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- PDB-1fev: CRYSTAL STRUCTURE OF THE ALA4AIB MUTATION IN RNASE S -

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Basic information

Entry
Database: PDB / ID: 1fev
TitleCRYSTAL STRUCTURE OF THE ALA4AIB MUTATION IN RNASE S
Components
  • S PEPTIDE
  • S PROTEINCoronavirus spike protein
KeywordsHYDROLASE / alpha aminoisobutyric acid / AIB
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
Ribonuclease pancreatic
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / Resolution: 2.25 Å
AuthorsRatnaparkhi, G.S. / Varadarajan, R.
Citation
Journal: Protein Eng. / Year: 2000
Title: Structural and thermodynamic consequences of introducing alpha-aminoisobutyric acid in the S peptide of ribonuclease S.
Authors: Ratnaparkhi, G.S. / Awasthi, S.K. / Rani, P. / Balaram, P. / Varadarajan, R.
#1: Journal: To be Published
Title: Thermodynamic and Structural Studies of Cavity Formation in Proteins Suggest that Loss of Packing Interactions Rather than the Hydrophobic Effect Dominates the Observed Energetics
Authors: Ratnaparkhi, G.S. / Varadarajan, R.
#2: Journal: Proteins / Year: 1999
Title: X-ray Crystallographic Studies of the Denaturation of Ribonuclease S
Authors: Ratnaparkhi, G.S. / Varadarajan, R.
History
DepositionJul 23, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 9, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Nov 3, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: S PEPTIDE
B: S PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,1403
Polymers13,0442
Non-polymers961
Water75742
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1620 Å2
ΔGint-23 kcal/mol
Surface area6540 Å2
MethodPISA
2
A: S PEPTIDE
B: S PROTEIN
hetero molecules

A: S PEPTIDE
B: S PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,2796
Polymers26,0874
Non-polymers1922
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area5210 Å2
ΔGint-52 kcal/mol
Surface area11110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.580, 44.580, 97.780
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein/peptide S PEPTIDE


Mass: 1748.933 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: S peptide is a 16 residue synthetic peptide with Ala4Aib replacement
References: UniProt: P61823
#2: Protein S PROTEIN / Coronavirus spike protein / RNASE S


Mass: 11294.749 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Tissue: PANCREAS / References: UniProt: P61823, EC: 3.1.27.5
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 42 / Source method: isolated from a natural source / Formula: H2O

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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: 2.15 Å3/Da / Density % sol: 42.78 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.75
Details: 3M CsCl, 35% Ammonium Sulphate, 50 mM Sodium Acetate, pH=5.75 , VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
14-12 mg/mlprotein1drop
23 M1dropCsCl
30.1 Macetate1drop
435 %ammonium sulfate1drop

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 26, 1996
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→25 Å / Num. obs: 52509 / % possible obs: 99.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 8.26 % / Biso Wilson estimate: 24.2 Å2 / Rmerge(I) obs: 0.095 / Net I/σ(I): 23.3
Reflection shellResolution: 2.15→2.25 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.38 / Num. unique all: 739 / % possible all: 83.9

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Processing

Software
NameVersionClassification
XDSdata scaling
AUTOMARdata reduction
X-PLORmodel building
X-PLOR3.851refinement
XDSdata reduction
X-PLORphasing
RefinementResolution: 2.25→10 Å / Rfactor Rfree error: 0.011 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 1
RfactorNum. reflection% reflectionSelection details
Rfree0.229 476 10.2 %RANDOM
Rwork0.191 ---
obs0.191 4654 82.3 %-
Displacement parametersBiso mean: 17.5 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.3 Å0.3 Å
Luzzati d res low-3.8 Å
Luzzati sigma a0.24 Å0.3 Å
Refinement stepCycle: LAST / Resolution: 2.25→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1140 0 5 126 1271
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.006
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.6
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d25.2
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d2.13
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it2.371.5
X-RAY DIFFRACTIONx_mcangle_it3.522
X-RAY DIFFRACTIONx_scbond_it4.192
X-RAY DIFFRACTIONx_scangle_it6.182.5
LS refinement shellResolution: 2.25→2.37 Å / Rfactor Rfree error: 0.043 / Total num. of bins used: 7
RfactorNum. reflection% reflection
Rfree0.326 57 10.4 %
Rwork0.305 490 -
obs--68.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1parhcsdx_rv.proTOPHCSD.pro
X-RAY DIFFRACTION2param19.solTOPH.SO4
X-RAY DIFFRACTION3TOPH19X_WAT.PRO
Software
*PLUS
Name: X-PLOR(ONLINE) / Version: 3.851 / Classification: refinement
Refinement
*PLUS
σ(F): 1 / % reflection Rfree: 10.2 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 17.5 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.006
X-RAY DIFFRACTIONx_angle_deg1.6
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg25.2
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg2.13
X-RAY DIFFRACTIONx_mcbond_it1.5
X-RAY DIFFRACTIONx_scbond_it2
X-RAY DIFFRACTIONx_mcangle_it2
X-RAY DIFFRACTIONx_scangle_it2.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.326 / % reflection Rfree: 10.4 % / Rfactor Rwork: 0.305

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