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- PDB-1ifg: CRYSTAL STRUCTURE OF A MONOMERIC FORM OF GENERAL PROTEASE INHIBIT... -

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Basic information

Entry
Database: PDB / ID: 1ifg
TitleCRYSTAL STRUCTURE OF A MONOMERIC FORM OF GENERAL PROTEASE INHIBITOR, ECOTIN IN ABSENCE OF A PROTEASE
ComponentsECOTIN
Keywordshydrolase inhibitor / monomeric ecotin / serine protease inhibitor
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsEggers, C.T. / Wang, S.X. / Fletterick, R.J. / Craik, C.S.
CitationJournal: J.Mol.Biol. / Year: 2001
Title: The role of ecotin dimerization in protease inhibition.
Authors: Eggers, C.T. / Wang, S.X. / Fletterick, R.J. / Craik, C.S.
History
DepositionApr 12, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 18, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 16, 2011Group: Atomic model
Revision 1.4Oct 4, 2017Group: Refinement description / Category: software
Revision 1.5Aug 16, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.6Nov 20, 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


Theoretical massNumber of molelcules
Total (without water)15,8491
Polymers15,8491
Non-polymers00
Water99155
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)97.235, 97.235, 37.233
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Cell settingtetragonal
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-177-

HOH

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Components

#1: Protein ECOTIN


Mass: 15849.198 Da / Num. of mol.: 1 / Fragment: RESIDUES 26-162 OF ECOTIN PRECURSOR
Mutation: INSERTION AFTER TRP130 THE SEQUENCE OF ALA-ASP-GLY
Source method: isolated from a genetically manipulated source
Details: MONOMERIC FORM / Source: (gene. exp.) Escherichia coli (E. coli) / Gene: ECO OR ETI OR B2209 / Plasmid: PTACTAC / Production host: Escherichia coli (E. coli) / Strain (production host): JM101 / References: UniProt: P23827
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 55 / 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: 2.77 Å3/Da / Density % sol: 55.67 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: PEG 4000, glycerol, Tris, Sodium Acetate, pH 8.0, VAPOR DIFFUSION, HANGING DROP at 298K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
112-15 mg/mlprotein1drop
228-30 %PEG40001reservoir
30.2 Msodium acetate1reservoir
415 %(v/v)glycerol1reservoir
50.1 MTris1reservoir

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 1.08 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 15, 1999 / Details: mirrors
RadiationMonochromator: 0.87 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. all: 12036 / Num. obs: 11496 / % possible obs: 95.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Redundancy: 6 % / Biso Wilson estimate: 21.2 Å2 / Rmerge(I) obs: 0.093 / Net I/σ(I): 19
Reflection shellResolution: 1.98→2.02 Å / Redundancy: 6 % / Rmerge(I) obs: 0.472 / Mean I/σ(I) obs: 4.7 / Num. unique all: 835 / Rsym value: 0.472 / % possible all: 99.9
Reflection
*PLUS
Num. measured all: 200193

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Processing

Software
NameVersionClassification
MAR345data collection
SCALEPACKdata scaling
X-PLORmodel building
CNS1refinement
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ECY with last ten residues deleted

1ecy


Resolution: 2→19.92 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 593458.54 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 1
RfactorNum. reflection% reflectionSelection details
Rfree0.267 1174 10.2 %RANDOM
Rwork0.248 ---
obs0.248 11481 91.4 %-
all-12036 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 71.32 Å2 / ksol: 0.523 e/Å3
Displacement parametersBiso mean: 42.7 Å2
Baniso -1Baniso -2Baniso -3
1--7.9 Å20 Å20 Å2
2---7.9 Å20 Å2
3---15.81 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.32 Å0.29 Å
Luzzati d res low-5 Å
Luzzati sigma a0.2 Å0.21 Å
Refinement stepCycle: LAST / Resolution: 2→19.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1112 0 0 55 1167
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d26.2
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.85
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.311.5
X-RAY DIFFRACTIONc_mcangle_it2.222
X-RAY DIFFRACTIONc_scbond_it1.832
X-RAY DIFFRACTIONc_scangle_it2.812.5
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.284 152 9.3 %
Rwork0.271 1482 -
obs--80 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PAPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
σ(F): 2 / % reflection Rfree: 10.2 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 42.7 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg26.2
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.85
X-RAY DIFFRACTIONc_mcbond_it1.5
X-RAY DIFFRACTIONc_scbond_it2
X-RAY DIFFRACTIONc_mcangle_it2
X-RAY DIFFRACTIONc_scangle_it2.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.284 / % reflection Rfree: 9.3 % / Rfactor Rwork: 0.271

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