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- PDB-7bfk: X-ray structure of SS-RNase-2 -

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Basic information

Entry
Database: PDB / ID: 7bfk
TitleX-ray structure of SS-RNase-2
ComponentsAngiogenin-1
KeywordsHYDROLASE / RNase / auto-inhibition / Salmo salar / ancient ribonuclease
Function / homology
Function and homology information


endonuclease activity / nucleic acid binding
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
Biological speciesSalmo salar (Atlantic salmon)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.89 Å
AuthorsSica, F. / Russo Krauss, I. / Troisi, R.
CitationJournal: Int.J.Biol.Macromol. / Year: 2021
Title: The structural features of an ancient ribonuclease from Salmo salar reveal an intriguing case of auto-inhibition.
Authors: Sica, F. / Russo Krauss, I. / Troisi, R. / Bosso, A. / Culurciello, R. / Carluccio, C. / Trapani, M. / Merlino, A. / Mazzarella, L. / Pizzo, E.
History
DepositionJan 4, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 28, 2021Provider: repository / Type: Initial release
Revision 1.1May 5, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.name
Revision 1.2Jan 31, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Angiogenin-1
B: Angiogenin-1


Theoretical massNumber of molelcules
Total (without water)27,8902
Polymers27,8902
Non-polymers00
Water1,53185
1
A: Angiogenin-1


Theoretical massNumber of molelcules
Total (without water)13,9451
Polymers13,9451
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Angiogenin-1


Theoretical massNumber of molelcules
Total (without water)13,9451
Polymers13,9451
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)28.968, 70.747, 53.545
Angle α, β, γ (deg.)90.000, 90.930, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ASN / Beg label comp-ID: ASN / End auth comp-ID: ILE / End label comp-ID: ILE / Refine code: _ / Auth seq-ID: 3 - 122 / Label seq-ID: 4 - 123

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Angiogenin-1 / Angiogenin-1 precursor / SS-RNase-2


Mass: 13944.915 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmo salar (Atlantic salmon) / Gene: ANG1, ang1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B5XAZ0
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 85 / Source method: isolated from a natural source / Formula: H2O

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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: 1.97 Å3/Da / Density % sol: 37.56 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 32% w/v PEG 4000, 0.2 M sodium acetate trihydrate, 0.1 M Tris-HCl pH 7.4 and 1% v/v acetonitrile

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Dec 2, 2019
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.89→50 Å / Num. obs: 17350 / % possible obs: 99.4 % / Redundancy: 3 % / Rmerge(I) obs: 0.072 / Net I/σ(I): 15.2
Reflection shellResolution: 1.89→1.96 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.31 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 1684 / % possible all: 96.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2VQ8

2vq8


Resolution: 1.89→26.82 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.949 / SU B: 9.071 / SU ML: 0.118 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.169 / ESU R Free: 0.145 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2188 902 5.2 %RANDOM
Rwork0.184 ---
obs0.1859 16429 99.25 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 95.94 Å2 / Biso mean: 41.136 Å2 / Biso min: 21.93 Å2
Baniso -1Baniso -2Baniso -3
1--0.19 Å2-0 Å2-0.41 Å2
2--0.07 Å2-0 Å2
3---0.13 Å2
Refinement stepCycle: final / Resolution: 1.89→26.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1865 0 0 85 1950
Biso mean---45.54 -
Num. residues----246
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0131911
X-RAY DIFFRACTIONr_bond_other_d00.0171812
X-RAY DIFFRACTIONr_angle_refined_deg1.4491.6462583
X-RAY DIFFRACTIONr_angle_other_deg1.3021.5944198
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.5855246
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.61725.30183
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.09315345
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.769154
X-RAY DIFFRACTIONr_chiral_restr0.0590.2261
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022176
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02396
Refine LS restraints NCS

Ens-ID: 1 / Number: 3296 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.17 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.89→1.936 Å /
Num. reflection% reflection
Rwork1155 -
obs-94.12 %
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)
10.7541-0.42450.00091.2937-1.09121.2198-0.12210.03720.07460.13810.0986-0.0098-0.0945-0.08110.02360.0557-0.0136-0.0020.0625-0.00370.09633.8717.9630.236
20.21080.34360.24330.693-0.00233.3239-0.0326-0.03450.00270.00710.00070.05630.1655-0.07980.03180.1060.06530.05460.08310.00840.05836.255-8.30317.974
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 124
2X-RAY DIFFRACTION1A201 - 243
3X-RAY DIFFRACTION1B220 - 242
4X-RAY DIFFRACTION2B3 - 123
5X-RAY DIFFRACTION2B201 - 219

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