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- PDB-2fog: Structure of porcine pancreatic elastase in 40% trifluoroethanol -

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Basic information

Entry
Database: PDB / ID: 2fog
TitleStructure of porcine pancreatic elastase in 40% trifluoroethanol
Componentselastase-1
KeywordsHYDROLASE / elastase / solvent mapping / organic solvents / protein binding sites / multiple solvent crystal structures
Function / homology
Function and homology information


pancreatic elastase / proteolysis / serine-type endopeptidase activity / extracellular space / metal ion binding
Similarity search - Function
Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, histidine active site. / Serine proteases, trypsin domain profile. / Trypsin-like serine protease / Serine proteases, trypsin family, serine active site. / Serine proteases, trypsin domain / Trypsin / Trypsin-like serine proteases ...Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, histidine active site. / Serine proteases, trypsin domain profile. / Trypsin-like serine protease / Serine proteases, trypsin family, serine active site. / Serine proteases, trypsin domain / Trypsin / Trypsin-like serine proteases / Thrombin, subunit H / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
TRIFLUOROETHANOL / Chymotrypsin-like elastase family member 1
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsMattos, C. / Bellamacina, C.R. / Peisach, E. / Pereira, A. / Vitkup, D. / Petsko, G.A. / Ringe, D.
CitationJournal: J.Mol.Biol. / Year: 2006
Title: Multiple solvent crystal structures: Probing binding sites, plasticity and hydration
Authors: Mattos, C. / Bellamacina, C.R. / Peisach, E. / Pereira, A. / Vitkup, D. / Petsko, G.A. / Ringe, D.
History
DepositionJan 13, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 18, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: elastase-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,4647
Polymers25,9281
Non-polymers5366
Water3,225179
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.600, 58.070, 75.460
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 elastase-1 / / E.C.3.4.21.36 / pancreatic elastase


Mass: 25928.031 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: Pancreas / References: UniProt: P00772, pancreatic elastase
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-ETF / TRIFLUOROETHANOL / 2,2,2-Trifluoroethanol


Mass: 100.040 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3F3O
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 179 / 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: 2.22 Å3/Da / Density % sol: 44.64 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 15 mg/ml elastase, 25 mM Sodium Acetate, 135 mM Sodium sulfate, 10 ul drop (5x5). See also: Sawyer et al., J.Mol.Biol. 118, 137-208 (1978), pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: ROTATING ANODE / Type: ELLIOTT GX-6 / Wavelength: 1.5418 Å
DetectorType: SIEMENS-NICOLET X100 / Detector: AREA DETECTOR
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→500 Å / Num. obs: 14069 / % possible obs: 40 %

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Processing

Software
NameClassification
XDSdata reduction
CNSrefinement
XDSdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1ELC
Resolution: 1.9→500 Å / FOM work R set: 0.891 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.22 771 2.2 %Random
Rwork0.172 ---
obs-14069 40 %-
Solvent computationBsol: 72.016 Å2
Displacement parametersBiso mean: 20.133 Å2
Baniso -1Baniso -2Baniso -3
1--4.293 Å20 Å20 Å2
2--3.378 Å20 Å2
3---0.915 Å2
Refinement stepCycle: LAST / Resolution: 1.9→500 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1822 0 30 179 2031
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0047
X-RAY DIFFRACTIONc_angle_deg1.2251
X-RAY DIFFRACTIONc_dihedral_angle_d25.4393
X-RAY DIFFRACTIONc_improper_angle_d0.6283
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs
1.9-1.940.303340.233627661
1.94-1.990.188430.208748791
1.99-2.050.298350.206791826
2.05-2.110.3540.2796850
2.11-2.170.202520.171831883
2.17-2.250.292570.21836893
2.25-2.340.219500.185892942
2.34-2.450.22490.168892941
2.45-2.580.231490.179915964
2.58-2.740.232480.171938986
2.74-2.950.218540.16910051059
2.95-3.250.219720.1689781050
3.25-3.720.194600.15410081068
3.72-4.690.158550.13510181073
4.69-500.010.239590.17710231082
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.paramCNS_TOPPAR:protein.top
X-RAY DIFFRACTION2CNS_TOPPAR:dna-rna_rep.paramCNS_TOPPAR:dna-rna.top
X-RAY DIFFRACTION3CNS_TOPPAR:water_rep.paramCNS_TOPPAR:water.top
X-RAY DIFFRACTION4CNS_TOPPAR:ion.paramCNS_TOPPAR:ion.top
X-RAY DIFFRACTION5tfe.partfe.top

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