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- PDB-4zz4: Neutron crystal structure of ribonuclease A determined by the rea... -

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Basic information

Entry
Database: PDB / ID: 4zz4
TitleNeutron crystal structure of ribonuclease A determined by the real space D/H contrast method
ComponentsRibonuclease pancreaticPancreatic ribonuclease family
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
DEUTERATED WATER / ISOPROPYL ALCOHOL / Ribonuclease pancreatic
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodNEUTRON DIFFRACTION / NUCLEAR REACTOR / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.798 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
DepositionMay 22, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 6, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 28, 2018Group: Data collection / Derived calculations / Category: diffrn_source / pdbx_struct_oper_list
Item: _diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.pdbx_synchrotron_site ..._diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.pdbx_synchrotron_site / _diffrn_source.type / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)13,7682
Polymers13,7081
Non-polymers601
Water1,928107
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11140 Å2
ΔGint62 kcal/mol
Surface area7490 Å2
MethodPISA
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 / 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 / References: UniProt: P61823, EC: 3.1.27.5
#2: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL / Isopropyl alcohol


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


Mass: 18.015 Da / Num. of mol.: 107 / Source method: isolated from a natural source / Formula: D2O

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Experimental details

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Experiment

ExperimentMethod: NEUTRON DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.17 Å3/Da / Density % sol: 43.41 % / Description: D2O-solvent crystal of ribonuclease A
Crystal growTemperature: 293 K / Method: liquid diffusion
Details: a H2O-solvent crystal was sealed in a capillary with D2O-buffer containing 20 mg/mL ribonuclease A, 0.05 M sodium acetate, and 50% 2-d8-propanol (pD 5.8) to exchange hydrogen atoms in the ...Details: a H2O-solvent crystal was sealed in a capillary with D2O-buffer containing 20 mg/mL ribonuclease A, 0.05 M sodium acetate, and 50% 2-d8-propanol (pD 5.8) to exchange hydrogen atoms in the crystal with deuterium atoms.

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: NUCLEAR REACTOR / Site: JRR-3M / Beamline: 1G-A / Wavelength: 2.9 Å
DetectorType: MACSCIENCE / Detector: IMAGE PLATE / Date: Mar 4, 2009 / Details: The BIX-3 neutron diffractometer at JRR-3M of JAEA
RadiationMonochromator: Si monochormator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: neutron
Radiation wavelengthWavelength: 2.9 Å / Relative weight: 1
ReflectionResolution: 1.798→100 Å / Num. obs: 7960 / % possible obs: 72.1 % / Redundancy: 1.8 % / Biso Wilson estimate: 14.96 Å2 / Rmerge(I) obs: 0.114 / Χ2: 1.131 / Net I/av σ(I): 5.489 / Net I/σ(I): 7.3 / Num. measured all: 14629
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.798-1.861.40.3445621.09251.3
1.86-1.941.60.325861.10453.4
1.94-2.031.60.2886320.95657.6
2.03-2.131.60.2466890.87462.9
2.13-2.271.60.2137400.8368.5
2.27-2.441.70.1768240.79174.6
2.44-2.691.80.1458420.78877
2.69-3.081.90.1049450.95885
3.08-3.882.20.07210311.30892
3.881-1002.30.05611091.61796.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
HKL-2000data scaling
AMoREphasing
Cootmodel building
PDB_EXTRACT3.15data extraction
DENZOdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1KF5

1kf5


Resolution: 1.798→51.19 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / Phase error: 20.09
RfactorNum. reflection% reflectionSelection details
Rfree0.2205 801 10.07 %Random selection
Rwork0.1967 7152 --
obs0.1991 7953 71.56 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 80.74 Å2 / Biso mean: 22.3728 Å2 / Biso min: 9.3 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
NEUTRON DIFFRACTIONf_bond_d0.012047
NEUTRON DIFFRACTIONf_angle_d0.983584
NEUTRON DIFFRACTIONf_chiral_restr0.054148
NEUTRON DIFFRACTIONf_plane_restr0.005422
NEUTRON DIFFRACTIONf_dihedral_angle_d16.486497
LS refinement shell

Refine-ID: NEUTRON DIFFRACTION / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7977-1.91040.3164930.293481190449
1.9104-2.05790.2751050.2552942104757
2.0579-2.2650.24641230.21091095121866
2.265-2.59270.1821380.17791248138675
2.5927-3.26640.19361610.18041421158285
3.2664-51.21050.20141810.16581635181695

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