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- PDB-1js0: Crystal Structure of 3D Domain-swapped RNase A Minor Trimer -

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Basic information

Entry
Database: PDB / ID: 1js0
TitleCrystal Structure of 3D Domain-swapped RNase A Minor Trimer
ComponentsRIBONUCLEASE A
KeywordsHYDROLASE / 3D domain swapping / RNase A
Function / homology
Function and homology information


pancreatic ribonuclease / ribonuclease A activity / RNA nuclease activity / nucleic acid binding / defense response to Gram-positive bacterium / lyase activity / 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
Ribonuclease pancreatic
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsLiu, Y. / Gotte, G. / Libonati, M. / Eisenberg, D.
Citation
Journal: Protein Sci. / Year: 2002
Title: Structures of the two 3D domain-swapped RNase A trimers.
Authors: Liu, Y. / Gotte, G. / Libonati, M. / Eisenberg, D.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 1998
Title: The Crystal Structure of a 3D Domain-swapped Dimer of RNase A at a 2.1 A Resolution
Authors: Liu, Y. / Hart, P.J. / Schlunegger, M.P. / Eisenberg, D.
#2: Journal: Nat.Struct.Biol. / Year: 2001
Title: A domain-swapped RNase A dimer with implications for amyloid formation
Authors: Liu, Y. / Gotte, G. / Libonati, M. / Eisenberg, D.
History
DepositionAug 15, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 13, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 2023Group: Data collection / Database references ...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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RIBONUCLEASE A
B: RIBONUCLEASE A
C: RIBONUCLEASE A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,5097
Polymers41,1253
Non-polymers3844
Water4,810267
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7470 Å2
ΔGint-111 kcal/mol
Surface area18520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.590, 122.170, 26.840
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11C-1249-

HOH

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Components

#1: Protein RIBONUCLEASE A / RNASE 1 / RNASE A / RIBONUCLEASE PANCREATIC


Mass: 13708.326 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / Organ: PANCREAS / References: UniProt: P61823, EC: 3.1.27.5
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 267 / 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: 2.28 Å3/Da / Density % sol: 46.13 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 3.7
Details: PEG 10,000, amonium sulfate, pH 3.7, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 6.7
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 mg/mlprotein1drop
20.18 Mphosphate1droppH6.7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 1.072 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 10, 2001 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.072 Å / Relative weight: 1
ReflectionResolution: 2.1→100 Å / Num. all: 22989 / Num. obs: 22989 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 14 % / Biso Wilson estimate: 26 Å2 / Rsym value: 0.096 / Net I/σ(I): 18.6
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 5.6 % / Mean I/σ(I) obs: 4.4 / Num. unique all: 2250 / Rsym value: 0.412 / % possible all: 99.8
Reflection
*PLUS
Lowest resolution: 40 Å / Num. measured all: 327545 / Rmerge(I) obs: 0.096

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1RTB

1rtb


Resolution: 2.2→10 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.257 1896 10.9 %random
Rwork0.184 ---
all0.201 19343 --
obs0.201 19343 97.6 %-
Displacement parametersBiso mean: 21.9 Å2
Refinement stepCycle: LAST / Resolution: 2.2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2853 0 20 267 3140
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.73
X-RAY DIFFRACTIONc_bond_d0.014
LS refinement shellResolution: 2.2→2.22 Å
RfactorNum. reflection% reflection
Rfree0.348 456 -
Rwork0.245 --
obs-510 99.8 %
Refinement
*PLUS
Lowest resolution: 10 Å / σ(F): 0 / % reflection Rfree: 10.9 % / Rfactor obs: 0.184
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 21.9 Å2
Refine LS restraints
*PLUS
Type: c_angle_deg / Dev ideal: 1.906
LS refinement shell
*PLUS
Rfactor Rfree: 0.348 / Rfactor Rwork: 0.245

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