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- PDB-1h8x: Domain-swapped Dimer of a Human Pancreatic Ribonuclease Variant -

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Basic information

Entry
Database: PDB / ID: 1h8x
TitleDomain-swapped Dimer of a Human Pancreatic Ribonuclease Variant
ComponentsRIBONUCLEASE 1
KeywordsHYDROLASE / RIBONUCLEASE / RNASE / HUMAN PANCREATIC RIBONUCLEASE / DOMAIN- SWAPPED DIMER
Function / homology
Function and homology information


pancreatic ribonuclease / ribonuclease A activity / RNA nuclease activity / Late endosomal microautophagy / Chaperone Mediated Autophagy / nucleic acid binding / lyase activity / defense response to Gram-positive bacterium / 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 / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsCanals, A. / Pous, J. / Guasch, A. / Benito, A. / Ribo, M. / Vilanova, M. / Coll, M.
CitationJournal: Structure / Year: 2001
Title: The Structure of an Engineered Domain-Swapped Ribonuclease Dimer and its Implications for the Evolution of Proteins Toward Oligomerization
Authors: Canals, A. / Pous, J. / Guasch, A. / Benito, A. / Ribo, M. / Vilanova, M. / Coll, M.
History
DepositionFeb 16, 2001Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 14, 2002Provider: repository / Type: Initial release
Revision 1.1May 7, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 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

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Assembly

Deposited unit
A: RIBONUCLEASE 1
B: RIBONUCLEASE 1


Theoretical massNumber of molelcules
Total (without water)28,9082
Polymers28,9082
Non-polymers00
Water6,125340
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)50.610, 61.430, 75.140
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


Mass: 14454.169 Da / Num. of mol.: 2 / Fragment: RNASE 1, HP-RNASE / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: RESIDIE 100 IS A FORMILMETHIONINE (FME) / Source: (gene. exp.) HOMO SAPIENS (human) / Description: SYNTHETIC GENE / Gene: PM8 / Organ: PANCREAS / Plasmid: PM8 / Gene (production host): PM8 / 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.: 340 / Source method: isolated from a natural source / Formula: H2O
Compound detailsCHAIN A, B ENGINEERED MUTATION ARG104ALA, LYS106ALA, GLN109GLU, ASP116GLY, SER117ASN, PRO201GLN

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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: 2.13 Å3/Da / Density % sol: 30 %
Crystal growpH: 9 / Details: pH 9.00
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 mg/mlprotein1drop
220 %(v/v)ethanol1reservoir
30.1 MBicine1reservoirpH9.0

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 15, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→13 Å / Num. obs: 17315 / % possible obs: 99.4 % / Redundancy: 3.1 % / Biso Wilson estimate: 33.7 Å2 / Rmerge(I) obs: 0.076 / Net I/σ(I): 7.1
Reflection shellResolution: 1.9→2 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.315 / Mean I/σ(I) obs: 2.4 / % possible all: 99.8
Reflection
*PLUS
Highest resolution: 2 Å / Lowest resolution: 13 Å / Num. obs: 16247 / Redundancy: 3.4 % / Num. measured all: 56729
Reflection shell
*PLUS
Highest resolution: 2 Å / Lowest resolution: 2.12 Å

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Processing

Software
NameVersionClassification
CNS1refinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1DZA

1dza


Resolution: 2→12 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2427 1610 10 %RANDOM
Rwork0.1964 ---
obs0.1964 16245 99.6 %-
Solvent computationSolvent model: DENSITY MODIFICATION
Displacement parametersBiso mean: 29.3 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.29 Å0.22 Å
Luzzati d res low-0 Å
Luzzati sigma a0.22 Å0.2 Å
Refinement stepCycle: LAST / Resolution: 2→12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1964 0 0 340 2304
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
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_deg1.6
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.3
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.88
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it3.11.5
X-RAY DIFFRACTIONc_mcangle_it4.892
X-RAY DIFFRACTIONc_scbond_it4.52
X-RAY DIFFRACTIONc_scangle_it5.52.5
LS refinement shellResolution: 2→2.07 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.316 152 10 %
Rwork0.27 1399 -
obs--96.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1CIS_PEPTIDE.PARAMCNS_TOPPAR:PROTEIN_REP.PARAM
X-RAY DIFFRACTION2CNS_TOPPAR:WATER_REP.PARAM
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.565
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24.3
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.88
LS refinement shell
*PLUS
Rfactor Rwork: 0.27

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