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- PDB-1egp: PROTEINASE INHIBITOR EGLIN C WITH HYDROLYSED REACTIVE CENTER -

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Basic information

Entry
Database: PDB / ID: 1egp
TitlePROTEINASE INHIBITOR EGLIN C WITH HYDROLYSED REACTIVE CENTER
Components(EGLIN-C) x 2
KeywordsPROTEINASE INHIBITOR
Function / homologyProteinase inhibitor I13, potato inhibitor I / Proteinase inhibitor I13, potato inhibitor I superfamily / Potato inhibitor I family / Potato inhibitor I family signature. / serine-type endopeptidase inhibitor activity / response to wounding / Eglin C
Function and homology information
Biological speciesHirudo medicinalis (medicinal leech)
MethodX-RAY DIFFRACTION / Resolution: 2 Å
AuthorsDauter, Z. / Lamzin, V. / Betzel, C. / Wilson, K.S.
CitationJournal: FEBS Lett. / Year: 1993
Title: Structure of the proteinase inhibitor eglin c with hydrolysed reactive centre at 2.0 A resolution.
Authors: Betzel, C. / Dauter, Z. / Genov, N. / Lamzin, V. / Navaza, J. / Schnebli, H.P. / Visanji, M. / Wilson, K.S.
History
DepositionSep 1, 1995Processing site: BNL
Revision 1.0Dec 7, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: EGLIN-C
B: EGLIN-C


Theoretical massNumber of molelcules
Total (without water)8,1172
Polymers8,1172
Non-polymers00
Water2,252125
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1750 Å2
ΔGint-12 kcal/mol
Surface area4380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.000, 42.000, 35.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

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Components

#1: Protein/peptide EGLIN-C


Mass: 5188.748 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: CLEAVED BETWEEN RESIDUES 45 AND 46 / Source: (natural) Hirudo medicinalis (medicinal leech) / References: UniProt: P01051
#2: Protein/peptide EGLIN-C


Mass: 2928.290 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: CLEAVED BETWEEN RESIDUES 45 AND 46 / Source: (natural) Hirudo medicinalis (medicinal leech) / References: UniProt: P01051
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 125 / Source method: isolated from a natural source / Formula: H2O
Compound detailsSECONDARY STRUCTURE BOUNDARIES HAVE BEEN DETERMINED USING SS PROGRAM (V.S.LAMZIN, EMBL HAMBURG) AS ...SECONDARY STRUCTURE BOUNDARIES HAVE BEEN DETERMINED USING SS PROGRAM (V.S.LAMZIN, EMBL HAMBURG) AS DESCRIBED IN V.S.LAMZIN,Z.DAUTER,V.O.POPOV,E.H.HARUTYUNYAN,K.S.WILSON J.MOL.BIOL. (1994) V.236, 759-785.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 1.9 Å3/Da / Density % sol: 35.27 %
Crystal grow
*PLUS
Temperature: 16 ℃ / pH: 6 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mleglin c1drop
20.02 Macetic acid1drop
38 mg/mlsubstilin DY1reservoir
40.1 Msodium acetate1reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2 Å / Num. obs: 4131 / % possible obs: 98 % / Rmerge(I) obs: 0.06

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Processing

Software
NameClassification
ARP/wARPmodel building
PROLSQrefinement
RefinementResolution: 2→10 Å / σ(F): 0 /
RfactorNum. reflection
obs0.122 4107
Refinement stepCycle: LAST / Resolution: 2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms990 0 0 125 1115
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0220.02
X-RAY DIFFRACTIONp_angle_d0.0510.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0540.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it2.12
X-RAY DIFFRACTIONp_mcangle_it2.93
X-RAY DIFFRACTIONp_scbond_it5.34
X-RAY DIFFRACTIONp_scangle_it7.15
X-RAY DIFFRACTIONp_plane_restr0.0150.02
X-RAY DIFFRACTIONp_chiral_restr0.1760.15
X-RAY DIFFRACTIONp_singtor_nbd0.1940.3
X-RAY DIFFRACTIONp_multtor_nbd0.2810.3
X-RAY DIFFRACTIONp_xhyhbond_nbd0.2470.3
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor2.53
X-RAY DIFFRACTIONp_staggered_tor14.715
X-RAY DIFFRACTIONp_orthonormal_tor13.220
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor

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