0284-0.14670.0441-0.63290.8131-0.06490.71590.677700.22971.46340.29080.01510.5246-0.53091.3874-4.2136-32.2004-15.8432
130.9537-0.4915-1.1991.66320.85213.1646-0.29520.2241-0.7409-0.11870.0808-0.4130.90590.791-0.3180.8050.00340.21041.0867-0.68380.977-0.8099-16.2635-24.8415
147.14741.76061.55312.16270.81451.3016-0.4061.62110.0068-0.27610.4327-0.4795-0.05421.0379-0.04290.7457-0.414-0.00631.4849-0.28660.6239-9.8285-1.8995-40.6013
152.066-1.85750.16622.0859-0.61062.1779-0.02311.186-0.38560.16320.109-0.02770.0563-0.01630.04350.5396-0.30460.07961.0725-0.06190.4793-14.34212.3409-30.5049
161.32020.1077-0.39581.61080.18670.6795-0.07330.31071.02940.01150.20660.2389-0.36220.24940.04090.5032-0.4815-0.10210.77640.19220.612-12.734816.2159-24.4714
170.57320.3384-0.37620.7326-0.13150.26360.08730.14260.25390.00050.1053-0.0826-0.0516-0.0453-0.04510.3626-0.4698-0.08810.9670.3460.815-11.987521.772-21.711
181.21360.5878-0.39262.5966-0.9062.25450.2066-0.17880.1575-0.094-0.3753-0.6674-0.33280.21310.17450.5776-0.4335-0.0261.12040.37030.5208-15.067819.4034-35.4869
190.067-0.0683-0.28090.55840.14851.20980.0857-0.08580.07470.1646-0.077-0.0833-0.93380.1175-0.09970.6327-0.2340.01011.33550.55810.5932-17.664924.3756-41.3717
202.4210.2936-0.430.5109-0.38881.2685-0.0570.65750.84970.0452-0.00220.1309-0.61720.3412-0.30150.7267-0.5216-0.08611.1390.33210.6401-12.26119.7348-36.9768
211.14090.1276-1.42211.4386-0.02482.9863-0.27411.1661-0.068-0.65110.40730.15320.2923-1.0907-0.15810.8107-0.62660.02091.67490.32810.5871-8.889312.5794-43.458
220.31850.65870.03221.40160.09490.0718-0.11530.2760.0695-0.19760.01850.6160.039-0.3890.19550.5189-0.411-0.05651.4118-0.070.5761-21.22614.388-39.6708
230.28930.53680.10711.010.20040.0408-0.19520.609-0.0431-0.20180.1230.51230.0405-0.05390.0760.5455-0.49280.0781.3425-0.16850.6436-24.42370.0674-34.2173
241.34640.3389-0.70371.48740.76210.9960.03450.2453-0.2211-0.28510.05890.64450.1123-0.59850.07890.6402-0.2183-0.20481.989-0.3861.1431-33.8362-1.5574-43.3768
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 8 through 106 )A8 - 106
2X-RAY DIFFRACTION2chain 'A' and (resid 107 through 134 )A107 - 134
3X-RAY DIFFRACTION3chain 'A' and (resid 135 through 204 )A135 - 204
4X-RAY DIFFRACTION4chain 'A' and (resid 205 through 224 )A205 - 224
5X-RAY DIFFRACTION5chain 'B' and (resid 8 through 146 )B8 - 146
6X-RAY DIFFRACTION6chain 'B' and (resid 147 through 223 )B147 - 223
7X-RAY DIFFRACTION7chain 'C' and (resid 9 through 21 )C9 - 21
8X-RAY DIFFRACTION8chain 'C' and (resid 22 through 41 )C22 - 41
9X-RAY DIFFRACTION9chain 'C' and (resid 42 through 62 )C42 - 62
10X-RAY DIFFRACTION10chain 'C' and (resid 63 through 134 )C63 - 134
11X-RAY DIFFRACTION11chain 'C' and (resid 135 through 146 )C135 - 146
12X-RAY DIFFRACTION12chain 'C' and (resid 147 through 158 )C147 - 158
13X-RAY DIFFRACTION13chain 'C' and (resid 159 through 224 )C159 - 224
14X-RAY DIFFRACTION14chain 'D' and (resid 8 through 21 )D8 - 21
15X-RAY DIFFRACTION15chain 'D' and (resid 22 through 62 )D22 - 62
16X-RAY DIFFRACTION16chain 'D' and (resid 63 through 94 )D63 - 94
17X-RAY DIFFRACTION17chain 'D' and (resid 95 through 106 )D95 - 106
18X-RAY DIFFRACTION18chain 'D' and (resid 107 through 146 )D107 - 146
19X-RAY DIFFRACTION19chain 'D' and (resid 147 through 156 )D147 - 156
20X-RAY DIFFRACTION20chain 'D' and (resid 157 through 172 )D157 - 172
21X-RAY DIFFRACTION21chain 'D' and (resid 173 through 186 )D173 - 186
22X-RAY DIFFRACTION22chain 'D' and (resid 187 through 204 )D187 - 204
23X-RAY DIFFRACTION23chain 'D' and (resid 205 through 215 )D205 - 215
24X-RAY DIFFRACTION24chain 'D' and (resid 216 through 224 )D216 - 224

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