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- PDB-3of3: Crystal structure of PNP with an inhibitor DADME_immH from Vibrio... -

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Basic information

Entry
Database: PDB / ID: 3of3
TitleCrystal structure of PNP with an inhibitor DADME_immH from Vibrio cholerae
ComponentsPurine nucleoside phosphorylase deoD-type 1
KeywordsTRANSFERASE / Structural Genomics / PSI-2 / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC / phophoryl transferase / purine nucleosides / phosphate
Function / homology
Function and homology information


purine-nucleoside phosphorylase / purine-nucleoside phosphorylase activity / purine nucleoside catabolic process / 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
Chem-DIH / PHOSPHATE ION / Purine nucleoside phosphorylase DeoD-type 1
Similarity search - Component
Biological speciesVibrio cholerae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.83 Å
AuthorsKim, J. / Ramagopal, U.A. / Burley, S.K. / Almo, S.C. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Crystal structure of PNP with an inhibitor DADME_immH from Vibrio cholerae
Authors: Kim, J. / Ramagopal, U.A. / Burley, S.K. / Almo, S.C.
History
DepositionAug 13, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 1, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 2.0Dec 12, 2018Group: Data collection / Derived calculations ...Data collection / Derived calculations / Non-polymer description / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_entity_nonpoly / pdbx_validate_chiral
Item: _chem_comp.formula / _chem_comp.formula_weight ..._chem_comp.formula / _chem_comp.formula_weight / _chem_comp.name / _chem_comp.pdbx_synonyms / _entity.formula_weight / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Revision 2.1Feb 10, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.2Sep 6, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Purine nucleoside phosphorylase deoD-type 1
B: Purine nucleoside phosphorylase deoD-type 1
C: Purine nucleoside phosphorylase deoD-type 1
D: Purine nucleoside phosphorylase deoD-type 1
E: Purine nucleoside phosphorylase deoD-type 1
F: Purine nucleoside phosphorylase deoD-type 1
G: Purine nucleoside phosphorylase deoD-type 1
H: Purine nucleoside phosphorylase deoD-type 1
I: Purine nucleoside phosphorylase deoD-type 1
J: Purine nucleoside phosphorylase deoD-type 1
K: Purine nucleoside phosphorylase deoD-type 1
L: Purine nucleoside phosphorylase deoD-type 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)318,15936
Polymers313,83612
Non-polymers4,32324
Water36,2462012
1
A: Purine nucleoside phosphorylase deoD-type 1
B: Purine nucleoside phosphorylase deoD-type 1
C: Purine nucleoside phosphorylase deoD-type 1
D: Purine nucleoside phosphorylase deoD-type 1
E: Purine nucleoside phosphorylase deoD-type 1
L: Purine nucleoside phosphorylase deoD-type 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)159,08018
Polymers156,9186
Non-polymers2,16212
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area28110 Å2
ΔGint-140 kcal/mol
Surface area41570 Å2
MethodPISA
2
F: Purine nucleoside phosphorylase deoD-type 1
G: Purine nucleoside phosphorylase deoD-type 1
H: Purine nucleoside phosphorylase deoD-type 1
I: Purine nucleoside phosphorylase deoD-type 1
J: Purine nucleoside phosphorylase deoD-type 1
K: Purine nucleoside phosphorylase deoD-type 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)159,08018
Polymers156,9186
Non-polymers2,16212
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area28150 Å2
ΔGint-138 kcal/mol
Surface area41660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.375, 160.974, 188.685
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 26153.006 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae (bacteria) / Gene: deoD, deoD1, VC_2347 / Plasmid: LIC-PET30a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3)
References: UniProt: Q9KPM0, purine-nucleoside phosphorylase
#2: Chemical
ChemComp-DIH / 7-[[(3R,4R)-3-(hydroxymethyl)-4-oxidanyl-pyrrolidin-1-ium-1-yl]methyl]-3,5-dihydropyrrolo[3,2-d]pyrimidin-4-one


Mass: 265.288 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C12H17N4O3
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2012 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.45 Å3/Da / Density % sol: 49.85 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 0.2M sodium acetate, 0.1M tri-sodium citrate PH 5.6, 30% PEG 4000, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 24, 2009
RadiationMonochromator: Double silicon(111) crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 1.83→43.03 Å / Num. all: 270678 / Num. obs: 270346 / % possible obs: 99.9 % / Redundancy: 6.9 % / Biso Wilson estimate: 32.56 Å2 / Rmerge(I) obs: 0.125 / Rsym value: 0.091 / Net I/σ(I): 15.1
Reflection shellResolution: 1.83→1.9 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.672 / Mean I/σ(I) obs: 2.1 / Num. unique all: 26846 / Rsym value: 0.513 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREP10.2.23phasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1VHJ

1vhj


Resolution: 1.83→43.03 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.963 / SU B: 5.512 / SU ML: 0.074 / Cross valid method: THROUGHOUT / ESU R: 0.111 / ESU R Free: 0.107 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18765 13629 5 %RANDOM
Rwork0.15359 ---
obs0.15529 256929 99.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.334 Å2
Baniso -1Baniso -2Baniso -3
1-2.11 Å20 Å20 Å2
2---1.24 Å20 Å2
3----0.87 Å2
Refinement stepCycle: LAST / Resolution: 1.83→43.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21771 0 288 2012 24071
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.02222624
X-RAY DIFFRACTIONr_angle_refined_deg1.4541.97330569
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.05352911
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.59524.7949
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.441153876
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.27315108
X-RAY DIFFRACTIONr_chiral_restr0.1030.23406
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02116956
X-RAY DIFFRACTIONr_mcbond_it0.6751.514311
X-RAY DIFFRACTIONr_mcangle_it1.193222944
X-RAY DIFFRACTIONr_scbond_it2.08538313
X-RAY DIFFRACTIONr_scangle_it3.3414.57625
LS refinement shellResolution: 1.829→1.876 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.26 1013 -
Rwork0.243 18556 -
obs-18556 98.5 %
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)
10.05230.18530.03120.7703-0.01620.54070.06020.00410.0020.2333-0.0503-0.01420.0419-0.0022-0.00980.195-0.0592-0.00020.07450.00170.060842.8625.02185.054
20.01790.11530.03970.86780.29040.60850.0039-0.0032-0.0070.0207-0.05880.0636-0.1226-0.00210.05490.1358-0.0080.00970.0475-0.02210.107544.03368.021160.752
30.01130.06170.02290.5758-0.08560.47290.01-0.00140.01160.0013-0.02-0.03780.1007-0.01850.010.1263-0.0277-0.00520.0608-0.00070.111240.74310.933161.528
40.0386-0.0363-0.15370.35880.06820.749-0.00070.0013-0.0105-0.0681-0.0265-0.0131-0.0788-0.04320.02730.10720.00210.00490.0774-0.00340.112342.37852.229134.361
50.06360.17760.01620.53530.12380.67250.0542-0.0050.00360.1648-0.0540.0448-0.0728-0.0035-0.00020.2053-0.06250.03880.062-0.03860.065141.51455.236184.928
60.02370.01570.0890.5503-0.13150.7404-0.017-0.01510.0187-0.18880.04180.03080.13660.0094-0.02480.1725-0.018-0.01750.07390.00430.104344.60423.42941.718
70.0159-0.0089-0.03610.802-0.03340.5041-0.04050.020.01050.22530.04690.00950.06290.0133-0.00640.19780.01790.01130.07040.01140.074944.52522.83391.358
80.0569-0.0357-0.15920.8206-0.08180.57270.01730.0038-0.00590.05320.06130.0238-0.1521-0.0134-0.07860.1550.01630.02670.05490.00240.10943.14265.98366.911
90.0334-0.10450.12830.7668-0.38340.80850.0202-0.00920.0258-0.09850.02440.00640.2579-0.0135-0.04450.1834-0.0065-0.01020.05330.00170.109242.9358.32467.953
100.02420.004-0.11950.5007-0.01090.9061-0.0122-0.0159-0.0056-0.16520.05460.0285-0.098-0.0248-0.04240.1586-0.0098-0.01070.07240.01570.101641.75750.78240.936
110.02380.0859-0.02830.54340.03770.6890.00860.0204-0.00920.14920.02610.0403-0.1205-0.0126-0.03470.18730.01980.02650.0579-0.00710.081941.43952.87291.185
120.014-0.00440.06890.409-0.03670.58440.0035-0.01650.0182-0.0841-0.018-0.01550.0772-0.00730.01440.1157-0.00730.00670.0772-0.00480.107143.48425.147135.142
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
4X-RAY DIFFRACTION4D-10 - 9999
5X-RAY DIFFRACTION5E-10 - 9999
6X-RAY DIFFRACTION6F-10 - 9999
7X-RAY DIFFRACTION7G-10 - 9999
8X-RAY DIFFRACTION8H-10 - 9999
9X-RAY DIFFRACTION9I-10 - 9999
10X-RAY DIFFRACTION10J-10 - 9999
11X-RAY DIFFRACTION11K-10 - 9999
12X-RAY DIFFRACTION12L-10 - 9999

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