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- PDB-1fle: CRYSTAL STRUCTURE OF ELAFIN COMPLEXED WITH PORCINE PANCREATIC ELASTASE -

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Basic information

Entry
Database: PDB / ID: 1fle
TitleCRYSTAL STRUCTURE OF ELAFIN COMPLEXED WITH PORCINE PANCREATIC ELASTASE
Components
  • ELAFIN
  • ELASTASE
KeywordsCOMPLEX (SERINE PROTEASE/INHIBITOR) / HYDROLASE / SERINE PROTEASE / ZYMOGEN / PANCREAS / COMPLEX (SERINE PROTEASE-INHIBITOR) / COMPLEX (SERINE PROTEASE-INHIBITOR) complex
Function / homology
Function and homology information


structural constituent of skin epidermis / copulation / pancreatic elastase / Formation of the cornified envelope / peptide cross-linking / cornified envelope / Antimicrobial peptides / endopeptidase inhibitor activity / extracellular matrix / serine-type endopeptidase inhibitor activity ...structural constituent of skin epidermis / copulation / pancreatic elastase / Formation of the cornified envelope / peptide cross-linking / cornified envelope / Antimicrobial peptides / endopeptidase inhibitor activity / extracellular matrix / serine-type endopeptidase inhibitor activity / antibacterial humoral response / serine-type endopeptidase activity / innate immune response / proteolysis / extracellular space / extracellular region / metal ion binding / cytosol
Similarity search - Function
Seminal vesicle protein I / Trappin protein transglutaminase-binding repeat / Trappin protein transglutaminase binding domain / Seminal vesicle protein I repeats signature. / Elafin-like / R-elafin / WAP-type 'four-disulfide core' domain / Elafin-like superfamily / WAP-type (Whey Acidic Protein) 'four-disulfide core' / WAP-type 'four-disulfide core' domain profile. ...Seminal vesicle protein I / Trappin protein transglutaminase-binding repeat / Trappin protein transglutaminase binding domain / Seminal vesicle protein I repeats signature. / Elafin-like / R-elafin / WAP-type 'four-disulfide core' domain / Elafin-like superfamily / WAP-type (Whey Acidic Protein) 'four-disulfide core' / WAP-type 'four-disulfide core' domain profile. / Four-disulfide core domains / Few Secondary Structures / Irregular / 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
Chymotrypsin-like elastase family member 1 / Elafin
Similarity search - Component
Biological speciesHomo sapiens (human)
Sus scrofa (pig)
MethodX-RAY DIFFRACTION / Resolution: 1.9 Å
AuthorsTsunemi, M. / Matsuura, Y. / Sakakibara, S. / Katsube, Y.
Citation
Journal: Biochemistry / Year: 1996
Title: Crystal structure of an elastase-specific inhibitor elafin complexed with porcine pancreatic elastase determined at 1.9 A resolution.
Authors: Tsunemi, M. / Matsuura, Y. / Sakakibara, S. / Katsube, Y.
#1: Journal: J.Mol.Biol. / Year: 1993
Title: Crystallization of a Complex between an Elastase-Specific Inhibitor Elafin and Porcine Pancreatic Elastase
Authors: Tsunemi, M. / Matsuura, Y. / Sakakibara, S. / Katsube, Y.
#2: Journal: Biochem.Biophys.Res.Commun. / Year: 1992
Title: Synthesis and Structure-Activity Relationships of Elafin, an Elastase-Specific Inhibitor
Authors: Tsunemi, M. / Kato, H. / Nishiuchi, Y. / Kumagaye, S. / Sakakibara, S.
History
DepositionJul 4, 1996-
Revision 1.0Jan 11, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 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
E: ELASTASE
I: ELAFIN


Theoretical massNumber of molelcules
Total (without water)31,9422
Polymers31,9422
Non-polymers00
Water2,828157
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1770 Å2
ΔGint-12 kcal/mol
Surface area12400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.910, 73.320, 48.920
Angle α, β, γ (deg.)90.00, 105.40, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein 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: Protein ELAFIN / / SKIN-DERIVED ANTILEUKOPROTEINASE (SKALP)


Mass: 6014.225 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Organ: SKIN / References: UniProt: P19957
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 157 / 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: 2.05 Å3/Da / Density % sol: 40 %
Crystal growpH: 5.9 / Details: pH 5.9
Crystal
*PLUS
Crystal grow
*PLUS
Method: macroseeding
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
168-74 %(v/v)MPD11
210 mMphosphate11

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceWavelength: 1.5418
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Dec 1, 1992
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionNum. obs: 15809 / % possible obs: 76.8 % / Observed criterion σ(I): 1 / Redundancy: 1.7 % / Rmerge(I) obs: 0.058
Reflection
*PLUS
Highest resolution: 1.9 Å / Num. measured all: 20575

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Processing

Software
NameClassification
RAXISdata collection
PROFFTrefinement
R-AXISdata reduction
RefinementResolution: 1.9→10 Å / σ(F): 1
RfactorNum. reflection% reflection
Rwork0.197 --
obs-15809 76.8 %
Displacement parametersBiso mean: 24.81 Å2
Refine analyzeLuzzati coordinate error obs: 0.21 Å / Luzzati d res low obs: 10 Å
Refinement stepCycle: LAST / Resolution: 1.9→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2163 0 0 157 2320
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0160.02
X-RAY DIFFRACTIONp_angle_d0.0370.03
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0430.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it0.9241
X-RAY DIFFRACTIONp_mcangle_it1.6611.5
X-RAY DIFFRACTIONp_scbond_it1.5031.5
X-RAY DIFFRACTIONp_scangle_it2.4382
X-RAY DIFFRACTIONp_plane_restr0.0140.02
X-RAY DIFFRACTIONp_chiral_restr0.1670.15
X-RAY DIFFRACTIONp_singtor_nbd0.190.5
X-RAY DIFFRACTIONp_multtor_nbd0.240.5
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.1920.5
X-RAY DIFFRACTIONp_planar_tor2.73
X-RAY DIFFRACTIONp_staggered_tor20.915
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor21.920
X-RAY DIFFRACTIONp_special_tor015
Software
*PLUS
Name: PROFFT / Classification: refinement
Refinement
*PLUS
Num. reflection obs: 15659 / Rfactor obs: 0.197
Solvent computation
*PLUS
Displacement parameters
*PLUS

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