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- PDB-1ecz: PROTEASE INHIBITOR ECOTIN -

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Basic information

Entry
Database: PDB / ID: 1ecz
TitlePROTEASE INHIBITOR ECOTIN
ComponentsECOTIN
KeywordsPROTEASE INHIBITOR / BETA-SHEET STRUCTURE / SERINE PROTEASE INHIBITOR / PERIPLASMIC
Function / homology
Function and homology information


serine-type endopeptidase inhibitor activity / defense response / outer membrane-bounded periplasmic space / protein homodimerization activity
Similarity search - Function
Ecotin / Ecotin, C-terminal / Proteinase inhibitor I11, ecotin / Proteinase inhibitor I11, ecotin, gammaproteobacteria / Ecotin superfamily / Ecotin / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.68 Å
AuthorsShin, D.H. / Suh, S.W.
Citation
Journal: Protein Sci. / Year: 1996
Title: Crystal structure analyses of uncomplexed ecotin in two crystal forms: implications for its function and stability.
Authors: Shin, D.H. / Song, H.K. / Seong, I.S. / Lee, C.S. / Chung, C.H. / Suh, S.W.
#1: Journal: J.Mol.Biol. / Year: 1993
Title: Crystallization and Preliminary X-Ray Crystallographic Analysis of the Protease Inhibitor Ecotin
Authors: Shin, D.H. / Hwang, K.Y. / Kim, K.K. / Lee, H.R. / Lee, C.S. / Chung, C.H. / Suh, S.W.
History
DepositionAug 6, 1996Processing site: BNL
Revision 1.0Feb 12, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 18, 2018Group: Advisory / Data collection / Other
Category: diffrn_detector / pdbx_database_status / pdbx_unobs_or_zero_occ_atoms
Item: _diffrn_detector.detector / _pdbx_database_status.process_site / _pdbx_unobs_or_zero_occ_atoms.label_asym_id
Revision 1.4Jul 29, 2020Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Structure summary
Category: chem_comp / database_PDB_caveat ...chem_comp / database_PDB_caveat / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5Apr 3, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.6Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ECOTIN
B: ECOTIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,38123
Polymers32,2412
Non-polymers6,14021
Water1,71195
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.220, 84.860, 98.740
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.986319, -0.012247, 0.16439), (-0.009362, -0.999789, -0.018311), (0.16458, 0.016522, -0.986225)
Vector: -3.1364, 43.3112, 41.9268)

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Components

#1: Protein ECOTIN


Mass: 16120.507 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: ESCHERICHIA COLI PROTEASE INHIBITOR / Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: PBS / Gene (production host): ETI GENE / Production host: Escherichia coli (E. coli) / References: UniProt: P23827
#2: Sugar...
ChemComp-BOG / octyl beta-D-glucopyranoside / Beta-Octylglucoside / octyl beta-D-glucoside / octyl D-glucoside / octyl glucoside


Type: D-saccharide / Mass: 292.369 Da / Num. of mol.: 21
Source method: isolated from a genetically manipulated source
Formula: C14H28O6 / Comment: detergent*YM
IdentifierTypeProgram
b-octylglucosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 95 / 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: 1

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Sample preparation

CrystalDensity Matthews: 2.55 Å3/Da / Density % sol: 51.8 %
Crystal grow
*PLUS
Temperature: 24.5-25.5 K / pH: 8.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
130 mg/mlprotein1drop
250 mMADA1drop
350 mMTris-HCl1drop
420 %(w/v)PEG15001drop
50.10 %(w/v)beta-octyl glucoside1drop
650 mMTris-HCl1reservoir
736 %(w/v)PEG15001reservoir

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Data collection

DiffractionMean temperature: 287 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: ENRAF-NONIUS FAST / Detector: DIFFRACTOMETER / Date: May 14, 1992
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.68→30.7 Å / Num. obs: 7810 / % possible obs: 80 % / Observed criterion σ(I): 0.5 / Redundancy: 3.5 % / Rmerge(I) obs: 0.076
Reflection shellResolution: 2.68→2.8 Å / % possible all: 25.2
Reflection shell
*PLUS
% possible obs: 25.2 %

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Processing

Software
NameVersionClassification
MADNESdata collection
X-PLOR3.1model building
X-PLOR3.1refinement
MADNESdata reduction
X-PLOR3.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: ECOTIN PART OF ECOTIN-TRYPSIN COMPLEX

Resolution: 2.68→6 Å / σ(F): 2
RfactorNum. reflection% reflection
Rfree0.309 -10 %
Rwork0.195 --
obs0.195 6880 78.1 %
Displacement parametersBiso mean: 38 Å2
Refinement stepCycle: LAST / Resolution: 2.68→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2260 0 412 95 2767
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.009
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.317
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d27.64
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.276
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg27.64
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.276

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