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- PDB-8oqc: Dirhodium tetraacetate/ribonuclease A adduct in the P3221 space g... -

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Basic information

Entry
Database: PDB / ID: 8oqc
TitleDirhodium tetraacetate/ribonuclease A adduct in the P3221 space group (1 h soaking)
ComponentsRibonuclease pancreatic
KeywordsHYDROLASE / Metal/protein adduct / dirhodium tetraacettate / catalysis / porous material
Function / homology
Function and homology information


pancreatic ribonuclease / ribonuclease A activity / RNA nuclease activity / nucleic acid binding / defense response to Gram-positive bacterium / lyase activity / 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
tri-(mi2-acetato-(O, O')-diaqua-dirhodium(II, II) / FORMIC ACID / dirhodium (II) tetraacetate / Ribonuclease pancreatic
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsLoreto, D. / Merlino, A. / Maity, B. / Ueno, T.
Funding support Italy, Japan, 4items
OrganizationGrant numberCountry
Compagnia di San Paolo Foundation Italy
University of Naples Federico II Italy
Japan Society for the Promotion of Science (JSPS)22H00347 Japan
Japan Society for the Promotion of Science (JSPS)JP18H05421 Japan
CitationJournal: Inorg.Chem. / Year: 2023
Title: Cross-Linked Crystals of Dirhodium Tetraacetate/RNase A Adduct Can Be Used as Heterogeneous Catalysts.
Authors: Loreto, D. / Maity, B. / Morita, T. / Nakamura, H. / Merlino, A. / Ueno, T.
History
DepositionApr 12, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 14, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,6916
Polymers13,7081
Non-polymers9835
Water3,063170
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area340 Å2
ΔGint-14 kcal/mol
Surface area7190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.129, 67.129, 64.979
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-342-

HOH

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 13708.326 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: P61823, pancreatic ribonuclease

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Non-polymers , 5 types, 175 molecules

#2: Chemical ChemComp-D1O / tri-(mi2-acetato-(O, O')-diaqua-dirhodium(II, II)


Mass: 419.982 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O8Rh2
#3: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O2
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-VVU / dirhodium (II) tetraacetate / Rhodium(II) acetate


Mass: 446.019 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H16O8Rh2 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 170 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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: 3.08 Å3/Da / Density % sol: 60.11 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.2 / Details: 2.5 M NaCl 3.3 M HCOONa 0.1 M Acetate buffer / PH range: 4.7-5.2

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Data collection

DiffractionMean temperature: 93 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU PhotonJet-R / Wavelength: 1.5406 Å
DetectorType: RIGAKU HyPix-6000HE / Detector: PIXEL / Date: Aug 24, 2022
RadiationMonochromator: Cu filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5406 Å / Relative weight: 1
ReflectionResolution: 1.5→21.97 Å / Num. obs: 27554 / % possible obs: 100 % / Redundancy: 11.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.074 / Rpim(I) all: 0.022 / Net I/σ(I): 22.6
Reflection shellResolution: 1.5→1.53 Å / Rmerge(I) obs: 2.144 / Mean I/σ(I) obs: 0.9 / Num. unique obs: 1345 / CC1/2: 0.325 / Rpim(I) all: 0.875 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0405refinement
CrysalisProdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→21.97 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.954 / SU B: 1.573 / SU ML: 0.056 / Cross valid method: FREE R-VALUE / ESU R: 0.068 / ESU R Free: 0.073
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2151 1379 5.011 %
Rwork0.1804 26141 -
all0.182 --
obs-27520 99.949 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 20.74 Å2
Baniso -1Baniso -2Baniso -3
1--0.001 Å2-0 Å2-0 Å2
2---0.001 Å20 Å2
3---0.003 Å2
Refinement stepCycle: LAST / Resolution: 1.5→21.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms951 0 39 170 1160
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0121141
X-RAY DIFFRACTIONr_bond_other_d0.0010.016978
X-RAY DIFFRACTIONr_angle_refined_deg3.2271.711561
X-RAY DIFFRACTIONr_angle_other_deg0.5991.5922291
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7345146
X-RAY DIFFRACTIONr_dihedral_angle_2_deg8.41154
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.93210197
X-RAY DIFFRACTIONr_dihedral_angle_6_deg17.1111053
X-RAY DIFFRACTIONr_chiral_restr0.0870.2166
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.021408
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02252
X-RAY DIFFRACTIONr_nbd_refined0.2350.2260
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2150.2934
X-RAY DIFFRACTIONr_nbtor_refined0.180.2525
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0890.2585
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.30.2125
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0290.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1360.217
X-RAY DIFFRACTIONr_nbd_other0.1620.265
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2330.231
X-RAY DIFFRACTIONr_mcbond_it2.32.116551
X-RAY DIFFRACTIONr_mcbond_other2.2982.117552
X-RAY DIFFRACTIONr_mcangle_it3.4333.8705
X-RAY DIFFRACTIONr_mcangle_other3.4313.798706
X-RAY DIFFRACTIONr_scbond_it3.1772.424590
X-RAY DIFFRACTIONr_scbond_other3.2212.443550
X-RAY DIFFRACTIONr_scangle_it4.9164.356858
X-RAY DIFFRACTIONr_scangle_other5.0074.367822
X-RAY DIFFRACTIONr_lrange_it6.99525.4911380
X-RAY DIFFRACTIONr_lrange_other6.54123.051285
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.539-1.5810.291070.2731818X-RAY DIFFRACTION100
1.626-1.6760.246980.2441759X-RAY DIFFRACTION100
1.676-1.7310.261890.2121692X-RAY DIFFRACTION100
1.731-1.7910.253790.2011632X-RAY DIFFRACTION100
1.791-1.8580.24900.1951606X-RAY DIFFRACTION100
1.858-1.9330.242730.2011532X-RAY DIFFRACTION100
1.933-2.0190.215900.1761472X-RAY DIFFRACTION100
2.019-2.1160.2540.1691420X-RAY DIFFRACTION100
2.116-2.230.198640.1631374X-RAY DIFFRACTION100
2.23-2.3630.174700.1681247X-RAY DIFFRACTION100
2.363-2.5250.23630.1641230X-RAY DIFFRACTION100
2.525-2.7240.211620.1721117X-RAY DIFFRACTION100
2.724-2.9790.241550.1911043X-RAY DIFFRACTION100
2.979-3.3230.194560.178949X-RAY DIFFRACTION100
3.323-3.8230.192380.151846X-RAY DIFFRACTION99.7743
3.823-4.6470.197450.125725X-RAY DIFFRACTION99.8703
4.647-6.430.178440.165571X-RAY DIFFRACTION100

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