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- PDB-1o0o: Ribonuclease A in complex with adenosine-2',5'-diphosphate -

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Basic information

Entry
Database: PDB / ID: 1o0o
TitleRibonuclease A in complex with adenosine-2',5'-diphosphate
ComponentsRibonuclease pancreatic
KeywordsHYDROLASE / Ribonuclease
Function / homology
Function and homology information


pancreatic ribonuclease / ribonuclease A activity / RNA nuclease activity / nucleic acid binding / defense response to Gram-positive bacterium / lyase activity / 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
ADENOSINE-2'-5'-DIPHOSPHATE / Ribonuclease pancreatic
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.2 Å
AuthorsLeonidas, D.D. / Oikonomakos, N.G. / Chrysina, E.D. / Kosmopoulou, M.N. / Vlassi, M.
CitationJournal: PROTEIN SCI. / Year: 2003
Title: High-resolution crystal structures of ribonuclease A complexed with adenylic and uridylic nucleotide inhibitors. Implications for structure-based design of ribonucleolytic inhibitors
Authors: Leonidas, D.D. / Chavali, G.B. / Oikonomakos, N.G. / Chrysina, E.D. / Kosmopoulou, M.N. / Vlassi, M. / Frankling, C. / Acharya, K.R.
History
DepositionFeb 24, 2003Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 9, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Oct 25, 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
Revision 1.5Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)28,2714
Polymers27,4172
Non-polymers8542
Water10,052558
1
A: Ribonuclease pancreatic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,1362
Polymers13,7081
Non-polymers4271
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ribonuclease pancreatic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,1362
Polymers13,7081
Non-polymers4271
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)99.852, 32.528, 72.383
Angle α, β, γ (deg.)90.00, 90.11, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-1136-

HOH

21B-1196-

HOH

31B-1213-

HOH

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Components

#1: Protein Ribonuclease pancreatic / Ribonuclease A


Mass: 13708.326 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: P61823, EC: 3.1.27.5
#2: Chemical ChemComp-A2P / ADENOSINE-2'-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 558 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 1.67 Å3/Da / Density % sol: 25.77 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 20mM Sodium citrate Buffer, 20% PEG 4000, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Crystal grow
*PLUS
Temperature: 16 ℃ / Method: vapor diffusion, hanging drop / Details: Leonidas, D.D., (1997) Biochemistry, 36, 5578.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 mg/mlprotein1drop
210 mMsodium citrate1drop
310 %PEG40001drop
420 %PEG40001reservoir
520 Msodium citrate1reservoirpH5.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1.00061 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 21, 2000 / Details: Mirrors
RadiationMonochromator: YALE MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00061 Å / Relative weight: 1
ReflectionResolution: 1.2→30 Å / Num. all: 67242 / Num. obs: 67242 / % possible obs: 92.1 % / Observed criterion σ(F): 0.01 / Observed criterion σ(I): -3 / Redundancy: 14.1 % / Biso Wilson estimate: 12.9 Å2 / Rsym value: 0.038 / Net I/σ(I): 30.9
Reflection shellResolution: 1.2→1.22 Å / Redundancy: 2.8 % / Num. unique all: 2545 / Rsym value: 0.226 / % possible all: 71.2
Reflection
*PLUS
% possible obs: 92.9 % / Num. measured all: 949552 / Rmerge(I) obs: 0.038
Reflection shell
*PLUS
Highest resolution: 1.2 Å / % possible obs: 71.2 % / Rmerge(I) obs: 0.226 / Mean I/σ(I) obs: 10.8

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Processing

Software
NameVersionClassification
REFMAC5refinement
MAR345data collection
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 1AFU

1afu


Resolution: 1.2→29.36 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.94 / SU B: 1.953 / SU ML: 0.046 / Cross valid method: THROUGHOUT / σ(F): 0.001 / ESU R: 0.059 / ESU R Free: 0.056 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22824 3421 5.1 %RANDOM
Rwork0.19431 ---
all0.19602 63814 --
obs0.19431 63814 92.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 14.68 Å2
Baniso -1Baniso -2Baniso -3
1--0.11 Å20 Å2-0.05 Å2
2--0.31 Å20 Å2
3----0.2 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.2 Å0.18 Å
Luzzati d res low-5 Å
Luzzati sigma a0.14 Å0.14 Å
Refinement stepCycle: LAST / Resolution: 1.2→29.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1902 0 54 558 2514
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0212000
X-RAY DIFFRACTIONr_bond_other_d0.0010.021626
X-RAY DIFFRACTIONr_angle_refined_deg1.6611.9612716
X-RAY DIFFRACTIONr_angle_other_deg0.86333844
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.1363246
X-RAY DIFFRACTIONr_dihedral_angle_2_deg12.84215355
X-RAY DIFFRACTIONr_chiral_restr0.0920.2302
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022202
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02368
X-RAY DIFFRACTIONr_nbd_refined0.250.3495
X-RAY DIFFRACTIONr_nbd_other0.2220.31706
X-RAY DIFFRACTIONr_nbtor_other0.1910.51
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2690.5430
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.2310.52
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2350.328
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2790.362
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2950.573
X-RAY DIFFRACTIONr_mcbond_it1.2331.51242
X-RAY DIFFRACTIONr_mcangle_it1.92722006
X-RAY DIFFRACTIONr_scbond_it2.3453758
X-RAY DIFFRACTIONr_scangle_it3.544.5710
X-RAY DIFFRACTIONr_rigid_bond_restr1.33722000
X-RAY DIFFRACTIONr_sphericity_free2.4092558
X-RAY DIFFRACTIONr_sphericity_bonded2.70121956
LS refinement shellResolution: 1.204→1.236 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.277 205 -
Rwork0.261 3868 -
obs-3868 71.2 %
Software
*PLUS
Version: 5 / Classification: refinement
Refinement
*PLUS
% reflection Rfree: 5 % / Rfactor Rfree: 0.228 / Rfactor Rwork: 0.194
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.011
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.7

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