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- PDB-2f91: 1.2A resolution structure of a crayfish trypsin complexed with a ... -

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Basic information

Entry
Database: PDB / ID: 2f91
Title1.2A resolution structure of a crayfish trypsin complexed with a peptide inhibitor, SGTI
Components
  • Serine protease inhibitor I/II
  • hepatopancreas trypsin
KeywordsHYDROLASE/HYDROLASE INHIBITOR / SERINE PROTEASE / TRYPSIN / CANONICAL INHIBITOR / ATOMIC RESOLUTION / HYDROLASE-HYDROLASE INHIBITOR COMPLEX
Function / homology
Function and homology information


serine-type endopeptidase inhibitor activity / serine-type endopeptidase activity / proteolysis / extracellular region / metal ion binding
Similarity search - Function
Protease inhibitor with pacifastin repeats / Pacifastin domain / Pacifastin domain superfamily / Pacifastin inhibitor (LCMII) / Pacifastin domain profile. / 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. ...Protease inhibitor with pacifastin repeats / Pacifastin domain / Pacifastin domain superfamily / Pacifastin inhibitor (LCMII) / Pacifastin domain profile. / 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 / Mainly Beta
Similarity search - Domain/homology
: / Serine protease inhibitor I/II / Hepatopancreas trypsin
Similarity search - Component
Biological speciesPontastacus leptodactylus (narrow-clawed crayfish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å
AuthorsFodor, K. / Harmat, V. / Hetenyi, C. / Kardos, J. / Antal, J. / Perczel, A. / Patthy, A. / Katona, G. / Graf, L.
Citation
Journal: Biochemistry / Year: 2006
Title: Enzyme:Substrate Hydrogen Bond Shortening during the Acylation Phase of Serine Protease Catalysis.
Authors: Fodor, K. / Harmat, V. / Neutze, R. / Szilagyi, L. / Graf, L. / Katona, G.
#1: Journal: J.Mol.Biol. / Year: 2005
Title: Extended Intermolecular Interactions in a Serine Protease-Canonical Inhibitor Complex Account for Strong and Highly Specific Inhibition.
Authors: Fodor, K. / Harmat, V. / Hetenyi, C. / Kardos, J. / Antal, J. / Perczel, A. / Patthy, A. / Katona, G. / Graf, L.
History
DepositionDec 5, 2005Deposition site: RCSB / Processing site: RCSB
SupersessionApr 18, 2006ID: 1YR4
Revision 1.0Apr 18, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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_PDB_ins_code / _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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_PDB_ins_code / _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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_PDB_ins_code / _struct_conn.pdbx_ptnr2_PDB_ins_code / _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.ptnr1_symmetry / _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_conn.ptnr2_symmetry / _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: Structure summary / Category: 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: hepatopancreas trypsin
B: Serine protease inhibitor I/II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,64610
Polymers28,9012
Non-polymers7458
Water6,179343
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2430 Å2
ΔGint-45 kcal/mol
Surface area11030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.283, 59.673, 97.302
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein hepatopancreas trypsin


Mass: 25072.434 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Pontastacus leptodactylus (narrow-clawed crayfish)
Tissue: HEPATOPANCREAS / References: UniProt: Q52V24, trypsin
#2: Protein/peptide Serine protease inhibitor I/II / SCHISTOCERCA GREGARIA TRYPSIN INHIBITOR / SGTI


Mass: 3828.314 Da / Num. of mol.: 1 / Fragment: PROTEASE INHIBITOR SGPI-1, RESIDUES 20-54 / Source method: obtained synthetically
Details: THE PROTEIN WAS CHEMICALLY SYNTHESIZED, THIS SEQUENCE OCCURS NATURALLY IN SCHISTOCERCA GREGARIA (DESERT LOCUST)
References: UniProt: O46162
#3: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cd
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 343 / 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: 2.07 Å3/Da / Density % sol: 40.65 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 30% PEG 400, 0.1 M CD CHLORIDE, 0.1 M NA ACETATE, pH 4.60, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 / Wavelength: 0.933 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Details: MIRROR
RadiationMonochromator: DIAMOND (111), GE (220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.2→32.1 Å / Num. obs: 69145 / % possible obs: 91.1 % / Observed criterion σ(I): -3 / Redundancy: 3.4 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 7.1
Reflection shellResolution: 1.2→1.23 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.2 / Mean I/σ(I) obs: 3.3 / % possible all: 51.8

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
SHELXL-97refinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1H4W TRUNCATED TO POLYALANINE

1h4w


Resolution: 1.2→32.1 Å / Num. parameters: 21232 / Num. restraintsaints: 37511 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.182 3470 5.3 %RANDOM
all0.139 65673 --
obs-54446 91.1 %-
Solvent computationSolvent model: MOEWS & KRETSINGER
Refine analyzeNum. disordered residues: 3
Refinement stepCycle: LAST / Resolution: 1.2→32.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3802 0 8 343 4153
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.012
X-RAY DIFFRACTIONs_angle_d0.029
X-RAY DIFFRACTIONs_similar_dist
X-RAY DIFFRACTIONs_from_restr_planes0.428
X-RAY DIFFRACTIONs_zero_chiral_vol0.07
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.074
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.018
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.004
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.027
X-RAY DIFFRACTIONs_approx_iso_adps0.04

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