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- PDB-1o0h: Ribonuclease A in complex with 5'-ADP -

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Basic information

Entry
Database: PDB / ID: 1o0h
TitleRibonuclease A in complex with 5'-ADP
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-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 21, 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 2.0Oct 25, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Refinement description
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _atom_site.occupancy / _database_2.pdbx_DOI ..._atom_site.occupancy / _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 2.1Oct 16, 2024Group: Advisory / Derived calculations / Structure summary
Category: pdbx_entry_details / pdbx_modification_feature ...pdbx_entry_details / pdbx_modification_feature / pdbx_struct_special_symmetry / pdbx_validate_symm_contact

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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
Water9,746541
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
MethodPISA
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)99.722, 32.515, 72.164
Angle α, β, γ (deg.)90.00, 90.03, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-1406-

HOH

21A-1407-

HOH

31B-1292-

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-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 541 / 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: 25.92 %
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: ESRF / Beamline: ID14-2 / Wavelength: 0.933 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 6, 2001 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.2→30 Å / Num. all: 70118 / Num. obs: 70118 / % possible obs: 96.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 8.9 % / Biso Wilson estimate: 12.9 Å2 / Rsym value: 0.053 / Net I/σ(I): 20.9
Reflection shellResolution: 1.2→1.22 Å / Rsym value: 0.13 / % possible all: 96.9
Reflection
*PLUS
Num. measured all: 623242 / Rmerge(I) obs: 0.053
Reflection shell
*PLUS
Highest resolution: 1.2 Å / % possible obs: 96.9 % / Rmerge(I) obs: 0.13 / Mean I/σ(I) obs: 5.8

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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→29.24 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.944 / SU B: 1.755 / SU ML: 0.042 / Cross valid method: THROUGHOUT / σ(F): 0.1 / ESU R: 0.055 / ESU R Free: 0.052 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22108 3573 5.1 %RANDOM
Rwork0.18963 ---
all0.19124 66544 --
obs0.18963 66544 97.9 %-
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: 15.133 Å2
Baniso -1Baniso -2Baniso -3
1--0.09 Å20 Å20.08 Å2
2--0.45 Å20 Å2
3----0.36 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.18 Å0.16 Å
Luzzati d res low-5 Å
Luzzati sigma a0.09 Å0.1 Å
Refinement stepCycle: LAST / Resolution: 1.2→29.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1902 0 54 541 2497
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0212000
X-RAY DIFFRACTIONr_bond_other_d0.0010.021622
X-RAY DIFFRACTIONr_angle_refined_deg1.7831.9612716
X-RAY DIFFRACTIONr_angle_other_deg0.80933838
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0843246
X-RAY DIFFRACTIONr_dihedral_angle_2_deg14.19515355
X-RAY DIFFRACTIONr_chiral_restr0.10.2302
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022202
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02368
X-RAY DIFFRACTIONr_nbd_refined0.270.3528
X-RAY DIFFRACTIONr_nbd_other0.2360.31727
X-RAY DIFFRACTIONr_nbtor_other0.1490.51
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2960.5379
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.1770.51
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.5550.331
X-RAY DIFFRACTIONr_symmetry_vdw_other0.6060.385
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.6040.579
X-RAY DIFFRACTIONr_mcbond_it1.1731.51242
X-RAY DIFFRACTIONr_mcangle_it1.91122006
X-RAY DIFFRACTIONr_scbond_it2.1713758
X-RAY DIFFRACTIONr_scangle_it3.334.5710
X-RAY DIFFRACTIONr_rigid_bond_restr1.24222000
X-RAY DIFFRACTIONr_sphericity_free2.0122541
X-RAY DIFFRACTIONr_sphericity_bonded2.37521956
LS refinement shellResolution: 1.201→1.232 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.202 256
Rwork0.195 4791
Refinement
*PLUS
Highest resolution: 1.2 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.219 / Rfactor Rwork: 0.19
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_deg1.8
LS refinement shell
*PLUS
Highest resolution: 1.2 Å / Lowest resolution: 1.22 Å

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