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- PDB-3d6p: RNase A- 5'-Deoxy-5'-N-morpholinouridine complex -

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Basic information

Entry
Database: PDB / ID: 3d6p
TitleRNase A- 5'-Deoxy-5'-N-morpholinouridine complex
ComponentsRibonuclease pancreaticPancreatic ribonuclease family
KeywordsHYDROLASE / Ribonuclease A / ligand / 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
Chem-U2S / Ribonuclease pancreatic
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.6 Å
AuthorsLeonidas, D.D. / Zogrpahos, 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 20, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 10, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 11, 2017Group: Data collection / Category: reflns / Item: _reflns.percent_possible_obs
Revision 1.3Aug 30, 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)27,7303
Polymers27,4172
Non-polymers3131
Water5,603311
1
A: Ribonuclease pancreatic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,0222
Polymers13,7081
Non-polymers3131
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
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
MethodPISA
Unit cell
Length a, b, c (Å)100.239, 32.823, 72.466
Angle α, β, γ (deg.)90.00, 90.41, 90.00
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 13708.326 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P61823, EC: 3.1.27.5
#2: Chemical ChemComp-U2S / 1-(5-deoxy-5-morpholin-4-yl-alpha-L-arabinofuranosyl)pyrimidine-2,4(1H,3H)-dione


Mass: 313.306 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H19N3O6
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 311 / 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: 2.17 Å3/Da / Density % sol: 43.42 %
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 7, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 1.6→30 Å / Num. all: 31 / Num. obs: 31526 / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 8.2 % / Biso Wilson estimate: 16.8 Å2 / Rsym value: 0.038 / Net I/σ(I): 24
Reflection shellResolution: 1.6→1.64 Å / Redundancy: 2.8 % / Mean I/σ(I) obs: 7.2 / Num. unique all: 1573 / Rsym value: 0.147 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
ADSCQuantumdata collection
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.2phasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 2G8Q
Resolution: 1.6→30 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.934 / SU B: 2.895 / SU ML: 0.055 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.098 / ESU R Free: 0.099 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21927 1557 5 %RANDOM
Rwork0.18153 ---
obs0.18337 29458 98.39 %-
all-31015 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.73 Å2
Baniso -1Baniso -2Baniso -3
1--0.27 Å20 Å20.23 Å2
2--0.2 Å20 Å2
3---0.07 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.103 Å0.101 Å
Refinement stepCycle: LAST / Resolution: 1.6→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1902 0 22 311 2235
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0221966
X-RAY DIFFRACTIONr_angle_refined_deg1.2421.9422662
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7315246
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.7625.22788
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.71115336
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.546158
X-RAY DIFFRACTIONr_chiral_restr0.0850.2295
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021475
X-RAY DIFFRACTIONr_nbd_refined0.190.2912
X-RAY DIFFRACTIONr_nbtor_refined0.2940.21363
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1160.2230
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1990.258
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1720.231
X-RAY DIFFRACTIONr_mcbond_it0.6581.51271
X-RAY DIFFRACTIONr_mcangle_it1.09922008
X-RAY DIFFRACTIONr_scbond_it1.6933776
X-RAY DIFFRACTIONr_scangle_it2.6634.5654
LS refinement shellResolution: 1.6→1.643 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.264 114 -
Rwork0.205 2069 -
obs--94.42 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
114.4672-0.22422.3444.55069.035918.48-0.05360.23330.843-1.05430.6884-0.3994-2.25410.7331-0.63480.2928-0.11720.0925-0.0698-0.0057-0.01333.160315.126211.8441
23.5095-0.8096-0.41414.20510.80246.36310.0810.1881-0.0343-0.1743-0.0301-0.1111-0.2513-0.071-0.05090.0604-0.00040.02020.02850.0122-0.003629.27595.76927.7001
314.4841-11.5597-15.257619.374210.64739.8524-0.36980.6555-0.36151.20940.37491.10410.3855-3.4959-0.00510.01230.01890.04950.30250.0372-0.062224.6546-5.1796-1.8714
44.97982.2467-0.41259.26954.74366.02740.02160.633-0.0239-0.6791-0.01650.0323-0.3749-0.1009-0.00510.04310.01190.03090.1018-0.0307-0.052733.76690.1868-2.99
544.8303-9.9178-4.39256.71132.41792.0465-0.0695-0.93741.0342-0.27620.4718-1.1047-0.43090.3442-0.40230.0031-0.0740.09330.0168-0.05650.088640.57696.34772.5273
61.62440.0032-1.92390.97950.50323.4466-0.06350.0116-0.0766-0.11090.0665-0.0448-0.10510.0143-0.0030.031300.0020.04270.00640.015627.44691.155710.3736
75.28290.3571.18871.0312-0.2142.43110.0005-0.0144-0.10160.02260.02-0.0818-0.044-0.1217-0.02050.03380.0039-0.00040.03050.00770.034428.4138-1.814324.0593
89.53751.6068-5.06341.0522-0.84214.1963-0.27410.0714-0.4231-0.24160.1216-0.35590.32630.24150.15260.0346-0.00010.0580.0267-0.05430.059338.3818-4.64782.0918
92.04570.9448-2.35020.9358-0.3383.8186-0.18270.1025-0.3749-0.09770.0604-0.1910.3464-0.03570.12240.04-0.0080.01120.026-0.03350.027530.0729-8.05986.2876
101.7291-0.35110.02824.02570.48282.1521-0.0382-0.02360.0827-0.0570.062-0.0227-0.0791-0.1259-0.02380.03390.0088-0.00150.02520.00420.0329.56993.902919.1805
114.03840.24091.14342.0898-0.17124.8180.01310.1486-0.19920.12360.1653-0.05860.18040.0537-0.17840.01630.0035-0.00160.0368-0.00740.033716.1774-4.941630.3592
1281.3737-17.572528.36245.8275-8.142911.8892-0.7946-1.98395.37440.00640.1121-0.5497-1.0954-0.04320.68250.2454-0.04250.04210.2869-0.07210.306610.965610.904921.8625
136.9683-4.61260.74611.843-1.49180.19320.25760.8589-0.0642-1.0917-0.41020.1556-0.04480.11910.15260.07790.0139-0.00840.12370.0058-0.09129.8738-0.969419.2951
142.89732.1907-2.775111.491512.558145.29220.22790.1264-1.41260.55530.2249-0.23653.12681.0019-0.45270.13460.0881-0.0739-0.0242-0.09180.16065.3904-10.850721.3982
151.3009-0.18510.88611.38621.09121.6933-0.04830.12580.0378-0.09670.04840.0246-0.06750.0313-0.00010.0116-0.0130.00610.02020.01520.027513.52223.593133.4997
166.72064.76680.72849.43152.21920.5581-0.1-0.17-0.29750.13520.09880.34010.1573-0.09040.00110.0145-0.01210.0080.02180.04710.04537.7994-2.498746.6774
170.72670.4124-0.07830.68560.54610.7806-0.04170.0450.0383-0.0691-0.02280.0576-0.0626-0.05310.06440.01830.0083-0.01760.00890.00680.04629.19085.514138.7281
185.6556-5.4373-2.86237.38826.016610.35050.23760.9221-0.6281-0.6665-0.46480.56560.4603-0.63270.22720.0549-0.0175-0.06260.0465-0.11170.0286-1.2997-5.275717.1666
191.63250.72422.25441.55461.91145.6282-0.16330.09440.0655-0.22970.01570.1802-0.4442-0.15980.14760.03380.0073-0.0450.03030.0210.0463.94337.269429.0816
204.8151-1.81450.77592.0024-0.99053.0855-0.02850.0376-0.1081-0.0721-0.01710.10690.07670.04130.04560.0478-0.0141-0.00610.0090.00280.048513.0433-2.863740.345
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 61 - 6
2X-RAY DIFFRACTION2AA7 - 167 - 16
3X-RAY DIFFRACTION3AA17 - 2317 - 23
4X-RAY DIFFRACTION4AA24 - 3224 - 32
5X-RAY DIFFRACTION5AA33 - 3933 - 39
6X-RAY DIFFRACTION6AA40 - 5840 - 58
7X-RAY DIFFRACTION7AA59 - 7759 - 77
8X-RAY DIFFRACTION8AA78 - 9578 - 95
9X-RAY DIFFRACTION9AA96 - 10696 - 106
10X-RAY DIFFRACTION10AA107 - 124107 - 124
11X-RAY DIFFRACTION11BB1 - 151 - 15
12X-RAY DIFFRACTION12BB16 - 2316 - 23
13X-RAY DIFFRACTION13BB24 - 3624 - 36
14X-RAY DIFFRACTION14BB37 - 4137 - 41
15X-RAY DIFFRACTION15BB42 - 5842 - 58
16X-RAY DIFFRACTION16BB59 - 7059 - 70
17X-RAY DIFFRACTION17BB71 - 8471 - 84
18X-RAY DIFFRACTION18BB85 - 9685 - 96
19X-RAY DIFFRACTION19BB97 - 10697 - 106
20X-RAY DIFFRACTION20BB107 - 124107 - 124

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