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- PDB-5d6u: X-ray crystal structure of ribonuclease A determined for the real... -

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Basic information

Entry
Database: PDB / ID: 5d6u
TitleX-ray crystal structure of ribonuclease A determined for the real space D/H contrast method
ComponentsRibonuclease pancreatic
KeywordsHYDROLASE / Ribonuclease A / D/H contrast
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
ISOPROPYL ALCOHOL / Ribonuclease pancreatic
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.52 Å
AuthorsChatake, T. / Fujiwara, S.
Funding support Japan, 1items
OrganizationGrant numberCountry
JSPS KAKENHI23770176 Japan
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2016
Title: A technique for determining the deuterium/hydrogen contrast map in neutron macromolecular crystallography
Authors: Chatake, T. / Fujiwara, S.
History
DepositionAug 13, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 6, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 19, 2020Group: Data collection / Derived calculations / Category: diffrn_source / pdbx_struct_oper_list
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Oct 23, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)13,7682
Polymers13,7081
Non-polymers601
Water1,69394
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area230 Å2
ΔGint4 kcal/mol
Surface area6940 Å2
Unit cell
Length a, b, c (Å)30.340, 38.369, 53.188
Angle α, β, γ (deg.)90.00, 105.75, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#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 (cattle) / Organ: Pancreas / References: UniProt: P61823, EC: 3.1.27.5
#2: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 94 / Source method: isolated from a natural source / Formula: H2O
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: 2.17 Å3/Da / Density % sol: 43.41 % / Description: H2O-solvent crystal of ribonuclease A
Crystal growTemperature: 293 K / Method: liquid diffusion / pH: 5.8
Details: 20 mg/mL ribonuclease A, 0.05 M sodium acetate, 50% 2-propanol

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 23, 2012
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.52→16.9 Å / Num. obs: 16748 / % possible obs: 91.7 % / Redundancy: 7.5 % / Rmerge(I) obs: 0.058 / Net I/σ(I): 43.3
Reflection shellResolution: 1.52→1.57 Å / Redundancy: 7.6 % / Rmerge(I) obs: 0.136 / Mean I/σ(I) obs: 20.8 / % possible all: 95.2

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Processing

Software
NameVersionClassification
PHENIX1.6.4_486refinement
HKL-2000data reduction
HKL-2000data scaling
AMoREphasing
RefinementResolution: 1.52→16.861 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 11.84 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1557 858 5.14 %
Rwork0.1305 --
obs0.1318 16708 91.49 %
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 51.799 Å2 / ksol: 0.368 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.0204 Å20 Å21.2671 Å2
2--1.2624 Å20 Å2
3----1.2828 Å2
Refinement stepCycle: LAST / Resolution: 1.52→16.861 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms951 0 4 94 1049
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006999
X-RAY DIFFRACTIONf_angle_d1.0081342
X-RAY DIFFRACTIONf_dihedral_angle_d10.652373
X-RAY DIFFRACTIONf_chiral_restr0.068148
X-RAY DIFFRACTIONf_plane_restr0.005176
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5202-1.61540.17261420.12892678X-RAY DIFFRACTION94
1.6154-1.740.12211400.10642707X-RAY DIFFRACTION94
1.74-1.91490.13331530.09432704X-RAY DIFFRACTION94
1.9149-2.19140.1451480.10682723X-RAY DIFFRACTION95
2.1914-2.7590.15781450.13052750X-RAY DIFFRACTION94
2.759-16.8620.17211300.16032288X-RAY DIFFRACTION78

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