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

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Basic information

Entry
Database: PDB / ID: 4mar
TitleCrystal structure of purine nucleoside phosphorylase from Meiothermus ruber DSM 1279 complexed with sulfate.
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


uridine phosphorylase / purine nucleoside catabolic process / purine-nucleoside phosphorylase activity / cytosol
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
Uridine phosphorylase
Similarity search - Component
Biological speciesMeiothermus ruber (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.16 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 complexed with sulfate.
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 16, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 9, 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
Revision 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)86,31515
Polymers85,2343
Non-polymers1,08112
Water5,098283
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)172,62930
Polymers170,4676
Non-polymers2,16224
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Buried area22740 Å2
ΔGint-423 kcal/mol
Surface area47450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.403, 189.103, 152.235
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11B-404-

HOH

21B-411-

HOH

31B-442-

HOH

41C-408-

HOH

51C-506-

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 (bacteria) / Strain: DSM 1279 / Gene: deoD, K649_07785, Mrub_2947 / 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-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 283 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.42 Å3/Da / Density % sol: 49.25 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4
Details: 0.1M citrte, pH 4.0, 0.8M ammonium 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: Aug 12, 2013
RadiationProtocol: SAD / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.16→50 Å / Num. obs: 44423 / % possible obs: 99.1 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.143 / Χ2: 1.006 / Net I/σ(I): 8.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.16-2.25.10.42920890.989193.2
2.2-2.245.60.43621030.989195.3
2.24-2.286.10.45321210.982197.5
2.28-2.336.40.37421710.965198
2.33-2.386.60.39622120.984199.8
2.38-2.436.70.32921910.958199.9
2.43-2.496.90.33622530.9591100
2.49-2.566.90.30121880.9711100
2.56-2.646.90.2622270.9631100
2.64-2.7270.23422280.9721100
2.72-2.8270.20822240.9551100
2.82-2.937.10.18522180.9691100
2.93-3.067.10.15222490.9311100
3.06-3.237.10.13122260.915199.9
3.23-3.437.20.10922400.936199.9
3.43-3.697.20.10522440.962199.9
3.69-4.0670.11222671.204199.9
4.06-4.656.80.11422611.411199.8
4.65-5.866.90.10223151.169199.8
5.86-506.60.07523960.924199.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
HKL-3000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4M3N

4m3n


Resolution: 2.16→32.56 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.94 / WRfactor Rfree: 0.2208 / WRfactor Rwork: 0.1858 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.862 / SU B: 7.942 / SU ML: 0.105 / SU R Cruickshank DPI: 0.0484 / SU Rfree: 0.039 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.048 / ESU R Free: 0.039 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.2256 2239 5.1 %RANDOM
Rwork0.1884 ---
obs0.1903 44335 99.04 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 98.35 Å2 / Biso mean: 33.8488 Å2 / Biso min: 14.9 Å2
Baniso -1Baniso -2Baniso -3
1-44.46 Å20 Å20 Å2
2---15.22 Å2-0 Å2
3----29.24 Å2
Refinement stepCycle: LAST / Resolution: 2.16→32.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5361 0 56 283 5700
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0195588
X-RAY DIFFRACTIONr_angle_refined_deg1.1941.987629
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8625711
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.45724.008247
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.61115852
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.2011535
X-RAY DIFFRACTIONr_chiral_restr0.0810.2877
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0214252
X-RAY DIFFRACTIONr_mcbond_it1.4354.1422796
X-RAY DIFFRACTIONr_mcangle_it2.49655.8373496
X-RAY DIFFRACTIONr_scbond_it2.1234.7612791
LS refinement shellResolution: 2.162→2.218 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.26 192 -
Rwork0.239 2786 -
all-2978 -
obs--92.03 %
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)
10.1169-0.07990.09360.6558-0.08420.89370.02550.02240.0245-0.1316-0.0303-0.02310.03840.04480.00480.03240.018-0.00330.05280.00130.033529.005725.92248.7739
20.3623-0.0349-0.04111.1524-0.08340.8130.003-0.00320.0139-0.0301-0.00130.05320.318-0.0221-0.00170.13420.0003-0.00670.0101-0.00730.008327.0897-0.627424.1986
30.16610.075-0.1940.6071-0.11820.86910.04280.0270.0347-0.0813-0.00170.0331-0.1119-0.1069-0.04110.03680.01910.01410.06170.00780.067227.250750.034122.7577
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 504
2X-RAY DIFFRACTION2B2 - 504
3X-RAY DIFFRACTION3C2 - 504

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