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- PDB-6xw0: X-ray structure obtained upon reaction of dirhodium tetraacetate ... -

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Basic information

Entry
Database: PDB / ID: 6xw0
TitleX-ray structure obtained upon reaction of dirhodium tetraacetate with RNase A (low 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: 1.8 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 / software / 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 / _software.name / _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)28,94822
Polymers27,4172
Non-polymers1,53220
Water5,729318
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)14,3569
Polymers13,7081
Non-polymers6488
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)99.660, 32.440, 68.020
Angle α, β, γ (deg.)90.000, 92.920, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11AAA-306-

HOH

21AAA-429-

HOH

31AAA-460-

HOH

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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-RH3 / RHODIUM(III) ION


Mass: 102.906 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Rh / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 318 / 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 Å3/Da / Density % sol: 38.58 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.1 / Details: 22% PEG4K 10 mM sodium citrate 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: 1.8→67.93 Å / Num. obs: 19347 / % possible obs: 94.9 % / Redundancy: 4.6 % / Biso Wilson estimate: 16.6 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.099 / Rpim(I) all: 0.051 / Rrim(I) all: 0.112 / Net I/σ(I): 8.8
Reflection shellResolution: 1.8→1.84 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.256 / Mean I/σ(I) obs: 3.4 / Num. unique obs: 1111 / CC1/2: 0.854 / Rpim(I) all: 0.14 / Rrim(I) all: 0.294 / % possible all: 92.9

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Processing

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

4ot4


Resolution: 1.8→67.93 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.927 / SU B: 3.113 / SU ML: 0.096 / Cross valid method: NONE / ESU R: 0.159 / ESU R Free: 0.145
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2185 993 5.14 %
Rwork0.1694 --
all0.172 --
obs-19319 94.12 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 23.197 Å2
Baniso -1Baniso -2Baniso -3
1--1.082 Å20 Å20.356 Å2
2--1.19 Å2-0 Å2
3----0.144 Å2
Refinement stepCycle: LAST / Resolution: 1.8→67.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1867 0 56 318 2241
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0132014
X-RAY DIFFRACTIONr_bond_other_d0.0010.0181729
X-RAY DIFFRACTIONr_angle_refined_deg1.5981.6572722
X-RAY DIFFRACTIONr_angle_other_deg1.421.584059
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2795255
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.70623.922102
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.51515345
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.947159
X-RAY DIFFRACTIONr_chiral_restr0.0770.2269
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022329
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02386
X-RAY DIFFRACTIONr_nbd_refined0.1990.2441
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1820.21545
X-RAY DIFFRACTIONr_nbtor_refined0.1570.2950
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.080.2859
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2090.2218
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1210.22
X-RAY DIFFRACTIONr_metal_ion_refined0.270.212
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2740.222
X-RAY DIFFRACTIONr_nbd_other0.1650.268
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1980.237
X-RAY DIFFRACTIONr_mcbond_it2.1712.2361017
X-RAY DIFFRACTIONr_mcbond_other2.1382.2271004
X-RAY DIFFRACTIONr_mcangle_it3.3083.3251265
X-RAY DIFFRACTIONr_mcangle_other3.3083.3261266
X-RAY DIFFRACTIONr_scbond_it2.6472.476997
X-RAY DIFFRACTIONr_scbond_other2.6462.476998
X-RAY DIFFRACTIONr_scangle_it4.1053.5861457
X-RAY DIFFRACTIONr_scangle_other4.1043.5861458
X-RAY DIFFRACTIONr_lrange_it6.45128.312341
X-RAY DIFFRACTIONr_lrange_other6.43728.3062340
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.8470.264650.241281X-RAY DIFFRACTION92.1918
1.847-1.8970.243810.2161283X-RAY DIFFRACTION92.1622
1.897-1.9520.236620.1981257X-RAY DIFFRACTION92.1733
1.952-2.0120.337570.1961202X-RAY DIFFRACTION91.298
2.012-2.0780.201620.1861163X-RAY DIFFRACTION91.4179
2.078-2.1510.245770.1841135X-RAY DIFFRACTION92.1673
2.151-2.2320.209640.1561081X-RAY DIFFRACTION93.5458
2.232-2.3230.209560.1561109X-RAY DIFFRACTION93.4242
2.323-2.4260.226430.1571046X-RAY DIFFRACTION95.1923
2.426-2.5450.161480.1461015X-RAY DIFFRACTION96.1991
2.545-2.6820.235610.157984X-RAY DIFFRACTION96.8489
2.682-2.8450.228500.178896X-RAY DIFFRACTION95.9432
2.845-3.0410.244490.168876X-RAY DIFFRACTION96.4546
3.041-3.2840.22370.158829X-RAY DIFFRACTION97.0852
3.284-3.5960.191480.149728X-RAY DIFFRACTION95.8025
3.596-4.0190.179310.146688X-RAY DIFFRACTION96.9003
4.019-4.6380.149400.133596X-RAY DIFFRACTION96.2178
4.638-5.6740.238290.159506X-RAY DIFFRACTION96.0503
5.674-7.9970.164180.222415X-RAY DIFFRACTION96.6518
7.997-67.930.357150.242236X-RAY DIFFRACTION94.0075

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