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- PDB-1cjq: X-RAY CRYSTALLOGRAPHIC STUDIES OF THE DENATURATION OF THE DENATUR... -

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Basic information

Entry
Database: PDB / ID: 1cjq
TitleX-RAY CRYSTALLOGRAPHIC STUDIES OF THE DENATURATION OF THE DENATURATION OF RIBONUCLEASE S.
Components(PROTEIN (RIBONUCLEASE S)) x 2
KeywordsHYDROLASE / RIBONUCLEASE / DENATURATION
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 family signature. / Pancreatic ribonuclease / Pancreatic ribonuclease / Roll / Alpha Beta
Similarity search - Domain/homology
Ribonuclease pancreatic
Similarity search - Component
Biological speciessynthetic construct (others)
Bos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsRatnaparkhi, G.S. / Varadarajan, R.
CitationJournal: Proteins / Year: 1999
Title: X-ray crystallographic studies of the denaturation of ribonuclease S.
Authors: Ratnaparkhi, G.S. / Varadarajan, R.
History
DepositionApr 19, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0May 7, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Aug 9, 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 1.5Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROTEIN (RIBONUCLEASE S)
B: PROTEIN (RIBONUCLEASE S)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,1443
Polymers13,0482
Non-polymers961
Water1267
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1600 Å2
ΔGint-22 kcal/mol
Surface area6440 Å2
MethodPISA
2
A: PROTEIN (RIBONUCLEASE S)
B: PROTEIN (RIBONUCLEASE S)
hetero molecules

A: PROTEIN (RIBONUCLEASE S)
B: PROTEIN (RIBONUCLEASE S)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,2886
Polymers26,0954
Non-polymers1922
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area5080 Å2
ΔGint-49 kcal/mol
Surface area10990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.800, 44.800, 98.620
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 PROTEIN (RIBONUCLEASE S)


Mass: 1752.944 Da / Num. of mol.: 1 / Fragment: S PEPTIDE / Source method: isolated from a natural source / Details: SYNTHETIC S PEPTIDE / Source: (natural) synthetic construct (others) / References: UniProt: P61823
#2: Protein PROTEIN (RIBONUCLEASE S) / RNASE S


Mass: 11294.749 Da / Num. of mol.: 1 / Fragment: S PROTEIN / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / Organ: PANCREAS / References: UniProt: P61823
#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.: 7 / 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

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Sample preparation

CrystalDensity Matthews: 2.19 Å3/Da / Density % sol: 43.81 %
Crystal growpH: 4.75
Details: THE RNASE S CRYSTAL HAS BEEN STABILIZED BY GLUTARALDEHYDE CROSSLINKING AND THEN THE CRYSTAL HAS BEEN SOAKED IN 5M UREA., pH 4.75 DATA COLLECTED ON A CRYSTAL SOAKED IN 5M UREA. THE CRYSTAL ...Details: THE RNASE S CRYSTAL HAS BEEN STABILIZED BY GLUTARALDEHYDE CROSSLINKING AND THEN THE CRYSTAL HAS BEEN SOAKED IN 5M UREA., pH 4.75 DATA COLLECTED ON A CRYSTAL SOAKED IN 5M UREA. THE CRYSTAL WAS STABILIZED BY GLUTARALDEHYDE CROSSLINKING
Crystal grow
*PLUS
pH: 5.5 / Method: unknown / Details: Kim, E.E., (1992) Biochemistry, 31, 12304.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
112.5 mg/mlprotein1drop
26.0 M1dropCsCl
30.1 Msodium acetate1drop
480 %sat1reservoir(NH4)2SO4
50.1 Msodium acetate1reservoir

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorDetector: IMAGE PLATE / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3→15 Å / Num. obs: 2233 / % possible obs: 76.6 % / Redundancy: 2.5 % / Biso Wilson estimate: 53.1 Å2 / Rmerge(I) obs: 0.09
Reflection shellResolution: 3→3.2 Å / % possible all: 49.3
Reflection
*PLUS
Rmerge(I) obs: 0.09

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Processing

Software
NameVersionClassification
XDSdata scaling
AUTOMARdata reduction
AMoREphasing
X-PLOR3.851refinement
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1RNV

1rnv


Resolution: 3→15 Å / Rfactor Rfree error: 0.015 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 1
RfactorNum. reflection% reflectionSelection details
Rfree0.253 245 14.7 %RANDOM
Rwork0.175 ---
obs-2233 76.6 %-
Displacement parametersBiso mean: 27.2 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.31 Å0.26 Å
Luzzati d res low-4 Å
Luzzati sigma a0.37 Å0.37 Å
Refinement stepCycle: LAST / Resolution: 3→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms905 0 5 7 917
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.011
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_deg1.2
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24.4
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.05
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it6.261.5
X-RAY DIFFRACTIONx_mcangle_it9.582
X-RAY DIFFRACTIONx_scbond_it9.222
X-RAY DIFFRACTIONx_scangle_it12.842.5
LS refinement shellResolution: 3→3.19 Å / Rfactor Rfree error: 0.039 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.237 37 18.7 %
Rwork0.217 161 -
obs--49.3 %
Xplor fileSerial no: 1 / Param file: PARHCSDX.PRO / Topol file: TOPHCSDX.PRO
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
σ(F): 1 / % reflection Rfree: 14.7 % / Rfactor obs: 0.175
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 27.2 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.011
X-RAY DIFFRACTIONx_angle_deg1.2
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24.4
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.05
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: 0.237 / % reflection Rfree: 18.7 % / Rfactor Rwork: 0.217

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