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- PDB-3d8y: RNase A- 5'-Deoxy-5'-N-piperidinothymidine complex -

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Basic information

Entry
Database: PDB / ID: 3d8y
TitleRNase A- 5'-Deoxy-5'-N-piperidinothymidine complex
ComponentsRibonuclease pancreaticPancreatic ribonuclease family
KeywordsHYDROLASE / RIBONUCLEASE / LIGAND BINDING / Endonuclease / Glycation / Glycoprotein / Nuclease / Secreted
Function / homology
Function and homology information


pancreatic ribonuclease / ribonuclease A activity / RNA nuclease activity / nucleic acid binding / lyase activity / defense response to Gram-positive bacterium / extracellular region
Similarity search - Function
P-30 Protein / Ribonuclease A-like domain / Pancreatic ribonuclease / Ribonuclease A, active site / Ribonuclease A-domain / Ribonuclease A-like domain superfamily / Pancreatic ribonuclease / Pancreatic ribonuclease family signature. / Pancreatic ribonuclease / Roll / Alpha Beta
Similarity search - Domain/homology
CITRATE ANION / 5'-deoxy-5'-piperidin-1-ylthymidine / Ribonuclease pancreatic
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.72 Å
AuthorsLeonidas, D.D. / Zographos, S.E. / Oikonomakos, N.G.
CitationJournal: J.Med.Chem. / Year: 2009
Title: Morpholino, piperidino, and pyrrolidino derivatives of pyrimidine nucleosides as inhibitors of ribonuclease A: synthesis, biochemical, and crystallographic evaluation
Authors: Samanta, A. / Leonidas, D.D. / Dasgupta, S. / Pathak, T. / Zographos, S.E. / Oikonomakos, N.G.
History
DepositionMay 26, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 10, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Jan 29, 2014Group: Database references
Revision 1.3Nov 1, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ribonuclease pancreatic
B: Ribonuclease pancreatic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,1045
Polymers27,4172
Non-polymers6883
Water3,837213
1
A: Ribonuclease pancreatic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,3964
Polymers13,7081
Non-polymers6883
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ribonuclease pancreatic


Theoretical massNumber of molelcules
Total (without water)13,7081
Polymers13,7081
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)100.161, 32.421, 72.567
Angle α, β, γ (deg.)90.00, 90.90, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Ribonuclease pancreatic / Pancreatic ribonuclease family / Ribonuclease A / RNase 1 / RNase A


Mass: 13708.326 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Tissue: PANCREAS / References: UniProt: P61823, EC: 3.1.27.5
#2: Chemical ChemComp-FLC / CITRATE ANION / Citric acid


Mass: 189.100 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H5O7
#3: Chemical ChemComp-T3S / 5'-deoxy-5'-piperidin-1-ylthymidine


Mass: 309.361 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H23N3O4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 213 / 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: 2.15 Å3/Da / Density % sol: 42.75 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: PEG 4000, SODIUM CITRATE, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.92 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 8, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 1.72→30 Å / Num. all: 25226 / Num. obs: 24530 / % possible obs: 97.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 10.8 % / Biso Wilson estimate: 19.5 Å2 / Rsym value: 0.078 / Net I/σ(I): 9.2
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 3.1 % / Mean I/σ(I) obs: 3 / Num. unique all: 1218 / Rsym value: 0.47 / % possible all: 96.7

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Processing

Software
NameVersionClassification
REFMAC5.3.0037refinement
ADSCQuantumdata collection
DENZOdata reduction
SCALEPACKdata scaling
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB entry 2G8Q

2g8q


Resolution: 1.72→30 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.922 / SU B: 4.603 / SU ML: 0.08 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.129 / ESU R Free: 0.124 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2296 1258 5.1 %RANDOM
Rwork0.18926 ---
obs0.19137 23272 97.24 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.746 Å2
Baniso -1Baniso -2Baniso -3
1--0.39 Å20 Å20.17 Å2
2--0.73 Å20 Å2
3----0.34 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.124 Å0.129 Å
Refinement stepCycle: LAST / Resolution: 1.72→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1901 0 48 213 2162
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0212003
X-RAY DIFFRACTIONr_angle_refined_deg1.2041.952713
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8625246
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.19525.22290
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.59315341
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.506158
X-RAY DIFFRACTIONr_chiral_restr0.0760.2298
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021506
X-RAY DIFFRACTIONr_nbd_refined0.1840.2891
X-RAY DIFFRACTIONr_nbtor_refined0.2920.21387
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1340.2175
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.230.265
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1760.228
X-RAY DIFFRACTIONr_mcbond_it0.5531.51274
X-RAY DIFFRACTIONr_mcangle_it0.94822023
X-RAY DIFFRACTIONr_scbond_it1.5723810
X-RAY DIFFRACTIONr_scangle_it2.4984.5690
LS refinement shellResolution: 1.72→1.765 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.27 90 -
Rwork0.229 1539 -
obs--88.29 %
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)
12.5009-0.4859-0.43213.63430.50667.97140.17930.10580.2624-0.0357-0.0126-0.2608-0.65910.0724-0.16670.0563-0.00230.050.03320.04980.004830.89129.00389.677
236.4039-29.4277-30.111233.03735.050537.3076-1.45572.6373-2.26511.8524-0.76382.32471.404-2.6642.21950.12070.14010.21330.40990.01860.05824.676-4.4083-1.7844
33.6531-0.911-2.60741.2050.63253.69970.17470.3730.1864-0.21970.0573-0.1382-0.1493-0.1318-0.2320.022-0.01080.01390.06530.037-0.00632.07822.15745.1426
47.8390.78811.47753.2824-0.45973.5072-0.1087-0.0862-0.07310.15490.1084-0.11390.0043-0.28210.00030.0396-0.0054-0.00030.01650.01010.017528.3211-1.714824.1818
512.2191.595-6.88110.6802-1.05957.3804-0.3540.3652-0.4671-0.1720.1759-0.28980.73040.15870.17810.0376-0.01450.02940.0315-0.0641-0.012538.2631-4.90171.6439
63.93491.8504-5.76096.27693.230114.9584-0.30670.4053-0.5797-0.4994-0.018-0.06360.6364-0.63690.32480.0198-0.0916-0.01520.0441-0.0294-0.050825.8308-8.896110.0774
72.7751-0.5878-0.89046.42760.42872.9978-0.04140.01580.1277-0.1090.148-0.0292-0.072-0.2145-0.10650.0216-0.0012-0.00950.0270.01660.030629.33843.883619.2891
85.61911.68363.262.89021.00179.6574-0.12590.5582-0.74390.08180.3629-0.17770.83650.4059-0.2370.0188-0.01130.02210.0287-0.05470.02216.427-7.585330.647
95.76750.29581.07221.29490.720.5448-0.47621.00331.0351-0.50410.1222-0.0452-0.39430.2710.3540.0827-0.1295-0.07580.09280.17280.011910.01386.753322.9552
1014.19041.02034.25968.79343.88933.5255-0.17761.2401-0.6352-0.62010.0621-0.0186-0.09380.29880.1155-0.0242-0.09020.03880.2213-0.0477-0.1519.449-5.499619.7119
112.29140.19560.59410.91880.96111.0728-0.113-0.0050.0185-0.05510.04070.0675-0.0285-0.02310.07230.0226-0.0125-0.0016-0.01090.0090.068710.29140.180338.3077
121.13650.7486-0.04311.96840.99160.7068-0.23240.04110.2569-0.25440.04270.1618-0.22-0.08790.18970.0342-0.0131-0.0615-0.0310.01620.06368.48946.938137.7501
133.29040.6441.35432.31921.84294.5709-0.31870.48960.0828-0.4292-0.0020.191-0.32540.06950.32070.1006-0.0222-0.03170.11170.00780.0469-0.2166-0.618920.3413
143.0394-0.11130.90382.3769-0.03122.7257-0.06290.0537-0.1011-0.1153-0.00330.16390.0326-0.03680.06620.0286-0.02280.0034-0.00160.01150.046511.5847-1.492639.8662
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 151 - 15
2X-RAY DIFFRACTION2AA16 - 2316 - 23
3X-RAY DIFFRACTION3AA24 - 5824 - 58
4X-RAY DIFFRACTION4AA59 - 7759 - 77
5X-RAY DIFFRACTION5AA78 - 9978 - 99
6X-RAY DIFFRACTION6AA100 - 106100 - 106
7X-RAY DIFFRACTION7AA107 - 124107 - 124
8X-RAY DIFFRACTION8BB1 - 111 - 11
9X-RAY DIFFRACTION9BB12 - 2712 - 27
10X-RAY DIFFRACTION10BB28 - 3928 - 39
11X-RAY DIFFRACTION11BB40 - 7240 - 72
12X-RAY DIFFRACTION12BB73 - 8473 - 84
13X-RAY DIFFRACTION13BB85 - 10385 - 103
14X-RAY DIFFRACTION14BB104 - 124104 - 124

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