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- PDB-4lna: CRYSTAL STRUCTURE OF purine nucleoside phosphorylase I from Spiro... -

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Basic information

Entry
Database: PDB / ID: 4lna
TitleCRYSTAL STRUCTURE OF purine nucleoside phosphorylase I from Spirosoma linguale DSM 74, NYSGRC Target 029362
ComponentsPurine nucleoside phosphorylase
KeywordsTRANSFERASE / STRUCTURAL GENOMICS / PROTEIN STRUCTURE INITIATIVE / NYSGRC / PSI-Biology / New York Structural Genomics Research Consortium
Function / homology
Function and homology information


nucleoside metabolic process / purine-nucleoside phosphorylase / purine-nucleoside phosphorylase activity
Similarity search - Function
Purine nucleoside phosphorylase I, inosine/guanosine-specific / Purine phosphorylase, family 2, conserved site / Purine and other phosphorylases family 2 signature. / Purine nucleoside phosphorylase / Nucleoside phosphorylase domain / Nucleoside phosphorylase domain / Phosphorylase superfamily / Nucleoside phosphorylase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENINE / PHOSPHATE ION / Purine nucleoside phosphorylase
Similarity search - Component
Biological speciesSpirosoma linguale (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 Å
AuthorsMalashkevich, V.N. / Bonanno, J.B. / Bhosle, R. / Toro, R. / Hillerich, B. / Gizzi, A. / Garforth, S. / Kar, A. / Chan, M.K. / Lafluer, J. ...Malashkevich, V.N. / Bonanno, J.B. / 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. / Almo, S.C. / New York Structural Genomics Research Consortium (NYSGRC)
CitationJournal: To be Published
Title: Crystal structure of purine nucleoside phosphorylase I from Spirosoma linguale DSM 74, NYSGRC Target 029362
Authors: Malashkevich, V.N. / Bonanno, J.B. / 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. ...Authors: Malashkevich, V.N. / Bonanno, J.B. / 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. / Almo, S.C.
History
DepositionJul 11, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 24, 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

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Assembly

Deposited unit
A: Purine nucleoside phosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,5256
Polymers33,0461
Non-polymers4795
Water2,450136
1
A: Purine nucleoside phosphorylase
hetero molecules

A: Purine nucleoside phosphorylase
hetero molecules

A: Purine nucleoside phosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,57418
Polymers99,1383
Non-polymers1,43615
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area10820 Å2
ΔGint-139 kcal/mol
Surface area29700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)125.561, 125.561, 125.561
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number212
Space group name H-MP4332
Components on special symmetry positions
IDModelComponents
11A-504-

CL

21A-671-

HOH

31A-699-

HOH

41A-710-

HOH

51A-721-

HOH

Detailstrimeric

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Purine nucleoside phosphorylase / Inosine-guanosine phosphorylase


Mass: 33046.051 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Spirosoma linguale (bacteria) / Strain: DSM 74 / Gene: 8727701, Slin_3943 / Plasmid: BC-PSGX3(BC) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)CODON+RIL
References: UniProt: D2QIK7, purine-nucleoside phosphorylase

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Non-polymers , 5 types, 141 molecules

#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-ADE / ADENINE


Mass: 135.127 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H5N5
#4: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 136 / 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: 2.5 Å3/Da / Density % sol: 50.72 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2 M sodium phosphate dibasic, 20% PEG3350, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 12, 2013
RadiationProtocol: SAD / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 20392 / % possible obs: 100 % / Redundancy: 41.9 % / Rmerge(I) obs: 0.073 / Χ2: 1.163 / Net I/σ(I): 11.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.1-2.1442.80.5489991.0811100
2.14-2.1843.10.59861.0821100
2.18-2.22430.41310061.0971100
2.22-2.2642.90.3939861.0921100
2.26-2.3142.90.2999971.1381100
2.31-2.3742.90.28510041.1341100
2.37-2.4242.80.2449811.1381100
2.42-2.4942.90.23110041.1421100
2.49-2.5642.60.1910171.1611100
2.56-2.65430.1689841.1671100
2.65-2.7442.60.13510081.2141100
2.74-2.8542.50.10910161.2711100
2.85-2.9842.30.09610141.3341100
2.98-3.1442.20.08710061.3961100
3.14-3.3341.90.07610311.471100
3.33-3.5941.20.06910281.3851100
3.59-3.9540.90.05910401.0841100
3.95-4.5239.80.04510430.9811100
4.52-5.739.60.04210730.9331100
5.7-5036.90.04111690.948199.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
CBASSdata collection
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1M73

1m73


Resolution: 2.1→20 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.95 / WRfactor Rfree: 0.2033 / WRfactor Rwork: 0.1684 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.8531 / SU ML: 0.098 / SU R Cruickshank DPI: 0.1716 / SU Rfree: 0.1572 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.172 / ESU R Free: 0.158 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.2157 1040 5.1 %RANDOM
Rwork0.1717 ---
obs0.1738 20288 99.67 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 110.17 Å2 / Biso mean: 42.9019 Å2 / Biso min: 22.8 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2071 0 29 136 2236
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0192152
X-RAY DIFFRACTIONr_angle_refined_deg1.4692.0232933
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5215273
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.59624.44481
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.33615335
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.581511
X-RAY DIFFRACTIONr_chiral_restr0.0770.2349
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211577
X-RAY DIFFRACTIONr_mcbond_it1.9945.4831080
X-RAY DIFFRACTIONr_mcangle_it3.24673.6931348
X-RAY DIFFRACTIONr_scbond_it3.2516.0721071
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.219 88 -
Rwork0.184 1377 -
all-1465 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: -15.5475 Å / Origin y: 9.4704 Å / Origin z: 11.6413 Å
111213212223313233
T0.0115 Å20.0116 Å20.0126 Å2-0.0642 Å20.0107 Å2--0.0269 Å2
L1.2935 °2-0.0614 °20.367 °2-0.8334 °2-0.2599 °2--0.9311 °2
S0.0196 Å °-0.1495 Å °0.0031 Å °0.0481 Å °0.0725 Å °0.1188 Å °-0.0716 Å °-0.2025 Å °-0.0921 Å °

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