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- PDB-8px0: Structure of ribonuclease A, solved at wavelength 2.75 A -

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Basic information

Entry
Database: PDB / ID: 8px0
TitleStructure of ribonuclease A, solved at wavelength 2.75 A
ComponentsRibonuclease pancreatic
KeywordsMEMBRANE PROTEIN / RNAse A
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
L-URIDINE-5'-MONOPHOSPHATE / Ribonuclease pancreatic
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å
AuthorsEl Omari, K. / Duman, R. / Mykhaylyk, V. / Orr, C. / Romano, M. / Beis, K. / Wagner, A.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Diamond Light Source United Kingdom
CitationJournal: Commun Chem / Year: 2023
Title: Experimental phasing opportunities for macromolecular crystallography at very long wavelengths.
Authors: El Omari, K. / Duman, R. / Mykhaylyk, V. / Orr, C.M. / Latimer-Smith, M. / Winter, G. / Grama, V. / Qu, F. / Bountra, K. / Kwong, H.S. / Romano, M. / Reis, R.I. / Vogeley, L. / Vecchia, L. / ...Authors: El Omari, K. / Duman, R. / Mykhaylyk, V. / Orr, C.M. / Latimer-Smith, M. / Winter, G. / Grama, V. / Qu, F. / Bountra, K. / Kwong, H.S. / Romano, M. / Reis, R.I. / Vogeley, L. / Vecchia, L. / Owen, C.D. / Wittmann, S. / Renner, M. / Senda, M. / Matsugaki, N. / Kawano, Y. / Bowden, T.A. / Moraes, I. / Grimes, J.M. / Mancini, E.J. / Walsh, M.A. / Guzzo, C.R. / Owens, R.J. / Jones, E.Y. / Brown, D.G. / Stuart, D.I. / Beis, K. / Wagner, A.
History
DepositionJul 22, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 25, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)27,7413
Polymers27,4172
Non-polymers3241
Water2,504139
1
A: Ribonuclease pancreatic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,0332
Polymers13,7081
Non-polymers3241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ribonuclease pancreatic


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)99.980, 32.620, 72.490
Angle α, β, γ (deg.)90.00, 90.16, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-353-

HOH

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Components

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


Mass: 13708.326 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Gene: RNASE1, RNS1 / Production host: Escherichia coli (E. coli) / References: UniProt: P61823, pancreatic ribonuclease
#2: Chemical ChemComp-0U / L-URIDINE-5'-MONOPHOSPHATE


Type: L-RNA linking / Mass: 324.181 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C9H13N2O9P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 139 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.16 Å3/Da / Density % sol: 43.11 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 20 mM sodium citrate pH 5.5, 28 % PEG 4000

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I23 / Wavelength: 2.7552 Å
DetectorType: DECTRIS PILATUS 12M / Detector: PIXEL / Date: Aug 1, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 2.7552 Å / Relative weight: 1
ReflectionResolution: 1.8→50.01 Å / Num. obs: 17977 / % possible obs: 81.29 % / Redundancy: 17.5 % / CC1/2: 0.995 / Rmerge(I) obs: 0.09291 / Rpim(I) all: 0.02108 / Rrim(I) all: 0.09543 / Net I/σ(I): 24.67
Reflection shellResolution: 1.8→1.864 Å / Redundancy: 8.2 % / Rmerge(I) obs: 0.3414 / Mean I/σ(I) obs: 5.03 / Num. unique obs: 1412 / CC1/2: 0.915 / Rpim(I) all: 0.12 / Rrim(I) all: 0.3644 / % possible all: 65.04

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
XDSdata reduction
Aimlessdata scaling
HKL2Mapphasing
RefinementMethod to determine structure: SAD / Resolution: 1.8→50.01 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.94 / SU B: 6.065 / SU ML: 0.097 / Cross valid method: THROUGHOUT / ESU R: 0.188 / ESU R Free: 0.162 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23851 903 5 %RANDOM
Rwork0.20063 ---
obs0.20252 17074 81.34 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.321 Å2
Baniso -1Baniso -2Baniso -3
1--1.05 Å2-0 Å20.28 Å2
2--1.7 Å2-0 Å2
3----0.65 Å2
Refinement stepCycle: 1 / Resolution: 1.8→50.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1875 0 21 139 2035
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0121935
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161726
X-RAY DIFFRACTIONr_angle_refined_deg1.421.6772618
X-RAY DIFFRACTIONr_angle_other_deg0.4671.5884000
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8885239
X-RAY DIFFRACTIONr_dihedral_angle_2_deg5.84858
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.02110334
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.070.2290
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022244
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02432
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_it2.1222.326968
X-RAY DIFFRACTIONr_mcbond_other2.1192.326968
X-RAY DIFFRACTIONr_mcangle_it3.1834.1531203
X-RAY DIFFRACTIONr_mcangle_other3.1824.1531204
X-RAY DIFFRACTIONr_scbond_it3.0122.628967
X-RAY DIFFRACTIONr_scbond_other3.0112.629968
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.4444.6931416
X-RAY DIFFRACTIONr_long_range_B_refined6.24424.972126
X-RAY DIFFRACTIONr_long_range_B_other6.24623.782096
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.332 51 -
Rwork0.245 942 -
obs--62.14 %
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)
11.42920.415-0.98151.21280.0133.14450.0733-0.18010.02860.22440.01510.2448-0.05-0.0024-0.08840.13360.01020.03170.0470.01830.062218.0992-10.587562.3835
22.16970.21460.74770.9493-0.75632.7029-0.0581-0.14720.03460.21030.0136-0.0768-0.07070.04310.04450.12280.0171-0.01540.025-0.01040.010440.1116-11.453341.1873
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 201
2X-RAY DIFFRACTION2B1 - 124

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