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- PDB-3djo: Bovine Seminal Ribonuclease uridine 2' phosphate complex -

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Basic information

Entry
Database: PDB / ID: 3djo
TitleBovine Seminal Ribonuclease uridine 2' phosphate complex
ComponentsSeminal ribonuclease
KeywordsHYDROLASE / Ribonuclease / Allosteric enzyme / Endonuclease / Nuclease / Secreted
Function / homology
Function and homology information


pancreatic ribonuclease / ribonuclease A activity / RNA phosphodiester bond hydrolysis / ribonuclease activity / nucleic acid binding / lyase activity / extracellular region / identical protein binding
Similarity search - Function
P-30 Protein / Ribonuclease A-like domain / Pancreatic ribonuclease / Ribonuclease A-like domain superfamily / Ribonuclease A-domain / Ribonuclease A, active site / Pancreatic ribonuclease family signature. / Pancreatic ribonuclease / Pancreatic ribonuclease / Roll / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / Chem-U2P / Seminal ribonuclease
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.6 Å
AuthorsDossi, K. / Leonidas, D.D. / Zographos, S.E. / Oikonomakos, N.G.
CitationJournal: Eur.J.Med.Chem. / Year: 2009
Title: Mapping the ribonucleolytic active site of bovine seminal ribonuclease. The binding of pyrimidinyl phosphonucleotide inhibitors
Authors: Dossi, K. / Tsirkone, V.G. / Hayes, J.M. / Matousek, J. / Pouckova, P. / Soucek, J. / Zadinova, M. / Zographos, S.E. / Leonidas, D.D.
History
DepositionJun 24, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 30, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software / Item: _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Seminal ribonuclease
B: Seminal ribonuclease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,0326
Polymers27,2652
Non-polymers7664
Water5,891327
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5040 Å2
ΔGint-31.2 kcal/mol
Surface area13180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.311, 59.067, 82.495
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 Seminal ribonuclease / Seminal RNase / S-RNase / Ribonuclease BS-1


Mass: 13632.640 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P00669, EC: 3.1.27.5
#2: Chemical ChemComp-U2P / PHOSPHORIC ACID MONO-[2-(2,4-DIOXO-3,4-DIHYDRO-2H-PYRIMIDIN-1-YL)-4-HYDROXY-5-HYDROXYMETHYL-TETRAHYDRO-FURAN-3-YL] ESTER / URIDINE-2'-PHOSPHATE / 2'-URIDINEMONOPHOSPHATE


Type: RNA linking / Mass: 324.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H13N2O9P
#3: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 327 / 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: 43.02 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 30% PEG4000, 0.1M sodium acetate, 0.1M Tris/HCl, pH8.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, Hamburg / Beamline: X13 / Wavelength: 0.8088 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Feb 14, 2007
RadiationMonochromator: Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8088 Å / Relative weight: 1
ReflectionResolution: 1.6→27.7 Å / Num. all: 31871 / Num. obs: 31815 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.9 % / Biso Wilson estimate: 15.6 Å2 / Rsym value: 0.066 / Net I/σ(I): 12.4
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 4.1 % / Mean I/σ(I) obs: 3 / Num. unique all: 9056 / Rsym value: 0.466 / % possible all: 98.4

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Processing

Software
NameVersionClassification
REFMAC5.3.0037refinement
MAR345data collection
DENZOdata reduction
SCALEPACKdata scaling
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 1R5D
Resolution: 1.6→27.7 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.937 / SU ML: 0.064 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.098 / ESU R Free: 0.101 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22638 1605 5 %RANDOM
Rwork0.18414 ---
obs0.18628 30202 99.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Refine analyzeLuzzati coordinate error obs: 0.206 Å
Refinement stepCycle: LAST / Resolution: 1.6→27.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1882 0 50 327 2259
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0221978
X-RAY DIFFRACTIONr_angle_refined_deg1.1711.9782667
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5175246
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.29624.86574
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.93615365
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.447158
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021428
X-RAY DIFFRACTIONr_nbd_refined0.1920.2991
X-RAY DIFFRACTIONr_nbtor_refined0.2910.21359
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1210.2263
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1680.253
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1370.244
LS refinement shellResolution: 1.6→1.641 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.282 114 -
Rwork0.229 2161 -
obs--98.4 %
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)
16.7081-0.1307-1.1133.12652.676212.73580.0871-0.43580.1230.3413-0.0743-0.13580.06150.4535-0.01280.0442-0.025-0.0040.0404-0.0002-0.00210.34819.940424.6128
21.6362-0.11060.90973.827-3.10145.60510.02810.00960.1013-0.1964-0.125-0.1080.03340.18810.09690.0264-0.00420.00720.03930.00430.02859.833620.678214.7305
36.4465-1.01894.06152.3833-3.79127.02180.54590.5591-0.08310.03750.08430.29220.5105-0.7-0.63020.02550.0141-0.0030.10390.0170.074610.698825.90451.047
41.38690.75990.29892.4264-1.39053.56070.0269-0.0975-0.05-0.0194-0.0550.1971-0.0108-0.03350.0281-0.0053-0.00130.0020.02430.00350.052121.012827.83567.247
512.1027-4.6938-2.23133.52292.81612.64640.0086-1.05770.03610.58820.1084-0.159-0.1552-0.049-0.1170.0738-0.02510.01030.14180.0224-0.030523.613332.173416.6379
63.18470.0864-0.69280.7019-0.1351.02010.12960.0352-0.17940.0138-0.0935-0.0178-0.03820.0048-0.03610.0320.0104-0.01610.0149-0.00810.052234.246431.43541.8107
72.1124-2.5756-1.80227.4175.06526.4980.15660.0324-0.0082-0.261-0.0167-0.1188-0.417-0.0411-0.13990.0466-0.01860.0169-0.00250.00140.005242.286843.81072.6759
83.5840.7452-0.04111.430.20120.90170.1130.2361-0.0232-0.039-0.0453-0.0204-0.04280.0257-0.06770.05640.0171-0.00890.02410.01340.031133.952436.831-1.0823
96.65462.5084-3.62687.9976-13.52422.93370.1146-0.48380.26980.56190.38080.8226-0.9657-0.8758-0.49540.02130.07070.08670.049-0.03660.037313.673337.851214.2641
105.45660.8431-3.13121.1193-0.56015.268-0.04810.26050.0831-0.06420.07430.14320.173-0.2133-0.02620.05470.0211-0.01950.00650.01090.056523.29735.6201-1.0898
113.8082-2.24733.52183.3248-2.60476.4102-0.11640.20660.03460.08760.0163-0.2189-0.11490.21510.10.0396-0.0072-0.01290.0390.00470.054542.831235.34734.8154
126.2026-4.35083.20414.5756-2.48783.17680.0548-0.09950.0239-0.12620.0281-0.0115-0.0469-0.1055-0.0830.0381-0.0172-0.01410.00990.01060.026538.613336.2254.3311
136.38010.76491.54992.14080.31861.93270.0368-0.3953-0.07310.2027-0.1223-0.0979-0.03540.00750.08540.0145-0.0253-0.01560.03540.02170.030534.902628.780310.54
146.42561.9764-1.46447.85523.8412.8749-0.46370.9345-0.0196-0.16160.21350.4426-0.0231-0.38140.25020.0011-0.04210.01580.03680.03710.034222.341522.1654-2.0687
154.80112.6771-0.83051.7636-0.84958.1189-0.105-0.07470.1192-0.25840.0694-0.15690.08450.19610.03560.03070.00550.0499-0.01080.01910.0518.366519.00577.147
163.5941.1696-2.04246.8093-0.96931.6090.1571-0.2697-0.08260.2437-0.1659-0.1659-0.04770.2380.00880.0064-0.0083-0.00510.05880.030.022618.762220.671315.6227
1717.21575.0733-4.39939.5687-0.98777.43910.2716-1.7705-0.34050.5527-0.3088-0.9443-0.04251.03180.0372-0.05580.0186-0.01440.17210.06670.081222.950412.914417.2418
182.01860.0287-0.15122.1066-0.95521.6667-0.0193-0.0293-0.0259-0.01910.05760.09640.0395-0.1799-0.03830.03130.0043-0.00810.04130.00550.01132.034517.025614.5976
1912.9111-8.0358.89239.7058-5.8396.14410.2493-0.1148-0.2954-0.25930.27010.45030.3546-0.1365-0.51940.0295-0.0186-0.00720.08680.046-0.00240.38843.275521.0796
200.9387-0.65711.86517.8534-7.803713.15190.00840.0497-0.0708-0.02520.3250.3710.0287-0.3902-0.3335-0.0079-0.0181-0.00080.05940.0230-3.0059.378519.224
218.6698-0.2343-0.4563.14320.6792.294-0.25470.12780.1297-0.20040.23880.0270.3582-0.14640.01590.096-0.0224-0.01190.02370.0046-0.00734.002415.43256.6348
221.73510.66362.14343.38-0.28247.010.08230.1544-0.2879-0.2072-0.1738-0.85140.25321.02350.0915-0.01890.07350.0820.05260.07510.145624.78649.50879.3399
238.07390.0789-0.73750.2263-0.69722.1783-0.15740.4669-0.0678-0.25190.072-0.09320.3496-0.14350.08550.1131-0.0120.036-0.0296-0.00920.01977.918212.14895.2143
241.047-0.9189-1.79097.44685.980610.52390.0423-0.0554-0.03350.020.0548-0.060.1525-0.2208-0.09710.0323-0.01-0.00110.04580.00780.00442.166812.952721.0459
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 91 - 9
2X-RAY DIFFRACTION2AA10 - 1610 - 16
3X-RAY DIFFRACTION3AA17 - 2317 - 23
4X-RAY DIFFRACTION4AA24 - 3324 - 33
5X-RAY DIFFRACTION5AA34 - 3934 - 39
6X-RAY DIFFRACTION6AA40 - 5940 - 59
7X-RAY DIFFRACTION7AA60 - 6960 - 69
8X-RAY DIFFRACTION8AA70 - 8670 - 86
9X-RAY DIFFRACTION9AA87 - 9487 - 94
10X-RAY DIFFRACTION10AA95 - 10595 - 105
11X-RAY DIFFRACTION11AA106 - 113106 - 113
12X-RAY DIFFRACTION12AA114 - 124114 - 124
13X-RAY DIFFRACTION13BB1 - 141 - 14
14X-RAY DIFFRACTION14BB15 - 2315 - 23
15X-RAY DIFFRACTION15BB24 - 3024 - 30
16X-RAY DIFFRACTION16BB31 - 3531 - 35
17X-RAY DIFFRACTION17BB36 - 4136 - 41
18X-RAY DIFFRACTION18BB42 - 6142 - 61
19X-RAY DIFFRACTION19BB62 - 6862 - 68
20X-RAY DIFFRACTION20BB69 - 7769 - 77
21X-RAY DIFFRACTION21BB78 - 8378 - 83
22X-RAY DIFFRACTION22BB84 - 9684 - 96
23X-RAY DIFFRACTION23BB97 - 10697 - 106
24X-RAY DIFFRACTION24BB107 - 124107 - 124

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