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- PDB-4m1e: Crystal structure of purine nucleoside phosphorylase I from Planc... -

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Entry
Database: PDB / ID: 4m1e
TitleCrystal structure of purine nucleoside phosphorylase I from Planctomyces limnophilus DSM 3776, NYSGRC Target 029364.
ComponentsPurine nucleoside phosphorylase
KeywordsTRANSFERASE / STRUCTURAL GENOMICS / PROTEIN STRUCTURE INITIATIVE / NYSGRC / purine nucleoside phosphorylase / 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
PYRIDINE-2-CARBOXYLIC ACID / ADENINE / Purine nucleoside phosphorylase
Similarity search - Component
Biological speciesPlanctomyces limnophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 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 Planctomyces limnophilus DSM 3776, NYSGRC Target 029364.
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
DepositionAug 2, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 21, 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: Purine nucleoside phosphorylase
B: Purine nucleoside phosphorylase
C: Purine nucleoside phosphorylase
E: Purine nucleoside phosphorylase
D: Purine nucleoside phosphorylase
F: Purine nucleoside phosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)200,07924
Polymers197,9536
Non-polymers2,12618
Water11,926662
1
A: Purine nucleoside phosphorylase
B: Purine nucleoside phosphorylase
C: Purine nucleoside phosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,04012
Polymers98,9773
Non-polymers1,0639
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8550 Å2
ΔGint-69 kcal/mol
Surface area30400 Å2
MethodPISA
2
E: Purine nucleoside phosphorylase
D: Purine nucleoside phosphorylase
F: Purine nucleoside phosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,04012
Polymers98,9773
Non-polymers1,0639
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8640 Å2
ΔGint-70 kcal/mol
Surface area29980 Å2
MethodPISA
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area23450 Å2
ΔGint-116 kcal/mol
Surface area54120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.950, 81.060, 91.616
Angle α, β, γ (deg.)103.420, 105.360, 112.730
Int Tables number1
Space group name H-MP1
Detailstrimeric

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Components

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


Mass: 32992.242 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Planctomyces limnophilus (bacteria) / Strain: DSM 3776 / Gene: Plim_2216 / Plasmid: BC-PSGX3(BC) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)CODON+RIL
References: UniProt: D5SMY7, purine-nucleoside phosphorylase
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-ADE / ADENINE / Adenine


Mass: 135.127 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C5H5N5
#4: Chemical
ChemComp-6PC / PYRIDINE-2-CARBOXYLIC ACID / PICOLINIC ACID / Picolinic acid


Mass: 123.109 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C6H5NO2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 662 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsLIGAND PYRIDINE-2-CARBOXYLIC ACID IS EXOGENOUS AND WAS NOT ADDED TO THE CRYSTALLIZATION BUFFER. IT ...LIGAND PYRIDINE-2-CARBOXYLIC ACID IS EXOGENOUS AND WAS NOT ADDED TO THE CRYSTALLIZATION BUFFER. IT IS ONLY SUGGESTED BASED ON THE ELECTRON DENSITY AND INTERACTIONS WITH SURROUNDING PROTEIN GROUPS. THERE ARE NO OTHER PROOFS IN SUPPORT OF ITS CHEMICAL NATURE.

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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: 50.85 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1 M MES:NaOH, pH 6.5, 1.6 Magnesium sulfate, 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: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 148934 / % possible obs: 97 % / Redundancy: 2.1 % / Rmerge(I) obs: 0.113 / Χ2: 1.149 / Net I/σ(I): 9.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.9-1.9320.71872531.297194.3
1.93-1.972.10.55772861.299194.7
1.97-2.012.10.45672151.324194.6
2.01-2.052.10.37773391.284195.3
2.05-2.092.10.31573421.265195.3
2.09-2.142.10.27873681.24195.9
2.14-2.192.10.23274221.222196.5
2.19-2.252.10.21273691.205196.7
2.25-2.322.10.18874471.192196.9
2.32-2.392.20.16675151.142197.3
2.39-2.482.20.16574061.157197.6
2.48-2.582.20.15175071.151198
2.58-2.72.20.13875541.179198
2.7-2.842.20.11675291.084198.2
2.84-3.022.20.10975551.084198.2
3.02-3.252.20.09875251.011198.4
3.25-3.582.20.0975560.979198.6
3.58-4.092.20.08975920.926198.8
4.09-5.162.20.08575730.923198.9
5.16-502.20.0975811.13198.7

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation5.54 Å31.42 Å
Translation5.54 Å31.42 Å

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHASER2.5.1phasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3LA8

3la8


Resolution: 1.9→20 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.912 / WRfactor Rfree: 0.2836 / WRfactor Rwork: 0.2337 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8176 / SU B: 8.152 / SU ML: 0.12 / SU R Cruickshank DPI: 0.163 / SU Rfree: 0.155 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.163 / ESU R Free: 0.155 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.2575 7374 5 %RANDOM
Rwork0.2132 ---
obs0.2154 146913 97.07 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 145.21 Å2 / Biso mean: 34.4156 Å2 / Biso min: 13 Å2
Baniso -1Baniso -2Baniso -3
1--0.07 Å20.66 Å20.46 Å2
2---0.26 Å20.78 Å2
3----0.36 Å2
Refinement stepCycle: LAST / Resolution: 1.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12435 0 144 662 13241
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01912850
X-RAY DIFFRACTIONr_angle_refined_deg1.4242.0217460
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.75151636
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.24523.886507
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.844151992
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.4271592
X-RAY DIFFRACTIONr_chiral_restr0.0930.22011
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0219642
X-RAY DIFFRACTIONr_mcbond_it1.6244.1186544
X-RAY DIFFRACTIONr_mcangle_it2.64455.4718171
X-RAY DIFFRACTIONr_scbond_it2.724.6546306
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.34 522 -
Rwork0.301 9962 -
all-10484 -
obs--94.38 %
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)
10.87030.15680.11640.1881-0.01320.7632-0.04160.10420.1487-0.0137-0.024-0.0606-0.07920.21610.06560.0129-0.0342-0.00470.11610.0420.07527.8606-27.223511.4729
20.37710.05250.02640.68380.1850.7785-0.00350.1566-0.0615-0.15430.0258-0.00550.07010.1067-0.02230.11740.0163-0.00810.0813-0.03110.0131-11.7678-53.1698-6.1077
30.8783-0.4173-0.15280.7615-0.23440.49520.06670.13020.1466-0.1185-0.04490.056-0.0182-0.0011-0.02180.04870.0009-0.02070.02290.03250.0694-27.8639-21.3193.3739
40.1776-0.09140.02950.8874-0.01520.596-0.0142-0.0412-0.12840.0730.01280.14180.1441-0.0130.00140.1170.0140.01960.01190.02840.1006-20.8875-69.933231.1608
51.0091-0.3118-0.07350.3707-0.08450.5331-0.055-0.1963-0.04490.04440.07580.13350.0137-0.0706-0.02080.00790.00710.01730.05420.00910.0581-39.7367-39.258639.269
60.66870.14710.19610.4104-0.02350.75460-0.1366-0.00420.12160.0014-0.07420.05260.0878-0.00150.06050.0102-0.02580.0978-0.01910.0202-4.0404-41.971348.5871
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 274
2X-RAY DIFFRACTION1A400 - 402
3X-RAY DIFFRACTION2B2 - 274
4X-RAY DIFFRACTION2B400 - 402
5X-RAY DIFFRACTION3C2 - 274
6X-RAY DIFFRACTION3C400
7X-RAY DIFFRACTION3D301
8X-RAY DIFFRACTION4E1 - 273
9X-RAY DIFFRACTION4E400 - 402
10X-RAY DIFFRACTION5D2 - 274
11X-RAY DIFFRACTION5C402
12X-RAY DIFFRACTION5D302
13X-RAY DIFFRACTION6F3 - 274
14X-RAY DIFFRACTION6F400 - 402

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