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- PDB-4lkr: Crystal structure of deoD-3 gene product from Shewanella oneidens... -

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Basic information

Entry
Database: PDB / ID: 4lkr
TitleCrystal structure of deoD-3 gene product from Shewanella oneidensis MR-1, NYSGRC target 029437
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


purine nucleoside metabolic process / purine-nucleoside phosphorylase / purine-nucleoside phosphorylase activity
Similarity search - Function
Purine nucleoside phosphorylase DeoD-type / Nucleoside phosphorylase domain / Nucleoside phosphorylase domain / Phosphorylase superfamily / Nucleoside phosphorylase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Purine nucleoside phosphorylase DeoD-type
Similarity search - Component
Biological speciesShewanella oneidensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.4 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 deoD-3 gene product from Shewanella oneidensis MR-1, NYSGRC target 029437
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 8, 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
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
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 DeoD-type


Theoretical massNumber of molelcules
Total (without water)28,6741
Polymers28,6741
Non-polymers00
Water2,090116
1
A: Purine nucleoside phosphorylase DeoD-type
x 6


Theoretical massNumber of molelcules
Total (without water)172,0476
Polymers172,0476
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
crystal symmetry operation10_664-y+1,-x+1,-z-1/21
crystal symmetry operation11_554-x+y,y,-z-1/21
crystal symmetry operation12_564x,x-y+1,-z-1/21
Buried area18160 Å2
ΔGint-126 kcal/mol
Surface area47950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)153.641, 153.641, 52.704
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number182
Space group name H-MP6322
Components on special symmetry positions
IDModelComponents
11A-312-

HOH

Detailshexameric

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Components

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


Mass: 28674.438 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shewanella oneidensis (bacteria) / Strain: MR-1 / Gene: deoD-3, deoD3, SO_2719 / Plasmid: BC-PSGX3(BC) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)CODON+RIL
References: UniProt: Q8EDM4, purine-nucleoside phosphorylase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 116 / 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: 3.13 Å3/Da / Density % sol: 60.72 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2M sodium citrate, 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 26, 2013
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 27227 / % possible obs: 100 % / Redundancy: 9 % / Rmerge(I) obs: 0.128 / Χ2: 1.219 / Net I/σ(I): 6.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.4-2.448.70.62113351.0451100
2.44-2.498.70.63313581.0121100
2.49-2.538.70.54613701.0481100
2.53-2.598.70.45613431.0541100
2.59-2.648.80.46213631.0631100
2.64-2.78.80.38413621.0741100
2.7-2.778.80.37213791.0861100
2.77-2.858.80.30713381.1231100
2.85-2.938.80.26313841.1471100
2.93-3.028.80.23113461.1491100
3.02-3.1390.19313661.1731100
3.13-3.2690.14613821.2611100
3.26-3.419.10.13913291.2781100
3.41-3.589.30.12513751.3731100
3.58-3.819.30.10913631.5781100
3.81-4.19.30.09213511.3711100
4.1-4.529.20.07713771.4481100
4.52-5.1790.06813571.2221100
5.17-6.519.60.0713811.2741100
6.51-509.40.07113681.5199.8

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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: 3OCC

3occ


Resolution: 2.4→20 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.958 / WRfactor Rfree: 0.178 / WRfactor Rwork: 0.1462 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8584 / SU B: 10.632 / SU ML: 0.121 / SU R Cruickshank DPI: 0.2199 / SU Rfree: 0.1819 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.218 / ESU R Free: 0.176 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.1953 749 5.1 %RANDOM
Rwork0.1638 ---
obs0.1654 14742 99.46 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 123.29 Å2 / Biso mean: 43.7178 Å2 / Biso min: 26.75 Å2
Baniso -1Baniso -2Baniso -3
1--2.56 Å2-2.56 Å2-0 Å2
2---2.56 Å2-0 Å2
3---8.3 Å2
Refinement stepCycle: LAST / Resolution: 2.4→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1782 0 0 116 1898
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0191813
X-RAY DIFFRACTIONr_angle_refined_deg1.2751.9732456
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0685232
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.61124.56881
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.16315274
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.132159
X-RAY DIFFRACTIONr_chiral_restr0.080.2281
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0211370
X-RAY DIFFRACTIONr_mcbond_it2.1315.854931
X-RAY DIFFRACTIONr_mcangle_it3.56178.7971162
X-RAY DIFFRACTIONr_scbond_it3.1486.366879
LS refinement shellResolution: 2.4→2.461 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.279 56 -
Rwork0.249 981 -
all-1037 -
obs--99.81 %
Refinement TLS params.Method: refined / Origin x: 14.3082 Å / Origin y: 114.6386 Å / Origin z: -12.2401 Å
111213212223313233
T0.0442 Å2-0.0076 Å2-0.0117 Å2-0.0284 Å20.0021 Å2--0.0427 Å2
L0.7224 °2-0.1723 °20.0348 °2-1.3932 °2-0.3013 °2--0.2181 °2
S0.0184 Å °-0.0409 Å °0.1412 Å °0.0804 Å °-0.0616 Å °-0.1686 Å °-0.0698 Å °0.0142 Å °0.0433 Å °

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