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- PDB-4lyy: Crystal structure of hypoxanthine phosphoribosyltransferase from ... -

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Basic information

Entry
Database: PDB / ID: 4lyy
TitleCrystal structure of hypoxanthine phosphoribosyltransferase from Shewanella pealeana ATCC 700345, NYSGRC Target 029677.
ComponentsHypoxanthine phosphoribosyltransferaseHypoxanthine-guanine phosphoribosyltransferase
KeywordsTRANSFERASE / STRUCTURAL GENOMICS / PROTEIN STRUCTURE INITIATIVE / NYSGRC / hypoxanthine phosphoribosyltransferase / PSI-Biology / New York Structural Genomics Research Consortium
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
PHOSPHATE ION / Hypoxanthine phosphoribosyltransferase
Similarity search - Component
Biological speciesShewanella pealeana (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.86 Å
AuthorsMalashkevich, V.N. / Bhosle, R. / Toro, R. / Hillerich, B. / Gizzi, A. / Garforth, S. / Kar, A. / Chan, M.K. / Lafluer, J. / Patel, H. ...Malashkevich, V.N. / Bhosle, R. / Toro, R. / Hillerich, B. / Gizzi, A. / Garforth, S. / Kar, A. / Chan, M.K. / Lafluer, J. / Patel, H. / Matikainen, B. / Chamala, S. / Lim, S. / Celikgil, A. / Villegas, G. / Evans, B. / Love, J. / Fiser, A. / Khafizov, K. / Seidel, R. / Bonanno, J.B. / Almo, S.C. / New York Structural Genomics Research Consortium (NYSGRC)
CitationJournal: To be Published
Title: Crystal structure of hypoxanthine phosphoribosyltransferase from Shewanella pealeana ATCC 700345, NYSGRC Target 029677.
Authors: Malashkevich, V.N. / Bhosle, R. / Toro, R. / Hillerich, B. / Gizzi, A. / Garforth, S. / Kar, A. / Chan, M.K. / Lafluer, J. / Patel, H. / Matikainen, B. / Chamala, S. / Lim, S. / Celikgil, A. ...Authors: Malashkevich, V.N. / Bhosle, R. / Toro, R. / Hillerich, B. / Gizzi, A. / Garforth, S. / Kar, A. / Chan, M.K. / Lafluer, J. / Patel, H. / Matikainen, B. / Chamala, S. / Lim, S. / Celikgil, A. / Villegas, G. / Evans, B. / Love, J. / Fiser, A. / Khafizov, K. / Seidel, R. / Bonanno, J.B. / Almo, S.C.
History
DepositionJul 31, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 14, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 20, 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_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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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)92,3306
Polymers92,1404
Non-polymers1902
Water5,711317
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8390 Å2
ΔGint-45 kcal/mol
Surface area27670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.514, 101.173, 73.844
Angle α, β, γ (deg.)90.000, 107.380, 90.000
Int Tables number4
Space group name H-MP1211
Detailstetrameric

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Components

#1: Protein
Hypoxanthine phosphoribosyltransferase / Hypoxanthine-guanine phosphoribosyltransferase


Mass: 23035.027 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shewanella pealeana (bacteria) / Strain: ATCC 700345 / Gene: 5661087, Spea_0688 / Plasmid: BC-PSGX3(BC) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)CODON+RIL
References: UniProt: A8H0C8, hypoxanthine phosphoribosyltransferase
#2: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 317 / 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: 1.99 Å3/Da / Density % sol: 38.29 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.2 M sodium chloride, 0.1 M Bis-Tris:HCl, pH 5.5, 25% PEG 3350 , VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.9791 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Jul 18, 2013
RadiationProtocol: SAD / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.86→101.173 Å / Num. all: 59642 / Num. obs: 59642 / % possible obs: 98.7 % / Redundancy: 7.5 % / Rsym value: 0.094 / Net I/σ(I): 13.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.86-1.967.70.5251.36652686650.52598.5
1.96-2.087.70.3282.16329682330.32898.6
2.08-2.227.70.2073.45931577190.20799
2.22-2.47.70.1464.85536672150.14699.1
2.4-2.637.60.1155.95096666750.11599.3
2.63-2.947.60.0976.84582160540.09799.4
2.94-3.47.50.07583975453320.07599.6
3.4-4.167.30.0678.83302445380.06799.6
4.16-5.8870.062102462134960.06298.9
5.88-101.1736.50.064101121717150.06487.1

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation4.53 Å70.47 Å
Translation4.53 Å70.47 Å

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Processing

Software
NameVersionClassificationNB
SCALA3.3.20data scaling
PHASER2.5.1phasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1J7J

1j7j


Resolution: 1.86→70.47 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.939 / WRfactor Rfree: 0.224 / WRfactor Rwork: 0.1873 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.887 / SU B: 4.713 / SU ML: 0.072 / SU R Cruickshank DPI: 0.0295 / SU Rfree: 0.0277 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.03 / ESU R Free: 0.028 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES: WITH TLS ADDED. HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.2165 3017 5.1 %RANDOM
Rwork0.1789 ---
obs0.1808 59581 98.56 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 93.63 Å2 / Biso mean: 31.1711 Å2 / Biso min: 14.94 Å2
Baniso -1Baniso -2Baniso -3
1-11.1 Å20 Å2-16.04 Å2
2---5.98 Å2-0 Å2
3----5.12 Å2
Refinement stepCycle: LAST / Resolution: 1.86→70.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5302 0 10 317 5629
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0195445
X-RAY DIFFRACTIONr_angle_refined_deg1.4582.0067372
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7975678
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.28424.538249
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.13115979
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.3361540
X-RAY DIFFRACTIONr_chiral_restr0.0890.2878
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213981
X-RAY DIFFRACTIONr_mcbond_it1.713.6812677
X-RAY DIFFRACTIONr_mcangle_it2.84949.3983339
X-RAY DIFFRACTIONr_scbond_it3.2044.5892768
LS refinement shellResolution: 1.861→1.909 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.269 218 -
Rwork0.196 4142 -
all-4360 -
obs--97.89 %
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)
10.30470.18960.06390.6147-0.01930.7531-0.05-0.0134-0.0994-0.0001-0.0085-0.05840.06890.00420.05850.0297-0.01190.02790.02240.00170.0418-2.57198.9502107.1102
20.4856-0.07770.21290.750.01251.07310.00460.0060.0575-0.03040.01190.0738-0.0528-0.0631-0.01650.0143-0.01270.00080.02930.00380.0185-12.34628.5599101.651
30.34320.19060.20630.83550.49081.42420.0813-0.0187-0.03940.1136-0.0302-0.02620.1497-0.0753-0.05110.0297-0.0067-0.00970.03560.01750.01231.223423.8008141.5871
40.6816-0.01840.3640.8502-0.3061.0550.00780.0450.0637-0.0338-0.0357-0.0711-0.10530.1580.02780.0223-0.01560.01440.03880.00480.03827.906142.281129.3885
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-3 - 175
2X-RAY DIFFRACTION2B3 - 174
3X-RAY DIFFRACTION3C2 - 173
4X-RAY DIFFRACTION4D2 - 174

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