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- PDB-7p4r: Ultra High Resolution X-ray Structure of Orthorhombic Bovine Panc... -

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Basic information

Entry
Database: PDB / ID: 7p4r
TitleUltra High Resolution X-ray Structure of Orthorhombic Bovine Pancreatic Ribonuclease at 100K
ComponentsRibonuclease pancreaticPancreatic ribonuclease family
KeywordsHYDROLASE / Nucleic acid / RNA / multiple conformations / water structure
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
Pancreatic ribonuclease / Ribonuclease A, active site / Ribonuclease A-domain / Ribonuclease A-like domain superfamily / Pancreatic ribonuclease / Pancreatic ribonuclease family signature. / Pancreatic ribonuclease
Similarity search - Domain/homology
ETHANOL / Ribonuclease pancreatic
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.85 Å
AuthorsLisgarten, D.R. / Palmer, R.A. / Cooper, J.B. / Naylor, C.E. / Howlin, B.J. / Lisgarten, J.N. / Najmudin, S. / Lobley, C.M.C.
Citation
Journal: BMC Chem / Year: 2023
Title: Ultra-high resolution X-ray structure of orthorhombic bovine pancreatic Ribonuclease A at 100K.
Authors: Lisgarten, D.R. / Palmer, R.A. / Cooper, J.B. / Naylor, C.E. / Talbert, R.C. / Howlin, B.J. / Lisgarten, J.N. / Konc, J. / Najmudin, S. / Lobley, C.M.C.
#1: Journal: Acta Crystallogr A / Year: 1989
Title: Segmented anisotropic refinement of bovine ribonuclease A by the application of the rigid-body TLS model.
Authors: Howlin, B. / Moss, D.S. / Harris, G.W.
History
DepositionJul 12, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 27, 2022Provider: repository / Type: Initial release
Revision 2.0Aug 16, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp_atom / chem_comp_bond / citation / citation_author / pdbx_validate_close_contact / struct_conn / struct_conn_type
Item: _atom_site.label_alt_id / _atom_site_anisotrop.pdbx_label_alt_id ..._atom_site.label_alt_id / _atom_site_anisotrop.pdbx_label_alt_id / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_validate_close_contact.label_alt_id_1
Revision 2.1Jan 31, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
AAA: Ribonuclease pancreatic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,88819
Polymers13,7081
Non-polymers1,17918
Water5,278293
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2330 Å2
ΔGint-62 kcal/mol
Surface area7790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.998, 45.697, 51.890
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Ribonuclease pancreatic / Pancreatic ribonuclease family / RNase 1 / RNase A


Mass: 13708.326 Da / Num. of mol.: 1 / Mutation: None
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Gene: RNASE1, RNS1 / Organ: Pancreas / Production host: Bos taurus (cattle) / References: UniProt: P61823, pancreatic ribonuclease
#2: Chemical
ChemComp-EOH / ETHANOL / Ethanol


Mass: 46.068 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C2H6O
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 293 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 1.87 Å3/Da / Density % sol: 34.3 %
Description: The Ribonuclease A crystals were long needles of the order of 0.5 mm long by about 0.05 mm by 0.05 mm.
Crystal growTemperature: 277 K / Method: evaporation / pH: 7
Details: 100mg of powdered Ribonuclease A in 1ml of distilled water dissolved in 2ml of ice cold absolute ethanol.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.77 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 1, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.77 Å / Relative weight: 1
ReflectionResolution: 0.85→51.89 Å / Num. obs: 87934 / % possible obs: 95.2 % / Redundancy: 6.2 % / Rmerge(I) obs: 0.076 / Rpim(I) all: 0.049 / Rrim(I) all: 0.091 / Net I/σ(I): 13.2
Reflection shellResolution: 0.85→0.86 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.697 / Mean I/σ(I) obs: 3.8 / Num. unique obs: 2925 / Rpim(I) all: 0.55 / Rrim(I) all: 0.893 / % possible all: 65.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
xia2data reduction
XDSdata reduction
xia2data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3rn3

3rn3


Resolution: 0.85→34.294 Å / Cor.coef. Fo:Fc: 0.982 / Cor.coef. Fo:Fc free: 0.977 / WRfactor Rfree: 0.122 / WRfactor Rwork: 0.106 / SU B: 0.399 / SU ML: 0.011 / Average fsc free: 0.9674 / Average fsc work: 0.9705 / Cross valid method: FREE R-VALUE / ESU R: 0.015 / ESU R Free: 0.016
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1291 4279 5.014 %
Rwork0.1123 81067 -
all0.113 --
obs-85346 92.225 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 7.596 Å2
Baniso -1Baniso -2Baniso -3
1-0.173 Å2-0 Å20 Å2
2--0.379 Å2-0 Å2
3----0.551 Å2
Refinement stepCycle: LAST / Resolution: 0.85→34.294 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms951 0 68 293 1312
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0131229
X-RAY DIFFRACTIONr_bond_other_d0.0020.0181185
X-RAY DIFFRACTIONr_angle_refined_deg2.4741.6661688
X-RAY DIFFRACTIONr_angle_other_deg1.681.6112766
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5035178
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.72224.51662
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.53715236
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.337155
X-RAY DIFFRACTIONr_chiral_restr0.1270.2167
X-RAY DIFFRACTIONr_gen_planes_refined0.0170.021429
X-RAY DIFFRACTIONr_gen_planes_other0.0060.02277
X-RAY DIFFRACTIONr_nbd_refined0.2630.2276
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2220.21065
X-RAY DIFFRACTIONr_nbtor_refined0.1890.2538
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.1070.2571
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.3310.2274
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.3010.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.3830.249
X-RAY DIFFRACTIONr_nbd_other0.3440.2152
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.3520.2104
X-RAY DIFFRACTIONr_mcbond_it0.9260.405565
X-RAY DIFFRACTIONr_mcbond_other0.9220.405564
X-RAY DIFFRACTIONr_mcangle_it1.2550.619718
X-RAY DIFFRACTIONr_mcangle_other1.2540.619719
X-RAY DIFFRACTIONr_scbond_it1.5820.594664
X-RAY DIFFRACTIONr_scbond_other1.450.577637
X-RAY DIFFRACTIONr_scangle_it1.7260.816941
X-RAY DIFFRACTIONr_scangle_other1.3480.774900
X-RAY DIFFRACTIONr_lrange_it5.4229.8291585
X-RAY DIFFRACTIONr_lrange_other3.2516.6331427
X-RAY DIFFRACTIONr_rigid_bond_restr5.28432414
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
0.85-0.8720.2831920.27339500.27367690.8240.85861.19070.243
0.872-0.8960.2382680.23148660.23166230.9130.91177.51770.202
0.896-0.9220.1772640.18353770.18364140.9530.94887.94820.156
0.922-0.950.1752700.15654460.15762010.9550.96192.17870.129
0.95-0.9810.153000.13653610.13760610.9650.96993.40040.114
0.981-1.0160.1282860.11652490.11758670.9740.97894.34120.098
1.016-1.0540.1132500.09950980.156280.9820.98495.02490.083
1.054-1.0970.12820.08749780.08754760.9850.98896.05550.074
1.097-1.1460.0992440.0848190.08152140.9870.9997.1040.069
1.146-1.2020.0872560.07446520.07550290.990.99297.5940.065
1.202-1.2670.0932400.07844530.07947830.990.99198.11830.07
1.267-1.3430.0982320.08342130.08445200.9880.98998.34070.076
1.343-1.4360.1062130.08240030.08342710.9850.98998.71220.076
1.436-1.5510.1052110.08437240.08539690.9860.98999.14340.08
1.551-1.6980.1091870.0934610.09136760.9860.98899.23830.089
1.698-1.8980.1211570.09731650.09833410.9830.98699.43130.1
1.898-2.1910.1251690.10128080.10229850.9820.98599.7320.108
2.191-2.6810.1411150.11424070.11525250.9770.98399.88120.126
2.681-3.7790.138880.13119120.13120070.980.9899.65120.155
3.779-34.2940.207550.16211250.16411820.9690.97499.83080.232

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