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- PDB-1jn4: The Crystal Structure of Ribonuclease A in complex with 2'-deoxyu... -

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Basic information

Entry
Database: PDB / ID: 1jn4
TitleThe Crystal Structure of Ribonuclease A in complex with 2'-deoxyuridine 3'-pyrophosphate (P'-5') adenosine
ComponentsPancreatic Ribonuclease A
KeywordsHYDROLASE / RIBONUCLEASE / ENDONUCLEASE / NUCLEOTIDE INHIBITOR
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-139 / Ribonuclease pancreatic
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsJardine, A.M. / Leonidas, D.D. / Jenkins, J.L. / Park, C. / Raines, R.T. / Acharya, K.R. / Shapiro, R.
CitationJournal: Biochemistry / Year: 2001
Title: Cleavage of 3',5'-Pyrophosphate-Linked Dinucleotides by Ribonuclease A and Angiogenin
Authors: Jardine, A.M. / Leonidas, D.D. / Jenkins, J.L. / Park, C. / Raines, R.T. / Acharya, K.R. / Shapiro, R.
History
DepositionJul 23, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 3, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Feb 7, 2018Group: Experimental preparation / Category: exptl_crystal_grow
Item: _exptl_crystal_grow.pdbx_details / _exptl_crystal_grow.temp
Revision 1.5Aug 16, 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)28,0543
Polymers27,4172
Non-polymers6371
Water4,774265
1
A: Pancreatic Ribonuclease A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,3462
Polymers13,7081
Non-polymers6371
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Pancreatic Ribonuclease A


Theoretical massNumber of molelcules
Total (without water)13,7081
Polymers13,7081
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)99.822, 32.291, 72.061
Angle α, β, γ (deg.)90.00, 90.04, 90.00
Int Tables number5
Cell settingmonoclinic
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-1016-

HOH

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Components

#1: Protein Pancreatic Ribonuclease A / E.C.3.1.27.5 / RNASE 1 / RNASE A


Mass: 13708.326 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Organ: pankreas / References: UniProt: P61823, EC: 3.1.27.5
#2: Chemical ChemComp-139 / ADENOSINE-5'-[TRIHYDROGEN DIPHOSPHATE] P'-3'-ESTER WITH 2'-DEOXYURIDINE


Mass: 637.388 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H25N7O14P2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 265 / 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: 2.12 Å3/Da / Density % sol: 41.91 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: PEG 4000, sodium citrate, pH 5.5, VAPOR DIFFUSION, HANGING DROP at 289K
Crystal grow
*PLUS
Temperature: 16 ℃ / 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: ROTATING ANODE / Type: ENRAF-NONIUS / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 22, 1998
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→30 Å / Num. all: 18095 / Num. obs: 18095 / % possible obs: 84.5 % / Observed criterion σ(I): -3 / Redundancy: 2.3 % / Biso Wilson estimate: 21.7 Å2 / Rsym value: 0.086
Reflection shellResolution: 1.8→1.91 Å / Rsym value: 0.262 / % possible all: 80.8
Reflection
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 30 Å / Num. measured all: 41852 / Rmerge(I) obs: 0.086
Reflection shell
*PLUS
% possible obs: 80.8 % / Rmerge(I) obs: 0.262

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Processing

Software
NameVersionClassification
XDSdata scaling
AUTOMARdata reduction
AMoREphasing
X-PLOR3.851refinement
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1afu

1afu


Resolution: 1.8→30 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.295 868 4.8 %RANDOM
Rwork0.225 ---
all0.2251 18095 --
obs0.2251 18095 84.5 %-
Displacement parametersBiso mean: 26.3 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.3 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.33 Å0.3 Å
Refinement stepCycle: LAST / Resolution: 1.8→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1902 0 42 265 2209
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.009
X-RAY DIFFRACTIONx_angle_deg1.4
X-RAY DIFFRACTIONx_dihedral_angle_d27
X-RAY DIFFRACTIONx_improper_angle_d0.88
X-RAY DIFFRACTIONx_mcbond_it1.671.5
X-RAY DIFFRACTIONx_mcangle_it2.622
X-RAY DIFFRACTIONx_scbond_it2.632
X-RAY DIFFRACTIONx_scangle_it3.942.5
LS refinement shellResolution: 1.8→1.91 Å / Rfactor Rfree error: 0.035 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.395 127 4.8 %
Rwork0.366 2506 -
obs--74.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMTOPHCSDX.TOP
X-RAY DIFFRACTION2PARAMTOP
X-RAY DIFFRACTION3LIG.PARAMLIG.TOP
Refinement
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 30 Å / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg27
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.88

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