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- PDB-7bfl: X-ray structure of SS-RNase-2 des116-120 -

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Basic information

Entry
Database: PDB / ID: 7bfl
TitleX-ray structure of SS-RNase-2 des116-120
ComponentsAngiogenin-1
KeywordsHYDROLASE / RNase / deletion mutant / 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: 2.88 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
C: Angiogenin-1
D: Angiogenin-1


Theoretical massNumber of molelcules
Total (without water)53,7824
Polymers53,7824
Non-polymers00
Water68538
1
A: Angiogenin-1


Theoretical massNumber of molelcules
Total (without water)13,4451
Polymers13,4451
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Angiogenin-1


Theoretical massNumber of molelcules
Total (without water)13,4451
Polymers13,4451
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Angiogenin-1


Theoretical massNumber of molelcules
Total (without water)13,4451
Polymers13,4451
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Angiogenin-1


Theoretical massNumber of molelcules
Total (without water)13,4451
Polymers13,4451
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)110.070, 93.070, 66.780
Angle α, β, γ (deg.)90.000, 117.190, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Refine code: _

Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111GLNGLNTHRTHRAA4 - 1185 - 119
211GLNGLNTHRTHRBB4 - 1185 - 119
122ASNASNTHRTHRAA3 - 1184 - 119
222ASNASNTHRTHRCC3 - 1184 - 119
133ASNASNGLYGLYAA3 - 1164 - 117
233ASNASNGLYGLYDD3 - 1164 - 117
144GLNGLNILEILEBB4 - 1175 - 118
244GLNGLNILEILECC4 - 1175 - 118
155GLNGLNILEILEBB4 - 1175 - 118
255GLNGLNILEILEDD4 - 1175 - 118
166ASNASNILEILECC3 - 1174 - 118
266ASNASNILEILEDD3 - 1174 - 118

NCS ensembles :
ID
1
2
3
4
5
6

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Components

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


Mass: 13445.399 Da / Num. of mol.: 4 / Mutation: des116-120
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.: 38 / 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: 2.83 Å3/Da / Density % sol: 56.55 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 25% w/v PEG 3350, 0.2 M sodium chloride and 0.1 M Bis-Tris pH 6.5

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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: Jul 6, 2020
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.88→70 Å / Num. obs: 13043 / % possible obs: 96.2 % / Redundancy: 3.4 % / CC1/2: 0.889 / Net I/σ(I): 3.4
Reflection shellResolution: 2.88→3.06 Å / Mean I/σ(I) obs: 1.2 / Num. unique obs: 1832 / CC1/2: 0.411

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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: 7BFK

7bfk


Resolution: 2.88→67.46 Å / Cor.coef. Fo:Fc: 0.874 / Cor.coef. Fo:Fc free: 0.806 / SU B: 27.65 / SU ML: 0.5 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.466 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.3076 705 5.2 %RANDOM
Rwork0.2588 ---
obs0.2613 12745 98.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 142.06 Å2 / Biso mean: 49.462 Å2 / Biso min: 3.34 Å2
Baniso -1Baniso -2Baniso -3
1--0.09 Å20 Å20.09 Å2
2--0.11 Å2-0 Å2
3----0.07 Å2
Refinement stepCycle: final / Resolution: 2.88→67.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3334 0 0 38 3372
Biso mean---28.85 -
Num. residues----442
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0133401
X-RAY DIFFRACTIONr_bond_other_d0.0020.0173211
X-RAY DIFFRACTIONr_angle_refined_deg1.1431.6434593
X-RAY DIFFRACTIONr_angle_other_deg1.0791.597436
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6835434
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.95326.277137
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.23815600
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.171151
X-RAY DIFFRACTIONr_chiral_restr0.0290.2468
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.023849
X-RAY DIFFRACTIONr_gen_planes_other00.02705
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A28290.13
12B28290.13
21A29130.12
22C29130.12
31A29130.12
32D29130.12
41B28320.12
42C28320.12
51B28700.11
52D28700.11
61C28540.11
62D28540.11
LS refinement shellResolution: 2.884→2.959 Å /
Num. reflection% reflection
Rwork885 -
obs-94.73 %

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