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- PDB-1slw: RAT ANIONIC N143H, E151H TRYPSIN COMPLEXED TO A86H ECOTIN; NICKEL... -

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Basic information

Entry
Database: PDB / ID: 1slw
TitleRAT ANIONIC N143H, E151H TRYPSIN COMPLEXED TO A86H ECOTIN; NICKEL-BOUND
Components
  • ANIONIC TRYPSIN
  • ECOTIN
KeywordsCOMPLEX (SERINE PROTEASE/INHIBITOR) / SERINE PROTEASE / INHIBITOR / COMPLEX / METAL BINDING SITES / PROTEIN ENGINEERING / PROTEASE-SUBSTRATE INTERACTIONS / METALLOPROTEINS / COMPLEX (SERINE PROTEASE-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 / Serine proteases, trypsin family, histidine active site. ...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 / 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 / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
ACETATE ION / NICKEL (II) ION / Anionic trypsin-2 / Ecotin
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Rattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / Resolution: 2 Å
AuthorsBrinen, L.S. / Fletterick, R.J.
Citation
Journal: Biochemistry / Year: 1996
Title: X-ray structures of a designed binding site in trypsin show metal-dependent geometry.
Authors: Brinen, L.S. / Willett, W.S. / Craik, C.S. / Fletterick, R.J.
#1: Journal: Embo J. / Year: 1994
Title: Macromolecular Chelation as an Improved Mechanism of Protease Inhibition: Structure of the Ecotin-Trypsin Complex
Authors: Mcgrath, M.E. / Erpel, T. / Bystroff, C. / Fletterick, R.J.
History
DepositionFeb 7, 1996Processing site: BNL
Revision 1.0Jul 11, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / 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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_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.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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_asym_id / _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_asym_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 1.4Oct 30, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ECOTIN
B: ANIONIC TRYPSIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,2075
Polymers40,0502
Non-polymers1583
Water93752
1
A: ECOTIN
B: ANIONIC TRYPSIN
hetero molecules

A: ECOTIN
B: ANIONIC TRYPSIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,41510
Polymers80,0994
Non-polymers3166
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_557-x,y,-z+21
Buried area9290 Å2
ΔGint-94 kcal/mol
Surface area29010 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)86.380, 56.230, 81.230
Angle α, β, γ (deg.)90.00, 92.81, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein ECOTIN / TRYPSIN INHIBITOR


Mass: 16187.577 Da / Num. of mol.: 1 / Mutation: CHAIN A, A86H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: RAT ANIONIC TRYPSIN / Plasmid: PTACTAC / Gene (production host): ECOTIN / Production host: Escherichia coli (E. coli) / References: UniProt: P23827
#2: Protein ANIONIC TRYPSIN


Mass: 23861.941 Da / Num. of mol.: 1 / Mutation: CHAIN B, V121I, N143H, E151H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: RAT ANIONIC TRYPSIN / Plasmid: PST / Gene (production host): RAT ANIONIC TRYPSIN / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P00763, trypsin

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Non-polymers , 4 types, 55 molecules

#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 52 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsSITE DIRECTED MUTAGENESIS WAS PERFORMED IN ORDER TO DESIGN A METAL BINDING SITE AT THE INTERFACE OF ...SITE DIRECTED MUTAGENESIS WAS PERFORMED IN ORDER TO DESIGN A METAL BINDING SITE AT THE INTERFACE OF TRYPSIN N143H,E151H AND ECOTIN A86H. METAL BINDING TAKES PLACE AT THE SITE OF THESE MUTATIONS.
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: 2.46 Å3/Da / Density % sol: 50 %
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 18 ℃ / pH: 8 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
10.375 mMtrypsin and ecotin1drop
2300 mM1dropNaOAc
3100 mMTris1drop
418-22 %PEG40001drop
5300 mM1dropNaOAc
6100 mMTris1drop
710 mM1dropCaCl2
818-22 %PEG40001reservoir
9300 mM1reservoirNaOAc
10100 mMTris1reservoir
1110 mM1reservoirCaCl2

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Data collection

DiffractionMean temperature: 198 K
Diffraction sourceWavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Feb 10, 1995
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 17281 / % possible obs: 95.5 % / Observed criterion σ(I): 1.5 / Redundancy: 3 % / Rmerge(I) obs: 0.054
Reflection
*PLUS
Num. measured all: 56521
Reflection shell
*PLUS
% possible obs: 90.4 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.1model building
X-PLOR3.1refinement
X-PLOR3.1phasing
RefinementResolution: 2→6 Å / σ(F): 1.5
RfactorNum. reflection% reflection
Rfree0.253 -10 %
Rwork0.179 --
obs0.179 7886 90.4 %
Displacement parametersBiso mean: 47.17 Å2
Refine analyzeLuzzati coordinate error obs: 0.25 Å
Refinement stepCycle: LAST / Resolution: 2→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2616 0 6 52 2674
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.006
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_deg1.3
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d25.09
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.14
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
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1PARAM19X.PRO
X-RAY DIFFRACTION2
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_deg25.09
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.14

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