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- PDB-3dxh: Ribonuclease A uridine 5' diphosphate complex -

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Basic information

Entry
Database: PDB / ID: 3dxh
TitleRibonuclease A uridine 5' diphosphate complex
ComponentsRibonuclease pancreatic
KeywordsHYDROLASE / RIBONUCLEASE / ENDONUCLEASE / NUCLEOTIDE INHIBITOR / Glycation / Glycoprotein / Nuclease / Secreted
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
URIDINE-5'-DIPHOSPHATE / Ribonuclease pancreatic
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.4 Å
AuthorsTsirkone, V.G. / Dossi, K. / Leonidas, D.D. / Zographos, S.E. / Oikonomakos, N.G. / Kontou, M.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2009
Title: Inhibitor design to Ribonuclease A: The binding of two 5'phosphate uridine analogues
Authors: Tsirkone, V.G. / Dossi, K. / Drakou, C. / Zographos, S.E. / Kontou, M. / Leonidas, D.D.
History
DepositionJul 24, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 16, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: 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 / 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 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)29,0336
Polymers27,4172
Non-polymers1,6174
Water6,612367
1
A: Ribonuclease pancreatic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,5173
Polymers13,7081
Non-polymers8082
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ribonuclease pancreatic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,5173
Polymers13,7081
Non-polymers8082
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)100.003, 32.337, 72.299
Angle α, β, γ (deg.)90.00, 90.72, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-300-

HOH

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Components

#1: Protein Ribonuclease pancreatic / Ribonuclease A / RNase 1 / RNase A


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


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C9H14N2O12P2 / Comment: UDP*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 367 / 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: 2.13 Å3/Da / Density % sol: 42.3 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: PEG 4000, sodium citrate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX10.1 / Wavelength: 1.0448 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Nov 17, 2007
RadiationMonochromator: crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0448 Å / Relative weight: 1
ReflectionResolution: 1.4→30 Å / Num. all: 45026 / Num. obs: 42757 / % possible obs: 97.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 2.9 % / Biso Wilson estimate: 14.5 Å2 / Rsym value: 0.044 / Net I/σ(I): 29
Reflection shellResolution: 1.4→1.42 Å / Redundancy: 2.9 % / Mean I/σ(I) obs: 8.2 / Num. unique all: 2290 / Rsym value: 0.111 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MAR345data collection
DENZOdata reduction
SCALEPACKdata scaling
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: pdb entry 2G8Q

2g8q


Resolution: 1.4→30 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.927 / SU B: 2.152 / SU ML: 0.04 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.09 / ESU R Free: 0.076 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22497 2266 5 %RANDOM
Rwork0.18791 ---
obs0.18976 42757 97.72 %-
all-45026 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.566 Å2
Baniso -1Baniso -2Baniso -3
1--0.35 Å20 Å20.04 Å2
2--0.34 Å20 Å2
3---0.01 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.076 Å0.09 Å
Refinement stepCycle: LAST / Resolution: 1.4→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1910 0 100 367 2377
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0212056
X-RAY DIFFRACTIONr_angle_refined_deg1.411.9862805
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9045250
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.33425.22788
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.53715339
X-RAY DIFFRACTIONr_dihedral_angle_4_deg7.989158
X-RAY DIFFRACTIONr_chiral_restr0.0810.2309
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021510
X-RAY DIFFRACTIONr_nbd_refined0.1930.2955
X-RAY DIFFRACTIONr_nbtor_refined0.2970.21418
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1550.2277
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2340.272
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.20.277
X-RAY DIFFRACTIONr_mcbond_it1.1491.51272
X-RAY DIFFRACTIONr_mcangle_it1.78722023
X-RAY DIFFRACTIONr_scbond_it2.4073873
X-RAY DIFFRACTIONr_scangle_it3.444.5780
X-RAY DIFFRACTIONr_rigid_bond_restr1.38132145
X-RAY DIFFRACTIONr_sphericity_free4.4093367
X-RAY DIFFRACTIONr_sphericity_bonded4.16732010
LS refinement shellResolution: 1.4→1.436 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.27 166 -
Rwork0.186 3178 -
obs--99.17 %

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