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- PDB-3ql2: Crystal Structure of Ribonuclease A Variant A4C/D83E/V118C -

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Basic information

Entry
Database: PDB / ID: 3ql2
TitleCrystal Structure of Ribonuclease A Variant A4C/D83E/V118C
ComponentsRibonuclease pancreatic
KeywordsHYDROLASE / Ribonuclease A / Disulfide Bond / Salt Bridge / Stability / Folding / Proteolysis / Site-Directed Mutagenesis
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: 1.49 Å
AuthorsArnold, U. / Schoepfel, M.
CitationJournal: Febs J. / Year: 2012
Title: Significant stabilization of ribonuclease A by additive effects
Authors: Arnold, U. / Schopfel, M.
History
DepositionFeb 2, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 29, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 13, 2012Group: Database references
Revision 1.2May 7, 2014Group: Database references
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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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)27,7094
Polymers27,5172
Non-polymers1922
Water4,486249
1
A: Ribonuclease pancreatic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,8542
Polymers13,7581
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ribonuclease pancreatic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,8542
Polymers13,7581
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)102.888, 30.694, 74.752
Angle α, β, γ (deg.)90.00, 93.15, 90.00
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 13758.430 Da / Num. of mol.: 2 / Mutation: A4C, D83E, V118C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / Gene: RNASE1, RNS1 / Production host: Escherichia coli (E. coli) / References: UniProt: P61823, EC: 3.1.27.5
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 249 / 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: 2.14 Å3/Da / Density % sol: 42.56 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.8
Details: 0.1M sodium acetate, 0.2M ammonium sulfate, 25% (w/v) PEG 4000, 10mM calcium chloride, pH 4.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 8, 2010
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 1.49→35.08 Å / Num. all: 38664 / Num. obs: 36486 / % possible obs: 94.4 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 22.686 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 15.23
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
1.49-1.530.8360.5021.893736284718890.64466.4
1.53-1.570.6380.3852.424605273121440.48678.5
1.57-1.620.4980.3123.075641271124520.39390.4
1.62-1.670.4040.2683.876653256025160.3398.3
1.67-1.720.3580.2324.596775257725340.28698.3
1.72-1.780.2620.1785.96514243924100.22198.8
1.78-1.850.220.1467.216372236723450.18199.1
1.85-1.920.1590.119.356253230422830.13699.1
1.92-2.010.1180.08511.645941215221370.10599.3
2.01-2.110.0890.06814.75681207920660.08499.4
2.11-2.220.0680.05417.85528201620030.06699.4
2.22-2.360.0550.04220.895267191118950.05299.2
2.36-2.520.0450.03624.474811175417370.04499
2.52-2.720.0380.03127.94572167216590.03999.2
2.72-2.980.0310.02830.644204154615260.03598.7
2.98-3.330.0240.02535.853748138913710.03198.7
3.33-3.850.020.02341.233339125212280.02898.1
3.85-4.710.0170.02143.962727103310110.02597.9
4.71-6.660.0170.0243.0321928388220.02598.1
6.660.0160.01843.6211584864580.02394.2

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 43.46 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å37.33 Å
Translation2.5 Å37.33 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER2.1.4phasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
MxCuBEdata collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7RSA

7rsa


Resolution: 1.49→31.01 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.946 / WRfactor Rfree: 0.2018 / WRfactor Rwork: 0.1634 / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.8727 / SU B: 3.166 / SU ML: 0.053 / SU R Cruickshank DPI: 0.0739 / SU Rfree: 0.0798 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.074 / ESU R Free: 0.08 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20913 1825 5 %RANDOM
Rwork0.16732 ---
all0.1694 38664 --
obs0.16939 34661 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 46.93 Å2 / Biso mean: 19.547 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1-0.28 Å20 Å2-0.72 Å2
2--0.99 Å20 Å2
3----1.35 Å2
Refinement stepCycle: LAST / Resolution: 1.49→31.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1904 0 10 249 2163
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.0211995
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.2441.9352715
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6395264
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.3625.22788
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.515349
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.671158
X-RAY DIFFRACTIONr_chiral_restr0.1480.2298
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.0211502
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2931.51269
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.02722063
X-RAY DIFFRACTIONr_scbond_it3.2843726
X-RAY DIFFRACTIONr_scangle_it5.2294.5643
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.49→1.529 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.305 95 -
Rwork0.249 1790 -
all-1885 -
obs--100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.70330.0403-0.10810.60970.35252.33460.0401-0.201-0.00130.087-0.00640.0390.04910.0474-0.03370.0611-0.00150.02860.0344-0.00260.195910.66612.4894.175
21.69560.05840.24310.52090.19271.61510.0173-0.30980.0873-0.03370.0203-0.05580.0653-0.0826-0.03760.0167-0.00320.03590.0771-0.01360.162730.99.74926.708
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 124
2X-RAY DIFFRACTION2B1 - 124

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