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- PDB-5xw8: Crystal Structure of Porcine pancreatic trypsin with tripeptide i... -

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Basic information

Entry
Database: PDB / ID: 5xw8
TitleCrystal Structure of Porcine pancreatic trypsin with tripeptide inhibitor, PRN, at pH 7
Components
  • (Trypsin) x 2
  • Acetylated-Pro-Arg-Asn Inhibitor
KeywordsHYDROLASE/HYDROLASE INHIBITOR / protease / inhibitor / complex / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


trypsin / digestion / serine-type endopeptidase activity / proteolysis / extracellular space / metal ion binding
Similarity search - Function
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 ...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
Biological speciesSus scrofa (pig)
Capsicum annuum (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.002 Å
AuthorsSaikhedkar, N.S. / Bhoite, A.S. / Giri, A.P. / Kulkarni, K.A.
Funding support India, 1items
OrganizationGrant numberCountry
CSIRBSC0120 India
CitationJournal: Insect Biochem. Mol. Biol. / Year: 2018
Title: Tripeptides derived from reactive centre loop of potato type II protease inhibitors preferentially inhibit midgut proteases of Helicoverpa armigera.
Authors: Saikhedkar, N.S. / Joshi, R.S. / Bhoite, A.S. / Mohandasan, R. / Yadav, A.K. / Fernandes, M. / Kulkarni, K.A. / Giri, A.P.
History
DepositionJun 29, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 28, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 11, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Nov 22, 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 / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_conn_type.id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Trypsin
B: Trypsin
C: Acetylated-Pro-Arg-Asn Inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,0175
Polymers24,8593
Non-polymers1582
Water4,540252
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6970 Å2
ΔGint-67 kcal/mol
Surface area8740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.881, 82.881, 135.643
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11B-410-

HOH

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein Trypsin / / Porcine pancreatic trypsin


Mass: 14238.919 Da / Num. of mol.: 1 / Fragment: UNP residues 1-133 / Source method: isolated from a natural source
Details: Commercially available trypsin from Sigma (Cat. No. T4799)
Source: (natural) Sus scrofa (pig) / References: UniProt: P00761, trypsin
#2: Protein Trypsin / / Porcine pancreatic trypsin


Mass: 10207.492 Da / Num. of mol.: 1 / Fragment: UNP residues 134-231 / Source method: isolated from a natural source
Details: Commercially available trypsin from Sigma (Cat. No. T4799)
Source: (natural) Sus scrofa (pig) / References: UniProt: P00761, trypsin

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Protein/peptide , 1 types, 1 molecules C

#3: Protein/peptide Acetylated-Pro-Arg-Asn Inhibitor


Mass: 412.464 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Capsicum annuum (plant)

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Non-polymers , 3 types, 254 molecules

#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 252 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsThere is autolysis of Trypsin at residue 133, thus Trypsin is split into two entities.

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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: 2.86 Å3/Da / Density % sol: 56.95 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.1M HEPES pH 7.5, 70% MPD

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: RRCAT INDUS-2 / Beamline: PX-BL21 / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 8, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→41.5 Å / Num. obs: 19102 / % possible obs: 99.9 % / Redundancy: 21.3 % / Rmerge(I) obs: 0.134 / Net I/σ(I): 22.4
Reflection shellResolution: 2.01→2.06 Å / Redundancy: 20.9 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 7.6 / Num. unique obs: 1868 / % possible all: 98.8

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4DOQ

4doq


Resolution: 2.002→41.44 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 15.61
RfactorNum. reflection% reflection
Rfree0.178 978 5.12 %
Rwork0.1491 --
obs0.1506 19099 99.24 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.002→41.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1654 0 9 252 1915
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061699
X-RAY DIFFRACTIONf_angle_d0.7792307
X-RAY DIFFRACTIONf_dihedral_angle_d6.1171348
X-RAY DIFFRACTIONf_chiral_restr0.057258
X-RAY DIFFRACTIONf_plane_restr0.004297
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0018-2.10730.1931200.14992536X-RAY DIFFRACTION99
2.1073-2.23930.19791500.14332550X-RAY DIFFRACTION100
2.2393-2.41220.16791350.14642544X-RAY DIFFRACTION100
2.4122-2.65490.20471550.14172561X-RAY DIFFRACTION100
2.6549-3.0390.18861460.14472569X-RAY DIFFRACTION99
3.039-3.82840.14071350.1392610X-RAY DIFFRACTION99
3.8284-41.44940.181370.16592751X-RAY DIFFRACTION97
Refinement TLS params.Method: refined / Origin x: -7.8049 Å / Origin y: 33.1643 Å / Origin z: -6.4751 Å
111213212223313233
T0.068 Å2-0.0007 Å20.0079 Å2-0.0781 Å20.0053 Å2--0.0696 Å2
L0.7851 °20.5339 °2-0.2686 °2-1.1199 °2-0.1265 °2--0.6649 °2
S0.0327 Å °0.0164 Å °0.0326 Å °0.0991 Å °-0.0019 Å °0.0727 Å °0.0004 Å °-0.0452 Å °-0.0184 Å °
Refinement TLS groupSelection details: (chain A and resseq 9:132) or (chain B and resseq 134:231)

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