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- PDB-3i6j: Ribonuclease A by Classical hanging drop method after high X-Ray ... -

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Basic information

Entry
Database: PDB / ID: 3i6j
TitleRibonuclease A by Classical hanging drop method after high X-Ray dose on ESRF ID14-2 beamline
ComponentsRibonuclease pancreatic
KeywordsHYDROLASE / Ribonuclease A / Disulfide bond / Endonuclease / Glycation / Glycoprotein / Nuclease / Secreted
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
Ribonuclease pancreatic
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.3 Å
AuthorsPechkova, E. / Tripathi, S.K. / Ravelli, R. / McSweeney, S. / Nicolini, C.
CitationJournal: To be Published
Title: Atomic structure and radiation resistance of langmuir-blodgett protein crystals
Authors: Pechkova, E. / McSweeney, S. / Nicolini, C.
History
DepositionJul 7, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 7, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Dec 25, 2019Group: Data collection / Category: reflns_shell
Item: _reflns_shell.Rmerge_I_obs / _reflns_shell.pdbx_Rsym_value
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

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Assembly

Deposited unit
A: Ribonuclease pancreatic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,7442
Polymers13,7081
Non-polymers351
Water3,153175
1
A: Ribonuclease pancreatic
hetero molecules

A: Ribonuclease pancreatic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,4884
Polymers27,4172
Non-polymers712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area2370 Å2
ΔGint-29 kcal/mol
Surface area12110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.362, 64.362, 63.745
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-286-

HOH

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Components

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


Mass: 13708.326 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / Tissue: Pancreas / References: UniProt: P61823, EC: 3.1.27.5
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 175 / 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: 2.78 Å3/Da / Density % sol: 55.76 % / Mosaicity: 0.43 °
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 1.75M ammonium sulphate, 2.0M Sodium Chloride, 100mM Na-acetate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 1.3 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: May 14, 2007 / Details: mirror
RadiationMonochromator: Diamond (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.3 Å / Relative weight: 1
ReflectionResolution: 1.3→55.739 Å / Num. obs: 37998 / % possible obs: 100 % / Redundancy: 5.3 % / Rmerge(I) obs: 0.095 / Rsym value: 0.095 / Net I/σ(I): 12.3
Reflection shellResolution: 1.3→1.37 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.14 / Mean I/σ(I) obs: 0.5 / Num. measured all: 28846 / Num. unique all: 5472 / Rsym value: 0.144 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.2.25data scaling
REFMACrefinement
PDB_EXTRACT3.005data extraction
ADSCQuantumdata collection
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2BLP

2blp


Resolution: 1.3→41.96 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.947 / WRfactor Rfree: 0.241 / WRfactor Rwork: 0.204 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.862 / SU B: 1.743 / SU ML: 0.038 / SU R Cruickshank DPI: 0.057 / SU Rfree: 0.055 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.057 / ESU R Free: 0.055 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.234 1881 5 %RANDOM
Rwork0.209 ---
obs0.21 37692 99.27 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 51.19 Å2 / Biso mean: 15.974 Å2 / Biso min: 6.29 Å2
Baniso -1Baniso -2Baniso -3
1-0.2 Å20.1 Å20 Å2
2--0.2 Å20 Å2
3----0.3 Å2
Refinement stepCycle: LAST / Resolution: 1.3→41.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms951 0 1 175 1127
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.021975
X-RAY DIFFRACTIONr_angle_refined_deg1.1021.9251321
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4115125
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.05225.22744
X-RAY DIFFRACTIONr_dihedral_angle_3_deg9.67915169
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.69154
X-RAY DIFFRACTIONr_chiral_restr0.0740.2146
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02737
X-RAY DIFFRACTIONr_nbd_refined0.2060.3417
X-RAY DIFFRACTIONr_nbtor_refined0.3080.5680
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1610.5203
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2380.332
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.170.527
X-RAY DIFFRACTIONr_mcbond_it1.3792634
X-RAY DIFFRACTIONr_mcangle_it2.15131010
X-RAY DIFFRACTIONr_scbond_it1.4682374
X-RAY DIFFRACTIONr_scangle_it2.0853310
LS refinement shellResolution: 1.3→1.334 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.481 138 -
Rwork0.408 2418 -
all-2556 -
obs--92.47 %

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