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- PDB-1e21: Ribonuclease 1 des1-7 Crystal Structure at 1.9A -

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Basic information

Entry
Database: PDB / ID: 1.0E+21
TitleRibonuclease 1 des1-7 Crystal Structure at 1.9A
ComponentsRIBONUCLEASE 1
KeywordsHYDROLASE / HUMAN PANCREATIC RIBONUCLEASE
Function / homology
Function and homology information


Developmental Lineage of Pancreatic Acinar Cells / pancreatic ribonuclease / ribonuclease A activity / RNA nuclease activity / Late endosomal microautophagy / Chaperone Mediated Autophagy / nucleic acid binding / defense response to Gram-positive bacterium / lyase activity / extracellular exosome
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
Ribonuclease pancreatic
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsPous, J. / Mallorqui-Fernandez, G. / Peracaula, R. / Terzyan, S.S. / Futami, J. / Tada, H. / Yamada, H. / Seno, M. / De Llorens, R. / Gomis-Ruth, F.X. / Coll, M.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2001
Title: Three-Dimensional Crystal Structure of Human Rnase 1Dn7 at 1.9A Resolution
Authors: Pous, J. / Mallorqui-Fernandez, G. / Peracaula, R. / Terzyan, S.S. / Futami, J. / Tada, H. / Yamada, H. / Seno, M. / De Llorens, R. / Gomis-Ruth, F.X. / Coll, M.
History
DepositionMay 15, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 3, 2001Provider: repository / Type: Initial release
Revision 1.1Jan 16, 2013Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Other / Refinement description / Source and taxonomy / Structure summary / Version format compliance
Revision 1.2Dec 6, 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
Revision 1.3Nov 6, 2024Group: Structure summary / Category: 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 1


Theoretical massNumber of molelcules
Total (without water)14,5391
Polymers14,5391
Non-polymers00
Water2,468137
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)32.691, 42.733, 79.894
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein RIBONUCLEASE 1 / RNASE 1


Mass: 14539.300 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Organ: PANCREAS / Plasmid: PET3A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P07998, EC: 3.1.27.5
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 137 / Source method: isolated from a natural source / Formula: H2O
Compound detailsCHAIN A AMINO-TERMINALLY TRUNCATED
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: 1.9 Å3/Da / Density % sol: 28 %
Crystal growpH: 8.5 / Details: 7% PEG 8K, 0.1M TRIS-HCL PH 8.5
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
120 mg/mlprotein1drop
27 %(v/v)PEG80001reservoir
30.1 MTris-HCl1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: ADSC CCD / Detector: CCD / Date: Feb 15, 2000
Details: SAGITALLY FOCUSING GE(220 MULTILAYER TOROIDAL MIRROR
RadiationMonochromator: DIAMOND (111), GE(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.9→20 Å / Num. obs: 8618 / % possible obs: 92.9 % / Observed criterion σ(I): 2 / Redundancy: 3.2 % / Biso Wilson estimate: 18.8 Å2 / Rmerge(I) obs: 0.135 / Rsym value: 0.113 / Net I/σ(I): 4.4
Reflection shellResolution: 1.9→2 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.426 / Mean I/σ(I) obs: 2 / Rsym value: 0.364 / % possible all: 87.2
Reflection
*PLUS
Num. measured all: 27390
Reflection shell
*PLUS
% possible obs: 87.2 % / Rmerge(I) obs: 0.364

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Processing

Software
NameVersionClassification
CNS1refinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 7RSA

7rsa


Resolution: 1.9→20 Å / Data cutoff high absF: 10000 / Cross valid method: THROUGHOUT / σ(F): 0 / Details: RESIDUES 126, 127 AND 128 NOT SEEN IN DENSITY MAPS
RfactorNum. reflection% reflectionSelection details
Rfree0.2511 449 5 %RANDOM
Rwork0.1959 ---
obs0.1959 8592 92.3 %-
Solvent computationBsol: 50.93 Å2 / ksol: 0.34 e/Å3
Displacement parametersBiso mean: 23.496 Å2
Refinement stepCycle: LAST / Resolution: 1.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms939 0 0 137 1076
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.61
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 1.9→1.99 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.298 60 6 %
Rwork0.2541 928 -
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
LS refinement shell
*PLUS
Rfactor Rfree: 0.298

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