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- PDB-1eai: COMPLEX OF ASCARIS CHYMOTRPSIN/ELASTASE INHIBITOR WITH PORCINE EL... -

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Basic information

Entry
Database: PDB / ID: 1eai
TitleCOMPLEX OF ASCARIS CHYMOTRPSIN/ELASTASE INHIBITOR WITH PORCINE ELASTASE
Components
  • PROTEIN (CHYMOTRYPSIN/ELASTASE ISOINHIBITOR 1)
  • PROTEIN (ELASTASE)
KeywordsSERINE PROTEINASE / ELASTASE / ASCARIS SUMM / PROTEIN INHIBITOR
Function / homology
Function and homology information


pancreatic elastase / serine-type endopeptidase inhibitor activity / serine-type endopeptidase activity / proteolysis / extracellular space / extracellular region / metal ion binding
Similarity search - Function
Trypsin Inhibitor-like, cysteine rich domain / Serine protease inhibitor-like superfamily / Trypsin Inhibitor like cysteine rich domain / : / Laminin / Laminin / Ribbon / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Serine proteases, trypsin family, histidine active site. ...Trypsin Inhibitor-like, cysteine rich domain / Serine protease inhibitor-like superfamily / Trypsin Inhibitor like cysteine rich domain / : / Laminin / Laminin / Ribbon / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Serine proteases, trypsin family, histidine active site. / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, serine active site. / Serine proteases, trypsin domain profile. / 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 / Chymotrypsin/elastase isoinhibitor 1
Similarity search - Component
Biological speciesSus scrofa (pig)
Ascaris suum (pig roundworm)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsHuang, K. / Strynadka, N.C.J. / Bernard, V.D. / Peanasky, R.J. / James, M.N.G.
Citation
Journal: Structure / Year: 1994
Title: The molecular structure of the complex of Ascaris chymotrypsin/elastase inhibitor with porcine elastase.
Authors: Huang, K. / Strynadka, N.C. / Bernard, V.D. / Peanasky, R.J. / James, M.N.
#1: Journal: Acta Crystallogr.,Sect.B / Year: 1988
Title: Structure of Native Porcine Pancreatic Elastase at 1.65 Resolution
Authors: Meyer, E. / Cole, G. / Radharkrishnan, R.
History
DepositionMar 25, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0Apr 5, 1999Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Aug 9, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Oct 9, 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 (ELASTASE)
B: PROTEIN (ELASTASE)
C: PROTEIN (CHYMOTRYPSIN/ELASTASE ISOINHIBITOR 1)
D: PROTEIN (CHYMOTRYPSIN/ELASTASE ISOINHIBITOR 1)


Theoretical massNumber of molelcules
Total (without water)65,0634
Polymers65,0634
Non-polymers00
Water2,630146
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: PROTEIN (ELASTASE)
D: PROTEIN (CHYMOTRYPSIN/ELASTASE ISOINHIBITOR 1)


Theoretical massNumber of molelcules
Total (without water)32,5322
Polymers32,5322
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2040 Å2
ΔGint-15 kcal/mol
Surface area13660 Å2
MethodPISA, PQS
3
A: PROTEIN (ELASTASE)
C: PROTEIN (CHYMOTRYPSIN/ELASTASE ISOINHIBITOR 1)


Theoretical massNumber of molelcules
Total (without water)32,5322
Polymers32,5322
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2020 Å2
ΔGint-15 kcal/mol
Surface area13880 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)84.020, 84.020, 190.930
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.9963, 0.0813, -0.0277), (0.0816, -0.9966, 0.0113), (-0.0267, -0.0135, -0.9996)
Vector: 2.0738, -7.0914, 160.3474)

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Components

#1: Protein PROTEIN (ELASTASE)


Mass: 25929.016 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: PANCREAS / References: UniProt: P00772, pancreatic elastase
#2: Protein PROTEIN (CHYMOTRYPSIN/ELASTASE ISOINHIBITOR 1)


Mass: 6602.523 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Ascaris suum (pig roundworm) / References: UniProt: P07851
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 146 / 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: 3

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Sample preparation

CrystalDensity Matthews: 2.99 Å3/Da / Density % sol: 58.84 %
Crystal growpH: 6.5 / Details: pH 6.5
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlprotein11
212 %PEG600011
350 mMsodium citrate11

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Data collection

DiffractionMean temperature: 287 K
Diffraction sourceSource: ROTATING ANODE / Type: SIEMENS / Wavelength: 1.5418
DetectorType: SIEMENS / Detector: AREA DETECTOR
RadiationMonochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→20 Å / Num. obs: 29261 / % possible obs: 99 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.07 / Rsym value: 0.07
Reflection shellHighest resolution: 2.4 Å / Rsym value: 0.07
Reflection
*PLUS
Num. measured all: 192689
Reflection shell
*PLUS
Highest resolution: 2.4 Å / Lowest resolution: 2.5 Å / % possible obs: 71 %

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Processing

Software
NameClassification
X-GENdata scaling
X-GENdata reduction
AMoREphasing
TNTrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1INC

1inc


Resolution: 2.4→20 Å / Isotropic thermal model: TNT BCOOREL / σ(F): 0 / Stereochemistry target values: TNT PROTGEO
RfactorNum. reflection% reflection
all0.191 29261 -
obs-29261 92 %
Refinement stepCycle: LAST / Resolution: 2.4→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4540 0 0 146 4686
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.021
X-RAY DIFFRACTIONt_angle_deg3.8
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes0.026
X-RAY DIFFRACTIONt_it
X-RAY DIFFRACTIONt_nbd
Software
*PLUS
Name: TNT / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.191
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: t_plane_restr / Dev ideal: 0.026

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