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- PDB-1d5d: The role of phenylalanine 8 in the stabilization of the s protein... -

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Basic information

Entry
Database: PDB / ID: 1d5d
TitleThe role of phenylalanine 8 in the stabilization of the s protein-s peptide interaction: packing and cavities
Components
  • RNASE S
  • S PEPTIDE
KeywordsHYDROLASE / RNASE S MUTANT(F8M) / CAVITY S PROTEIN / S PEPTIDE
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 / Ribonuclease pancreatic
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / Resolution: 2.25 Å
AuthorsRatnaparkhi, G.S. / Varadarajan, R.
Citation
Journal: Biochemistry / Year: 2000
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.
#1: Journal: Proteins: Struct.,Funct.,Genet. / Year: 1999
Title: X-ray crystallographic studies of the denaturation of ribonuclease S
Authors: Ratnaparkhi, G.S. / Varadarajan, R.
#2: Journal: Biochemistry / Year: 1992
Title: Crystallographic structures of ribonuclease S variants with nonpolar substitution at position 13: packing and cavities
Authors: Varadarajan, R. / Richards, F.M.
#3: Journal: Biochemistry / Year: 1994
Title: Thermodynamic and structural consequences of changing a sulfur atom to a methylene group in the M13Nle mutation in ribonuclease-S
Authors: Thomson, J. / Ratnaparkhi, G.S. / Varadarajan, R. / Sturtevant, J.M. / Richards, F.M.
History
DepositionOct 7, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 20, 1999Provider: 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 1.4Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.5Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.6Mar 14, 2018Group: Database references / Category: struct_ref_seq_dif / Item: _struct_ref_seq_dif.details
Revision 1.7Mar 26, 2025Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)13,1093
Polymers13,0132
Non-polymers961
Water82946
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1760 Å2
ΔGint-23 kcal/mol
Surface area6600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.840, 44.840, 98.000
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: 1717.943 Da / Num. of mol.: 1 / Fragment: RESIDUES 1-15 / Mutation: F8M / Source method: obtained synthetically
Details: S15 PEPTIDE SYNTHESIZED BY SOLID PHASE PEPTIDE SYNTHESIS
References: UniProt: P61823
#2: Protein RNASE S


Mass: 11294.749 Da / Num. of mol.: 1 / Fragment: RESIDUES 21-124 / Source method: isolated from a natural source
Details: DERIEVED FROM A LIMIT DIGEST OF BOVINE PANCREATIC RNASE A
Source: (natural) Bos taurus (domestic cattle) / References: UniProt: P00656, UniProt: P61823*PLUS
#3: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 46 / 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: 2.19 Å3/Da / Density % sol: 43.72 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.75
Details: 3M CSCL, 35% AMMONIUM SULFATE. 0.1 M SODIUM ACETATE, pH 5.75, VAPOR DIFFUSION, SITTING DROP, temperature 20K
Crystal grow
*PLUS
Method: unknown / Details: Thomson, J., (1994) Biochemistry, 33, 8587.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
14-5 mg/mlprotein1drop
23 M1dropCsCl
30.1 Macetate1drop
435 %ammonium sulfate1drop

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 26, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.19→10 Å / Num. all: 5293 / Num. obs: 4958 / % possible obs: 100 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 11 % / Biso Wilson estimate: 26.9 Å2 / Rmerge(I) obs: 0.117 / Net I/σ(I): 20.18
Reflection shellResolution: 2.19→2.4 Å / Redundancy: 11 % / Rmerge(I) obs: 0.42 / % possible all: 100
Reflection
*PLUS
Num. obs: 4492

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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: 0.01 / 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
Rfree0.218 474 10.6 %RANDOM
Rwork0.189 ---
obs0.189 4492 78.7 %-
Displacement parametersBiso mean: 19.3 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.32 Å0.28 Å
Luzzati d res low-3.8 Å
Luzzati sigma a0.17 Å0.28 Å
Refinement stepCycle: LAST / Resolution: 2.25→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1136 0 5 138 1279
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.005
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_deg1.3
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d25.5
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.54
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it2.261.5
X-RAY DIFFRACTIONx_mcangle_it3.572
X-RAY DIFFRACTIONx_scbond_it3.932
X-RAY DIFFRACTIONx_scangle_it5.872.5
LS refinement shellResolution: 2.25→2.37 Å / Rfactor Rfree error: 0.04 / Total num. of bins used: 7
RfactorNum. reflection% reflection
Rfree0.328 48 9.6 %
Rwork0.3 453 -
obs--63.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX_RV.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM19.SOLTOPH.SO4
X-RAY DIFFRACTION3TOPH19X_WAT.PRO
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
σ(F): 1 / % reflection Rfree: 10.6 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 19.3 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.005
X-RAY DIFFRACTIONx_angle_deg1.3
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg25.5
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.54
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: 0.328 / % reflection Rfree: 9.6 % / Rfactor Rwork: 0.3

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