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- PDB-6xvx: X-ray structure obtained upon reaction of dirhodium tetraacetate ... -

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Basic information

Entry
Database: PDB / ID: 6xvx
TitleX-ray structure obtained upon reaction of dirhodium tetraacetate with RNase A (high resolution)
ComponentsRibonuclease pancreaticPancreatic ribonuclease family
KeywordsUNKNOWN FUNCTION / dirhodium / model protein / metalation
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
ACETATE ION / RHODIUM(III) ION / Ribonuclease pancreatic
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsMerlino, A. / Ferraro, G.
Funding support Italy, 1items
OrganizationGrant numberCountry
Italian Association for Cancer Research22578 Italy
CitationJournal: Dalton Trans / Year: 2020
Title: Protein interactions of dirhodium tetraacetate: a structural study.
Authors: Ferraro, G. / Pratesi, A. / Messori, L. / Merlino, A.
History
DepositionJan 22, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 19, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 4, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AAA: Ribonuclease pancreatic
BBB: Ribonuclease pancreatic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,24427
Polymers27,4172
Non-polymers1,82725
Water5,314295
1
AAA: Ribonuclease pancreatic
hetero molecules


  • defined by author
  • 14.6 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)14,59213
Polymers13,7081
Non-polymers88412
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
BBB: Ribonuclease pancreatic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,65114
Polymers13,7081
Non-polymers94313
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)100.430, 32.750, 72.690
Angle α, β, γ (deg.)90.000, 90.380, 90.000
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 13708.326 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P61823, pancreatic ribonuclease
#2: Chemical
ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical
ChemComp-RH3 / RHODIUM(III) ION


Mass: 102.906 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Rh / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 295 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.18 Å3/Da / Density % sol: 43.58 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.1 / Details: 22% PEG 4K 10 mM sodium citrate buffer pH 5.1

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 11.2C / Wavelength: 0.96 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 1, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96 Å / Relative weight: 1
ReflectionResolution: 1.4→72.69 Å / Num. obs: 43787 / % possible obs: 93.4 % / Redundancy: 2.6 % / Biso Wilson estimate: 12.6 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.066 / Rpim(I) all: 0.055 / Rrim(I) all: 0.08 / Net I/σ(I): 8.5
Reflection shellResolution: 1.4→1.42 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.259 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 2120 / CC1/2: 0.861 / Rpim(I) all: 0.196 / Rrim(I) all: 0.327 / % possible all: 91.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
MOSFLMdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ot4

4ot4


Resolution: 1.4→72.688 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.931 / SU B: 1.349 / SU ML: 0.054 / Cross valid method: NONE / ESU R: 0.075 / ESU R Free: 0.082
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2326 2317 5.295 %
Rwork0.1876 --
all0.19 --
obs-43756 92.735 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 20.561 Å2
Baniso -1Baniso -2Baniso -3
1--0.069 Å20 Å20.074 Å2
2--0.025 Å2-0 Å2
3---0.042 Å2
Refinement stepCycle: LAST / Resolution: 1.4→72.688 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1902 0 76 295 2273
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0132109
X-RAY DIFFRACTIONr_bond_other_d0.0010.0181795
X-RAY DIFFRACTIONr_angle_refined_deg1.7991.6552855
X-RAY DIFFRACTIONr_angle_other_deg1.5081.5774219
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4965272
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.28424.272103
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.29815357
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.41158
X-RAY DIFFRACTIONr_chiral_restr0.0810.2281
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.022476
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02400
X-RAY DIFFRACTIONr_nbd_refined0.2210.2513
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1890.21658
X-RAY DIFFRACTIONr_nbtor_refined0.1650.2983
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0830.2870
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1640.2192
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0670.22
X-RAY DIFFRACTIONr_metal_ion_refined0.4620.27
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2160.228
X-RAY DIFFRACTIONr_nbd_other0.190.272
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1760.258
X-RAY DIFFRACTIONr_mcbond_it2.1972.0411072
X-RAY DIFFRACTIONr_mcbond_other2.1742.0341054
X-RAY DIFFRACTIONr_mcangle_it3.4243.0411338
X-RAY DIFFRACTIONr_mcangle_other3.4233.0411339
X-RAY DIFFRACTIONr_scbond_it2.4252.2021036
X-RAY DIFFRACTIONr_scbond_other2.4242.2031037
X-RAY DIFFRACTIONr_scangle_it3.763.1951517
X-RAY DIFFRACTIONr_scangle_other3.7593.1961518
X-RAY DIFFRACTIONr_lrange_it6.4425.3332448
X-RAY DIFFRACTIONr_lrange_other6.30924.7252368
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
1.399-1.4350.2451750.24129660.24134640.8930.88890.67550.218
1.435-1.4750.2581630.22229080.22433600.8880.89591.39880.201
1.475-1.5170.2521800.22529270.22732690.8820.89895.04440.22
1.517-1.5640.2721500.24428380.24631990.8750.8993.40420.252
1.564-1.6150.2461790.21927920.2230690.9140.91396.80680.223
1.615-1.6720.2391670.21427010.21630080.9180.9295.34570.223
1.672-1.7350.281380.20125710.20428950.880.9293.57510.199
1.735-1.8060.2631340.20724630.20927900.920.92793.08240.224
1.806-1.8860.2311130.21324170.21426630.9230.9395.00560.233
1.886-1.9780.2071150.20422840.20425420.940.93294.37450.23
1.978-2.0850.2441160.18121190.18424440.920.94291.44840.207
2.085-2.2110.2151050.220310.223160.9250.93592.2280.248
2.211-2.3640.2091210.17718790.17921660.9340.94392.33610.208
2.364-2.5530.1921100.16517780.16720270.9490.95493.14260.19
2.553-2.7960.231980.1715980.17318900.9310.9589.73550.198
2.796-3.1260.205610.16814490.1716790.9420.95589.93450.203
3.126-3.6080.223880.15912980.16315220.9350.95791.06440.201
3.608-4.4170.205530.15810850.1612840.9490.96288.62930.205
4.417-6.2350.211290.1668510.16810050.9570.96687.56220.232
6.235-72.6880.533220.2394850.2485930.7930.9285.49750.299

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