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- PDB-5ogh: Structure of RNase A at high resolution (1.16 A) in complex with ... -

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Basic information

Entry
Database: PDB / ID: 5ogh
TitleStructure of RNase A at high resolution (1.16 A) in complex with 3'-CMP and sulphate ions
ComponentsRibonuclease pancreaticPancreatic ribonuclease family
KeywordsHYDROLASE / Ribonuclease A / 3'-CMP / RNase A / mononucleotide inhibitor / high resolution
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
P-30 Protein / Ribonuclease A-like domain / Pancreatic ribonuclease / Ribonuclease A, active site / Ribonuclease A-domain / Ribonuclease A-like domain superfamily / Pancreatic ribonuclease / Pancreatic ribonuclease family signature. / Pancreatic ribonuclease / Roll / Alpha Beta
Similarity search - Domain/homology
CYTIDINE-3'-MONOPHOSPHATE / Ribonuclease pancreatic
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.16 Å
AuthorsBlanco, J.A. / Prats-Ejarque, G. / Salazar, V.A. / Moussaoui, M. / Boix, E.
Funding support Spain, 2items
OrganizationGrant numberCountry
MINECOSAF2015-66007-P Spain
Generalitat de Catalunya2014 SGR 728 Spain
CitationJournal: Biochim Biophys Acta Gen Subj / Year: 2019
Title: Characterization of an RNase with two catalytic centers. Human RNase6 catalytic and phosphate-binding site arrangement favors the endonuclease cleavage of polymeric substrates.
Authors: Prats-Ejarque, G. / Blanco, J.A. / Salazar, V.A. / Nogues, V.M. / Moussaoui, M. / Boix, E.
History
DepositionJul 13, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 1, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 24, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Sep 11, 2019Group: Data collection / Database references / Category: citation / Item: _citation.year
Revision 1.3Jan 17, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ribonuclease pancreatic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,67411
Polymers13,7081
Non-polymers96610
Water3,225179
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1780 Å2
ΔGint-69 kcal/mol
Surface area7130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.060, 64.060, 64.058
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-461-

HOH

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 13708.326 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Organ: Pancreas / Tissue: PancreaticPancreas / References: UniProt: P61823, EC: 3.1.27.5

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Non-polymers , 5 types, 189 molecules

#2: Chemical ChemComp-C3P / CYTIDINE-3'-MONOPHOSPHATE / Cytidine monophosphate


Mass: 323.197 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H14N3O8P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 179 / 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: 2.78 Å3/Da / Density % sol: 55.76 % / Description: Hexagonal
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.54 M ammonium sulphate, 1.25 M sodium chloride, 0.1 M sodium acetate pH 6.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 14, 2014
Details: VERTICAL FOCUSING MIRROR (VFM) AND A HORIZONTAL FOCUSING MIRROR (HFM), MANUFACTURED BY IRELEC
RadiationMonochromator: CHANNEL-CUT DOUBLE CRYSTAL MONOCHROMATOR (CINEL), CRYOCOOLED, 6MM GAP
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.16→28.65 Å / Num. obs: 52994 / % possible obs: 100 % / Redundancy: 10.65 % / Biso Wilson estimate: 14.4 Å2 / Rmerge(I) obs: 0.046 / Net I/σ(I): 20.9
Reflection shellResolution: 1.16→1.22 Å / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 3.6 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1KF3

1kf3


Resolution: 1.16→28.648 Å / SU ML: 0.08 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 10.73
RfactorNum. reflection% reflection
Rfree0.1354 2692 5.08 %
Rwork0.1206 --
obs0.1213 52947 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 17.13 Å2
Refinement stepCycle: LAST / Resolution: 1.16→28.648 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms951 0 54 179 1184
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011145
X-RAY DIFFRACTIONf_angle_d1.491573
X-RAY DIFFRACTIONf_dihedral_angle_d18.529453
X-RAY DIFFRACTIONf_chiral_restr0.086175
X-RAY DIFFRACTIONf_plane_restr0.009202
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.16-1.18110.18931330.16352594X-RAY DIFFRACTION100
1.1811-1.20380.16491350.14582644X-RAY DIFFRACTION100
1.2038-1.22840.18681420.14212627X-RAY DIFFRACTION100
1.2284-1.25510.15871580.13082620X-RAY DIFFRACTION100
1.2551-1.28430.13671420.12572594X-RAY DIFFRACTION100
1.2843-1.31640.15541550.11312604X-RAY DIFFRACTION100
1.3164-1.3520.11861640.10692623X-RAY DIFFRACTION100
1.352-1.39180.14181210.10632624X-RAY DIFFRACTION100
1.3918-1.43670.13231390.10242627X-RAY DIFFRACTION100
1.4367-1.48810.12531290.12630X-RAY DIFFRACTION100
1.4881-1.54770.1121290.09442631X-RAY DIFFRACTION100
1.5477-1.61810.10671350.08642645X-RAY DIFFRACTION100
1.6181-1.70340.10731550.08922623X-RAY DIFFRACTION100
1.7034-1.81010.09631540.09552645X-RAY DIFFRACTION100
1.8101-1.94980.12011220.09872678X-RAY DIFFRACTION100
1.9498-2.1460.10971700.10122630X-RAY DIFFRACTION100
2.146-2.45640.13111160.11142713X-RAY DIFFRACTION100
2.4564-3.09420.13711510.14092682X-RAY DIFFRACTION100
3.0942-28.640.16741420.14352821X-RAY DIFFRACTION100

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