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- PDB-3d8z: RNase A- 5'-Deoxy-5'-N-pyrrolidinothymidine complex -

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Basic information

Entry
Database: PDB / ID: 3d8z
TitleRNase A- 5'-Deoxy-5'-N-pyrrolidinothymidine 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 / Chem-TXS / Ribonuclease pancreatic
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.98 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)27,9014
Polymers27,4172
Non-polymers4842
Water2,990166
1
A: Ribonuclease pancreatic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,0042
Polymers13,7081
Non-polymers2951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Ribonuclease pancreatic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,8972
Polymers13,7081
Non-polymers1891
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)100.102, 32.678, 72.562
Angle α, β, γ (deg.)90.00, 90.51, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-153-

HOH

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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-TXS / 1-(2,5-dideoxy-5-pyrrolidin-1-yl-beta-L-erythro-pentofuranosyl)-5-methylpyrimidine-2,4(1H,3H)-dione / 5'-deoxy-5'-pyrrolidin-1-ylthymidine


Mass: 295.334 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H21N3O4
#3: Chemical ChemComp-FLC / CITRATE ANION / Citric acid


Mass: 189.100 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5O7
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 166 / 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: 2.16 Å3/Da / Density % sol: 43.17 %
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: 1.98→30 Å / Num. all: 16850 / Num. obs: 16481 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 2.9 % / Biso Wilson estimate: 21 Å2 / Rsym value: 0.091 / Net I/σ(I): 8.7
Reflection shellResolution: 1.98→2.03 Å / Redundancy: 2.9 % / Mean I/σ(I) obs: 2.8 / Num. unique all: 852 / Rsym value: 0.435 / % possible all: 100

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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: 1.98→28.6 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.905 / SU B: 7.784 / SU ML: 0.117 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.207 / ESU R Free: 0.179 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24022 832 5 %RANDOM
Rwork0.18929 ---
obs0.19178 15649 97.82 %-
all-16850 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.096 Å2
Baniso -1Baniso -2Baniso -3
1--0.14 Å20 Å2-0.1 Å2
2--0.29 Å20 Å2
3----0.16 Å2
Refine analyzeLuzzati coordinate error obs: 0.207 Å / Luzzati d res low obs: 0.179 Å
Refinement stepCycle: LAST / Resolution: 1.98→28.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1902 0 34 166 2102
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0211984
X-RAY DIFFRACTIONr_angle_refined_deg1.581.9442688
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.395246
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.95925.16989
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.30815337
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.076158
X-RAY DIFFRACTIONr_chiral_restr0.150.2296
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021494
X-RAY DIFFRACTIONr_nbd_refined0.1910.2861
X-RAY DIFFRACTIONr_nbtor_refined0.2910.21350
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1640.2162
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2010.255
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1370.221
X-RAY DIFFRACTIONr_mcbond_it0.5261.51277
X-RAY DIFFRACTIONr_mcangle_it0.8722016
X-RAY DIFFRACTIONr_scbond_it1.6023792
X-RAY DIFFRACTIONr_scangle_it2.54.5672
LS refinement shellResolution: 1.977→2.028 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.319 52 -
Rwork0.203 1021 -
obs--85.16 %
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)
15.1533-1.5917-0.38516.13991.86478.10820.08360.3654-0.0233-0.346-0.0394-0.0401-0.2923-0.1165-0.04420.07140.0140.02710.08190.0754-0.005928.92475.82546.9016
27.8066-1.7853-1.55364.88582.12843.32780.15220.46040.292-0.39440.0507-0.4257-0.32880.0118-0.2029-0.0022-0.01140.08190.04080.025-0.074937.11212.3667-0.1603
31.8921-0.18120.27051.2762-0.5513.8458-0.05160.1449-0.0265-0.07130.0702-0.07930.1074-0.157-0.01870.0053-0.0268-0.0109-0.01250.00530.037927.8582-1.636915.7498
42.43370.0632-0.9461.0067-0.11873.0889-0.04990.3355-0.148-0.16820.087-0.21940.2065-0.074-0.03710.0469-0.0069-0.00030.0376-0.0160.072933.5615-1.173910.3483
56.8803-1.211.41684.50141.14756.5339-0.08760.3201-0.3354-0.04980.2358-0.08060.37690.131-0.1481-0.0269-0.03250.02810.0146-0.0148-0.022615.9382-5.491430.4363
67.8054-1.66022.03191.2438-0.26074.3818-0.46390.75221.0865-0.78520.2052-0.0969-0.70960.18320.25870.183-0.0917-0.04650.15750.10780.06969.94925.294620.241
722.23795.59877.1577.68311.342.920.12020.6148-1.7154-0.6663-0.0238-0.00550.45110.07-0.0964-0.0183-0.01170.01140.0867-0.0895-0.03738.6028-8.641920.6371
81.79060.12540.48821.10590.34941.5713-0.07210.10070.0008-0.14450.0070.104-0.0346-0.080.0651-0.0029-0.0085-0.0106-0.01950.00850.04058.30730.824634.7012
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 221 - 22
2X-RAY DIFFRACTION2AA23 - 4123 - 41
3X-RAY DIFFRACTION3AA42 - 8642 - 86
4X-RAY DIFFRACTION4AA87 - 12487 - 124
5X-RAY DIFFRACTION5BB1 - 141 - 14
6X-RAY DIFFRACTION6BB15 - 3215 - 32
7X-RAY DIFFRACTION7BB33 - 4033 - 40
8X-RAY DIFFRACTION8BB41 - 12441 - 124

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