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- PDB-1ezs: CRYSTAL STRUCTURE OF ECOTIN MUTANT M84R, W67A, G68A, Y69A, D70A B... -

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Basic information

Entry
Database: PDB / ID: 1ezs
TitleCRYSTAL STRUCTURE OF ECOTIN MUTANT M84R, W67A, G68A, Y69A, D70A BOUND TO RAT ANIONIC TRYPSIN II
Components
  • ECOTIN
  • TRYPSIN II, ANIONIC
KeywordsHYDROLASE/INHIBITOR / protein-protein interactions / macromolecular complex / protease inhibitor / HYDROLASE-INHIBITOR COMPLEX
Function / homology
Function and homology information


Antimicrobial peptides / Alpha-defensins / Activation of Matrix Metalloproteinases / Neutrophil degranulation / collagen catabolic process / trypsin / digestion / response to nutrient / serine-type endopeptidase inhibitor activity / defense response ...Antimicrobial peptides / Alpha-defensins / Activation of Matrix Metalloproteinases / Neutrophil degranulation / collagen catabolic process / trypsin / digestion / response to nutrient / serine-type endopeptidase inhibitor activity / defense response / outer membrane-bounded periplasmic space / serine-type endopeptidase activity / calcium ion binding / protein homodimerization activity / proteolysis / extracellular space / extracellular region
Similarity search - Function
Ecotin / Ecotin, C-terminal / Proteinase inhibitor I11, ecotin / Proteinase inhibitor I11, ecotin, gammaproteobacteria / Ecotin superfamily / Ecotin / : / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Peptidase S1A, chymotrypsin family ...Ecotin / Ecotin, C-terminal / Proteinase inhibitor I11, ecotin / Proteinase inhibitor I11, ecotin, gammaproteobacteria / Ecotin superfamily / Ecotin / : / 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 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 / Immunoglobulin-like / Beta Barrel / Sandwich / Mainly Beta
Similarity search - Domain/homology
Anionic trypsin-2 / Ecotin
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Rattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / Resolution: 2.3 Å
AuthorsGillmor, S.A. / Takeuchi, T. / Yang, S.Q. / Craik, C.S. / Fletterick, R.J.
CitationJournal: J.Mol.Biol. / Year: 2000
Title: Compromise and accommodation in ecotin, a dimeric macromolecular inhibitor of serine proteases.
Authors: Gillmor, S.A. / Takeuchi, T. / Yang, S.Q. / Craik, C.S. / Fletterick, R.J.
History
DepositionMay 11, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 23, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 13, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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: ECOTIN
B: ECOTIN
C: TRYPSIN II, ANIONIC
D: TRYPSIN II, ANIONIC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,5286
Polymers79,4484
Non-polymers802
Water1,54986
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7740 Å2
ΔGint-54 kcal/mol
Surface area29400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.828, 59.682, 71.044
Angle α, β, γ (deg.)103.574, 93.274, 94.621
Int Tables number1
Space group name H-MP1
DetailsThe biological assembly is the two-ecotin, two-trypsin hetero tetramer in the asymmetric unit

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Components

#1: Protein ECOTIN


Mass: 15909.294 Da / Num. of mol.: 2 / Mutation: M84R, W67A, G68A, Y69A, D70A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: PTACTACECOTIN / Production host: Escherichia coli (E. coli) / Strain (production host): 25A6 / References: UniProt: P23827
#2: Protein TRYPSIN II, ANIONIC


Mass: 23814.840 Da / Num. of mol.: 2 / Mutation: D102N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Tissue: PANCREAS / Plasmid: PYTD102N TRYPSIN / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P00763, trypsin
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 86 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.36 Å3/Da / Density % sol: 47.91 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: protein: 15mg/ml complex in 10mM Tris pH 8.0 well: 0.15M Sodium Cacodylate, 0.3M Sodium Acetate, 14% Peg 4K, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal grow
*PLUS
Temperature: 18 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
10.15 MNa-cacodylate1reservoir
20.3 MNa acetate1reservoir
314 %PEG40001reservoir

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jan 12, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. all: 29967 / Num. obs: 29967 / % possible obs: 92.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 2.1 % / Biso Wilson estimate: 18.6 Å2 / Rmerge(I) obs: 0.088 / Net I/σ(I): 5.8
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 2 % / Rmerge(I) obs: 0.196 / Num. unique all: 2791 / % possible all: 87.2
Reflection
*PLUS
Num. measured all: 61752
Reflection shell
*PLUS
% possible obs: 87.2 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
X-PLOR3.851refinement
RefinementResolution: 2.3→25 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0.2 / σ(I): -3 / Stereochemistry target values: Engh & Huber
Details: used bulk solvent correction, B-factor refinement, positional refinement, and simulated annealing
RfactorNum. reflection% reflectionSelection details
Rfree0.235 1511 5.1 %RANDOM
Rwork0.188 ---
obs0.188 29880 92.7 %-
all-29967 --
Displacement parametersBiso mean: 38.3 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.34 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.39 Å0.34 Å
Refinement stepCycle: LAST / Resolution: 2.3→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5244 0 2 86 5332
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.013
X-RAY DIFFRACTIONx_angle_deg1.6
X-RAY DIFFRACTIONx_dihedral_angle_d26.8
X-RAY DIFFRACTIONx_improper_angle_d1.56
X-RAY DIFFRACTIONx_mcbond_it2.641.5
X-RAY DIFFRACTIONx_mcangle_it4.192
X-RAY DIFFRACTIONx_scbond_it4.052
X-RAY DIFFRACTIONx_scangle_it6.112.5
LS refinement shellResolution: 2.3→2.44 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.338 226 4.9 %
Rwork0.286 4429 -
obs--87.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM.WATTOPH.WAT
X-RAY DIFFRACTION3PARAM19.IONTOPH19.ION
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg26.8
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.56

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