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- PDB-3djx: Bovine Seminal Ribonuclease- cytidine 5' phosphate complex -

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Basic information

Entry
Database: PDB / ID: 3djx
TitleBovine Seminal Ribonuclease- cytidine 5' phosphate complex
ComponentsSeminal ribonuclease
KeywordsHYDROLASE / Ribonuclease / Allosteric enzyme / Endonuclease / Nuclease / Secreted
Function / homology
Function and homology information


pancreatic ribonuclease / ribonuclease A activity / RNA nuclease activity / metabolic process / nucleic acid binding / lyase activity / defense response to Gram-positive bacterium / extracellular region / identical protein binding
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
CYTIDINE-5'-MONOPHOSPHATE / Seminal ribonuclease
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.69 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
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 / diffrn_source / 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 / _diffrn_source.pdbx_synchrotron_site / _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: Seminal ribonuclease
B: Seminal ribonuclease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,9124
Polymers27,2652
Non-polymers6462
Water5,531307
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3840 Å2
ΔGint-26.2 kcal/mol
Surface area13940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.585, 59.016, 82.247
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-C5P / CYTIDINE-5'-MONOPHOSPHATE / Cytidine monophosphate


Mass: 323.197 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H14N3O8P
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 307 / 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: 43.12 %
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: 1.69→27.775 Å / Num. all: 26589 / Num. obs: 26554 / % possible obs: 98.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.9 % / Biso Wilson estimate: 16.968 Å2 / Rsym value: 0.059 / Net I/σ(I): 14.1
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 3.4 / Num. unique all: 4382 / Rsym value: 0.445 / % possible all: 98.7

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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: 1.69→27.77 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.948 / SU B: 3.413 / SU ML: 0.061 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.108 / ESU R Free: 0.105 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20428 1326 5 %RANDOM
Rwork0.16862 ---
obs0.17036 25228 97.45 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.364 Å2
Baniso -1Baniso -2Baniso -3
1--0.07 Å20 Å20 Å2
2---0.1 Å20 Å2
3---0.16 Å2
Refine analyzeLuzzati coordinate error obs: 0.196 Å
Refinement stepCycle: LAST / Resolution: 1.69→27.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1882 0 42 307 2231
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0221972
X-RAY DIFFRACTIONr_angle_refined_deg1.2841.9712661
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8445246
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.82524.86574
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.49815365
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.941158
X-RAY DIFFRACTIONr_chiral_restr0.0880.2295
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021420
X-RAY DIFFRACTIONr_nbd_refined0.190.2940
X-RAY DIFFRACTIONr_nbtor_refined0.2930.21347
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1330.2232
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1570.256
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1370.234
X-RAY DIFFRACTIONr_mcbond_it0.6851.51274
X-RAY DIFFRACTIONr_mcangle_it1.1422013
X-RAY DIFFRACTIONr_scbond_it1.8623777
X-RAY DIFFRACTIONr_scangle_it2.9074.5648
LS refinement shellResolution: 1.688→1.732 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.255 72 -
Rwork0.199 1706 -
obs--89.21 %
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)
16.4828-0.4176-1.06761.82741.15759.16380.0796-0.41020.07570.2785-0.0813-0.09810.0780.46730.00180.0324-0.0214-0.0110.0530.0098-0.000411.086919.563323.2512
26.1972-2.90732.32116.9707-5.04354.85530.17780.47620.2624-0.4547-0.16930.03830.26770.0696-0.00840.05210.009-0.00940.04810.01180.01346.915622.62489.5224
34.20871.3484-0.04792.3685-1.21083.6246-0.00080.08790.0281-0.20340.05840.25870.0907-0.2203-0.05760.0043-0.00360.00180.0185-0.00410.040718.664927.36735.5442
413.0913-7.0931-6.683814.069314.133814.21910.0627-0.99270.08751.1964-0.07820.00050.2167-0.05850.01550.0693-0.0170.02030.1233-0.0188-0.034723.840232.151716.7676
53.11940.4774-0.7451.06910.0031.17040.03360.0146-0.0166-0.0383-0.00890.0142-0.0322-0.0311-0.02470.0494-0.0016-0.00610.017-0.00490.045834.082531.29991.6962
61.5409-0.0243-0.64155.49574.44456.39740.1397-0.00630.0237-0.18910.091-0.1614-0.3394-0.0571-0.23060.053-0.02450.0083-0.01140.00030.014642.992443.39133.1774
75.15312.33960.80433.02430.74882.2369-0.06180.5198-0.1585-0.23750.1862-0.13960.02550.1631-0.12440.07710.0099-0.00710.04460.00510.023536.458535.2873-4.6086
83.52740.3059-2.73763.9664-1.76328.68950.5019-0.06050.66840.2711-0.09060.143-0.6892-0.6932-0.41130.01330.02570.02810.0005-0.03420.090518.172739.43696.4562
92.7156-1.7351-2.49212.2639-2.82519.17650.2919-0.7885-0.0080.33450.3930.6199-0.1352-0.5836-0.6849-0.0258-0.00030.07620.0936-0.02650.050315.326735.823214.5517
1021.53345.1156-19.42631.2188-4.446125.7071-0.17040.6104-0.053-0.18510.13980.24810.1969-0.59290.03060.06180.0211-0.0294-0.01450.03440.05722.093934.7179-3.7659
115.042-1.89344.78161.6843-1.69165.8969-0.10530.26110.0907-0.02410.026-0.0289-0.1980.16190.07930.0417-0.0194-0.00870.02330.01760.03538.347237.17850.4721
125.2289-4.12542.86674.6719-1.61913.0472-0.1375-0.14160.2166-0.0120.1138-0.1471-0.0764-0.08290.02380.0462-0.0271-0.01040.02560.01340.059439.934335.41285.0675
136.42530.54451.3182.5131-0.14083.2579-0.0278-0.4886-0.10470.1884-0.0784-0.1099-0.1123-0.01070.10620.0256-0.0116-0.00210.04450.01740.009234.874628.558210.5551
142.93130.6319-1.80760.8172-0.53271.1447-0.09680.32050.112-0.16410.1165-0.0078-0.0019-0.1276-0.01970.034-0.01860.01990.0343-0.00930.027920.719720.6980.6808
151.70611.76560.27253.95470.5652.39520.11280.0777-0.0253-0.111-0.0346-0.0709-0.07280.0973-0.07820.0003-0.00920.01220.04630.00850.032618.289120.961411.8511
1620.5434-17.451.783914.8991-2.28247.83830.1082-0.6337-0.09590.83670.1442-1.0039-0.04070.9486-0.25240.0076-0.0322-0.08560.14240.02240.067522.831815.864917.7353
172.0189-0.191-0.63961.2-0.41311.61270.0375-0.0276-0.05080.0325-0.01040.01360.0427-0.0483-0.02710.05330.0047-0.0120.0356-0.00930.03963.651916.241114.5518
1814.8873-8.98938.092311.0608-6.44164.82820.04530.0612-0.4562-0.07080.20050.35370.11290.0162-0.24580.0591-0.0307-0.01180.04350.0312-0.0150.64742.943720.9532
192.1505-0.65052.25316.4396-6.974613.50710.0342-0.0464-0.10830.0360.3250.29790.0334-0.4979-0.35920.0033-0.00670.00190.04590.01960.0173-2.81238.988119.1714
207.70680.1993-0.11541.83180.17321.52910.01250.0614-0.197-0.06670.0043-0.11220.16270.0395-0.01690.09270.0157-0.00340.031-0.00720.01398.585112.95317.1701
2112.98033.927314.736816.529315.53935.03390.08041.0311-0.0486-0.3018-0.0371-0.68780.37483.1176-0.0432-0.06810.15320.06290.25490.10870.051427.998910.04739.2945
2211.12554.0877-1.46023.24661.86734.3837-0.0910.67850.2306-0.19210.07220.01130.23560.21540.01880.05970.02770.01210.0187-0.00570.028915.5912.79063.6568
232.13030.53520.43351.6484-0.81838.560.06270.0992-0.0433-0.16440.00340.02430.3352-0.139-0.0660.06210.00030.00460.0205-0.00650.0111.265211.054511.6749
241.0046-0.7729-1.20673.83563.73258.39250.07040.0078-0.05820.01030.03310.00540.0557-0.0271-0.10350.0422-0.0054-0.00450.03140.00620.01842.593913.146421.198
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 111 - 11
2X-RAY DIFFRACTION2AA12 - 1812 - 18
3X-RAY DIFFRACTION3AA19 - 3319 - 33
4X-RAY DIFFRACTION4AA34 - 3934 - 39
5X-RAY DIFFRACTION5AA40 - 5940 - 59
6X-RAY DIFFRACTION6AA60 - 7160 - 71
7X-RAY DIFFRACTION7AA72 - 8272 - 82
8X-RAY DIFFRACTION8AA83 - 9083 - 90
9X-RAY DIFFRACTION9AA91 - 9791 - 97
10X-RAY DIFFRACTION10AA98 - 10398 - 103
11X-RAY DIFFRACTION11AA104 - 112104 - 112
12X-RAY DIFFRACTION12AA113 - 124113 - 124
13X-RAY DIFFRACTION13BB1 - 141 - 14
14X-RAY DIFFRACTION14BB15 - 2715 - 27
15X-RAY DIFFRACTION15BB28 - 3328 - 33
16X-RAY DIFFRACTION16BB34 - 3934 - 39
17X-RAY DIFFRACTION17BB40 - 6140 - 61
18X-RAY DIFFRACTION18BB62 - 6862 - 68
19X-RAY DIFFRACTION19BB69 - 7769 - 77
20X-RAY DIFFRACTION20BB78 - 8678 - 86
21X-RAY DIFFRACTION21BB87 - 9587 - 95
22X-RAY DIFFRACTION22BB96 - 10196 - 101
23X-RAY DIFFRACTION23BB102 - 110102 - 110
24X-RAY DIFFRACTION24BB111 - 124111 - 124

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