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- PDB-4m3n: Crystal structure of purine nucleoside phosphorylase from Meiothe... -

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Basic information

Entry
Database: PDB / ID: 4m3n
TitleCrystal structure of purine nucleoside phosphorylase from Meiothermus ruber DSM 1279, NYSGRC Target 029804.
ComponentsPurine nucleoside phosphorylase DeoD-type
KeywordsTRANSFERASE / STRUCTURAL GENOMICS / PROTEIN STRUCTURE INITIATIVE / NYSGRC / PSI-Biology / New York Structural Genomics Research Consortium
Function / homology
Function and homology information


nucleoside catabolic process / uridine phosphorylase / purine-nucleoside phosphorylase activity
Similarity search - Function
Purine nucleoside phosphorylase DeoD-type / Nucleoside phosphorylase, conserved site / Purine and other phosphorylases family 1 signature. / Nucleoside phosphorylase domain / Nucleoside phosphorylase domain / Phosphorylase superfamily / Nucleoside phosphorylase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Uridine phosphorylase
Similarity search - Component
Biological speciesMeiothermus ruber DSM 1279 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.6 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 purine nucleoside phosphorylase from Meiothermus ruber DSM 1279, NYSGRC Target 029804.
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
DepositionAug 6, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 28, 2013Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Purine nucleoside phosphorylase DeoD-type
B: Purine nucleoside phosphorylase DeoD-type
C: Purine nucleoside phosphorylase DeoD-type
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,4486
Polymers85,2343
Non-polymers2143
Water8,161453
1
A: Purine nucleoside phosphorylase DeoD-type
B: Purine nucleoside phosphorylase DeoD-type
C: Purine nucleoside phosphorylase DeoD-type
hetero molecules

A: Purine nucleoside phosphorylase DeoD-type
B: Purine nucleoside phosphorylase DeoD-type
C: Purine nucleoside phosphorylase DeoD-type
hetero molecules


Theoretical massNumber of molelcules
Total (without water)170,89612
Polymers170,4676
Non-polymers4286
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Buried area19330 Å2
ΔGint-141 kcal/mol
Surface area47380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.629, 188.930, 153.002
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11B-303-

HOH

21B-314-

HOH

31B-411-

HOH

41C-654-

HOH

51C-726-

HOH

Detailshexameric

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Components

#1: Protein Purine nucleoside phosphorylase DeoD-type / PNP


Mass: 28411.178 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Meiothermus ruber DSM 1279 (bacteria) / Strain: DSM 1279 / Gene: deoD, Mrub_2947, K649_07785 / Plasmid: BC-PSGX3(BC) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)CODON+RIL
References: UniProt: D3PPS9, purine-nucleoside phosphorylase
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


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


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 453 / 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: 2.4 Å3/Da / Density % sol: 48.76 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1 M Magnesium Chloride, 0.1 M MES:NaOH, pH 6.5, 30% PEG 400, 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 21, 2013
RadiationProtocol: SAD / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 107774 / % possible obs: 99.7 % / Redundancy: 13.2 % / Rmerge(I) obs: 0.107 / Χ2: 1.003 / Net I/σ(I): 8.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.6-1.6311.60.99551241196.1
1.63-1.6611.80.95252560.999198.2
1.66-1.6912.10.73252981.011199.5
1.69-1.7212.50.68253351.007199.8
1.72-1.7612.90.66454011.0071100
1.76-1.8130.58753231.0091100
1.8-1.8513.10.44453651.0081100
1.85-1.913.10.39153941.0291100
1.9-1.9513.20.28153810.9951100
1.95-2.0213.40.23453520.971100
2.02-2.0913.50.19753920.9591100
2.09-2.1713.60.1753780.9651100
2.17-2.2713.60.1653951.0591100
2.27-2.3913.70.15854041.1351100
2.39-2.5413.70.15653981.21100
2.54-2.7413.80.14754271.1711100
2.74-3.0113.80.12154521.0221100
3.01-3.4513.90.07654490.7741100
3.45-4.3413.80.05955350.8771100
4.34-5013.30.0657150.876199.7

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.11data extraction
HKL-2000data reduction
SHELXSphasing
RefinementMethod to determine structure: SAD / Resolution: 1.6→31.26 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.959 / WRfactor Rfree: 0.2306 / WRfactor Rwork: 0.2129 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.8014 / SU B: 3.749 / SU ML: 0.062 / SU R Cruickshank DPI: 0.0193 / SU Rfree: 0.0184 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.019 / ESU R Free: 0.018 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.221 5372 5 %RANDOM
Rwork0.203 ---
obs0.204 107668 99.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 83.79 Å2 / Biso mean: 30.7939 Å2 / Biso min: 13.86 Å2
Baniso -1Baniso -2Baniso -3
1-47.12 Å20 Å20 Å2
2---19.81 Å2-0 Å2
3----27.31 Å2
Refinement stepCycle: LAST / Resolution: 1.6→31.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5361 0 11 453 5825
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0195610
X-RAY DIFFRACTIONr_angle_refined_deg1.3641.9727663
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7645724
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.71523.944251
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.04115861
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.9221536
X-RAY DIFFRACTIONr_chiral_restr0.0860.2873
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0214315
X-RAY DIFFRACTIONr_mcbond_it1.3933.6842818
X-RAY DIFFRACTIONr_mcangle_it2.33849.6363529
X-RAY DIFFRACTIONr_scbond_it2.1444.2792791
LS refinement shellResolution: 1.601→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.361 340 -
Rwork0.355 7173 -
all-7513 -
obs--95.61 %
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)
10.0038-0.02020.01170.21640.02570.38490.0036-0.00290.0111-0.0339-0.0029-0.00860.02370.0139-0.00070.00790.007-0.00260.08230.00010.090528.471325.76218.8688
20.0115-0.01470.01380.3408-0.02550.36920.002-0.00370.02270.0017-0.00030.01790.1668-0.0126-0.00170.07780.0012-0.00730.0424-0.00370.053826.4961-0.849324.3278
30.00920.0295-0.04720.2263-0.02650.41040.0027-0.0013-0.0009-0.02430.01050.0134-0.0507-0.0398-0.01320.01030.00780.00750.09140.00240.102826.563949.935422.9567
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-10 - 9999
2X-RAY DIFFRACTION2B-10 - 9999
3X-RAY DIFFRACTION3C-10 - 9999

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