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- PDB-3e3t: Structure of porcine pancreatic elastase with the magic triangle I3C -

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Basic information

Entry
Database: PDB / ID: 3e3t
TitleStructure of porcine pancreatic elastase with the magic triangle I3C
ComponentsElastase-1
KeywordsHYDROLASE / Phasing tool / 5-amino-2 / 4 / 6-triiodoisophthalic acid / magic triangle / I3C / Metal-binding / Protease / Secreted / Serine protease / Zymogen
Function / homology
Function and homology information


pancreatic elastase / serine-type endopeptidase activity / proteolysis / 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. / Serine proteases, trypsin family, serine active site. / Trypsin-like serine protease / 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. / Serine proteases, trypsin family, serine active site. / Trypsin-like serine protease / 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
Chem-I3C / IODIDE ION / Chymotrypsin-like elastase family member 1
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodX-RAY DIFFRACTION / SAD / Resolution: 1.6 Å
AuthorsBeck, T. / Gruene, T. / Sheldrick, G.M.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2008
Title: A magic triangle for experimental phasing of macromolecules
Authors: Beck, T. / Krasauskas, A. / Gruene, T. / Sheldrick, G.M.
History
DepositionAug 8, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 28, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Apr 11, 2012Group: Database references

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: Elastase-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,5059
Polymers25,9281
Non-polymers2,5778
Water5,405300
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)50.096, 57.973, 74.395
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Elastase-1 /


Mass: 25928.031 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: P00772, pancreatic elastase

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Non-polymers , 5 types, 308 molecules

#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-IOD / IODIDE ION / Iodide


Mass: 126.904 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: I
#5: Chemical
ChemComp-I3C / 5-amino-2,4,6-triiodobenzene-1,3-dicarboxylic acid / 5-Amino-2,4,6-triiodoisophthalic acid


Mass: 558.835 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H4I3NO4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 300 / Source method: isolated from a natural source / Formula: H2O

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Details

Nonpolymer detailsTHE REFERENCE OF I3C IS ACTA CRYSTALLOGRAPHICA SECTION E(2008) E64, O1286 TITLE: 5-AMINO-2,4,6- ...THE REFERENCE OF I3C IS ACTA CRYSTALLOGRAPHICA SECTION E(2008) E64, O1286 TITLE: 5-AMINO-2,4,6-TRIIODOISOPHTHALIC ACID MONOHYDRATE AUTHOR: T. BECK AND G.M. SHELDRICK
Sequence detailsTHIS SEQUENCE IS FROM REFERENCE 3 IN UNP DATABASE, P00772. BIOCHEM. J. 131:643-675(1973) SHOTTON D. ...THIS SEQUENCE IS FROM REFERENCE 3 IN UNP DATABASE, P00772. BIOCHEM. J. 131:643-675(1973) SHOTTON D.M., HARTLEY B.S. EVIDENCE FOR THE AMINO ACID SEQUENCE OF PORCINE PANCREATIC ELASTASE

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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: 2.083245 Å3/Da / Density % sol: 40.96 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.1M HEPES, 0.6M sodium sulfate, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: MACSCIENCE / Wavelength: 1.54178 Å
DetectorType: BRUKER SMART 6000 / Detector: CCD / Date: Mar 28, 2008 / Details: MULTI-LAYER INCOATEC OPTICS
RadiationMonochromator: MULTI-LAYER INCOATEC OPTICS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.6→37.2 Å / Num. all: 28897 / Num. obs: 28897 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11.2 % / Rmerge(I) obs: 0.038 / Net I/σ(I): 40.6
Reflection shellResolution: 1.6→1.7 Å / Redundancy: 2.76 % / Rmerge(I) obs: 0.1 / Mean I/σ(I) obs: 8.38 / % possible all: 91.5

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Processing

Software
NameVersionClassificationNB
SHELXrefinement
PDB_EXTRACT3.006data extraction
APEXdata collection
SAINTdata reduction
SADABSdata scaling
SHELXDphasing
SHELXL-97refinement
RefinementMethod to determine structure: SAD / Resolution: 1.6→37.2 Å / Num. parameters: 9019 / Num. restraintsaints: 8280 / Occupancy max: 1 / Occupancy min: 0 / Cross valid method: FREE R / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
Details: Side chain is disordered and I3C site is also not fully occupied.
RfactorNum. reflection% reflectionSelection details
Rfree0.213 1443 5 %RANDOM
Rwork0.157 ---
all0.159 28897 --
obs0.157 28897 98.6 %-
Displacement parametersBiso max: 89.32 Å2 / Biso mean: 17.458 Å2 / Biso min: 0 Å2
Refine analyzeNum. disordered residues: 12
Refinement stepCycle: LAST / Resolution: 1.6→37.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1806 0 75 300 2181
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.008
X-RAY DIFFRACTIONs_angle_d0.024
X-RAY DIFFRACTIONs_similar_dist0.004
X-RAY DIFFRACTIONs_from_restr_planes0.5
X-RAY DIFFRACTIONs_zero_chiral_vol0.047
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.053
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.015
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.06
X-RAY DIFFRACTIONs_approx_iso_adps0

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