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- PDB-4doq: Crystal structure of the complex of Porcine Pancreatic Trypsin wi... -

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Basic information

Entry
Database: PDB / ID: 4doq
TitleCrystal structure of the complex of Porcine Pancreatic Trypsin with 1/2SLPI
Components
  • Antileukoproteinase
  • Trypsin
KeywordsHYDROLASE/HYDROLASE INHIBITOR / beta barrel / mainly bata / protease / protease inhibitor / Secretory Leukocyte / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


modulation of process of another organism / endopeptidase inhibitor activity / negative regulation of viral genome replication / trypsin / digestion / negative regulation of protein binding / serine-type endopeptidase inhibitor activity / specific granule lumen / antibacterial humoral response / collagen-containing extracellular matrix ...modulation of process of another organism / endopeptidase inhibitor activity / negative regulation of viral genome replication / trypsin / digestion / negative regulation of protein binding / serine-type endopeptidase inhibitor activity / specific granule lumen / antibacterial humoral response / collagen-containing extracellular matrix / response to lipopolysaccharide / immune response / serine-type endopeptidase activity / innate immune response / mRNA binding / Neutrophil degranulation / Golgi apparatus / enzyme binding / proteolysis / DNA binding / extracellular space / extracellular exosome / extracellular region / metal ion binding
Similarity search - Function
Elafin-like / R-elafin / WAP-type 'four-disulfide core' domain / Elafin-like superfamily / WAP-type (Whey Acidic Protein) 'four-disulfide core' / WAP-type 'four-disulfide core' domain profile. / Four-disulfide core domains / Few Secondary Structures / Irregular / Serine proteases, trypsin family, histidine active site ...Elafin-like / R-elafin / WAP-type 'four-disulfide core' domain / Elafin-like superfamily / WAP-type (Whey Acidic Protein) 'four-disulfide core' / WAP-type 'four-disulfide core' domain profile. / Four-disulfide core domains / Few Secondary Structures / Irregular / 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 domain profile. / Serine proteases, trypsin family, serine active site. / 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
Trypsin / Antileukoproteinase
Similarity search - Component
Biological speciesSus scrofa (pig)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å
AuthorsFukushima, K. / Takimoto-Kamimura, M.
CitationJournal: J.SYNCHROTRON RADIAT. / Year: 2013
Title: Structure basis 1/2SLPI and porcine pancreas trypsin interaction
Authors: Fukushima, K. / Kamimura, T. / Takimoto-Kamimura, M.
History
DepositionFeb 10, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 14, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2013Group: Database references
Revision 1.2Jul 25, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.source
Revision 1.3Nov 8, 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_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_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Trypsin
B: Antileukoproteinase
C: Trypsin
D: Antileukoproteinase
E: Trypsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,28917
Polymers80,7555
Non-polymers1,53412
Water9,296516
1
A: Trypsin
B: Antileukoproteinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,4187
Polymers28,6312
Non-polymers7875
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2820 Å2
ΔGint-57 kcal/mol
Surface area11230 Å2
MethodPISA
2
C: Trypsin
D: Antileukoproteinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,2417
Polymers28,6312
Non-polymers6115
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2810 Å2
ΔGint-64 kcal/mol
Surface area11650 Å2
MethodPISA
3
E: Trypsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,6303
Polymers23,4931
Non-polymers1362
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)40.535, 118.610, 93.393
Angle α, β, γ (deg.)90.00, 90.74, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein / Protein/peptide , 2 types, 5 molecules ACEBD

#1: Protein Trypsin


Mass: 23493.496 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Tissue: Pancreas / References: UniProt: P00761, trypsin
#2: Protein/peptide Antileukoproteinase / Secretory leukocyte protease inhibitor


Mass: 5137.271 Da / Num. of mol.: 2 / Fragment: C-terminal domain / Source method: obtained synthetically / Details: This sequence occurs naturally in humans. / Source: (synth.) Homo sapiens (human) / References: UniProt: P03973

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Non-polymers , 5 types, 528 molecules

#3: Chemical ChemComp-XPE / 3,6,9,12,15,18,21,24,27-NONAOXANONACOSANE-1,29-DIOL / DECAETHYLENE GLYCOL


Mass: 458.541 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H42O11 / Comment: precipitant*YM
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#6: Chemical ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


Mass: 282.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 516 / Source method: isolated from a natural source / Formula: H2O

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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: 2.78 Å3/Da / Density % sol: 55.75 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 25% PEG4000, 0.1M Na-Citrate, 200mM Ammonium Sulfate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1 Å
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Oct 10, 2005
RadiationMonochromator: RIGAKU FRE-D / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→93.25 Å / Num. obs: 57599 / % possible obs: 96.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 2→2.05 Å / % possible all: 95.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
d*TREKdata reduction
MOLREPphasing
REFMAC5.2.0019refinement
PDB_EXTRACT3.1data extraction
CrystalCleardata collection
d*TREKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1AVW, 2Z7F

1avw

2z7f


Resolution: 2→50.06 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.927 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 4.242 / SU ML: 0.119 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.174 / ESU R Free: 0.167 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2416 2911 5.1 %RANDOM
Rwork0.1867 ---
obs0.1895 54688 96.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 89.64 Å2 / Biso mean: 30.2024 Å2 / Biso min: 14.58 Å2
Baniso -1Baniso -2Baniso -3
1-0.15 Å20 Å2-0.18 Å2
2--0.02 Å20 Å2
3----0.17 Å2
Refinement stepCycle: LAST / Resolution: 2→50.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5568 0 88 516 6172
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0225782
X-RAY DIFFRACTIONr_angle_refined_deg1.7011.9637839
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1795748
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.09925.741216
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.72215932
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.5591514
X-RAY DIFFRACTIONr_chiral_restr0.1090.2860
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024268
X-RAY DIFFRACTIONr_nbd_refined0.2070.22715
X-RAY DIFFRACTIONr_nbtor_refined0.3010.23870
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1640.2486
X-RAY DIFFRACTIONr_metal_ion_refined0.1130.212
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2560.289
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1860.244
X-RAY DIFFRACTIONr_mcbond_it1.0681.53834
X-RAY DIFFRACTIONr_mcangle_it1.72225971
X-RAY DIFFRACTIONr_scbond_it2.53132261
X-RAY DIFFRACTIONr_scangle_it3.724.51867
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.33 204 -
Rwork0.235 3998 -
all-4202 -
obs--95.83 %

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