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- PDB-1uhb: Crystal structure of porcine alpha trypsin bound with auto cataly... -

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Basic information

Entry
Database: PDB / ID: 1uhb
TitleCrystal structure of porcine alpha trypsin bound with auto catalyticaly produced native peptide at 2.15 A resolution
Components
  • (Trypsin) x 2
  • 9-mer peptide from Trypsin
KeywordsHYDROLASE / Serine Protease / peptide trypsin 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 / 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 ...: / 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
ACETATE ION / Trypsin
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsPattabhi, V. / Syed Ibrahim, B. / Shamaladevi, N.
Citation
Journal: J.Biomol.Struct.Dyn. / Year: 2004
Title: Trypsin activity reduced by an autocatalytically produced nonapeptide.
Authors: Ibrahim, B.S. / Shamaladevi, N. / Pattabhi, V.
#1: Journal: BIOCHIM.BIOPHYS.ACTA / Year: 1999
Title: Crystal structure at 1.63 A resolution of the native form of porcine beta-trypsin: revealing an acetate ion binding site and functional water network
Authors: Johnson, A. / Gautham, N. / Pattabhi, V.
History
DepositionJun 27, 2003Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 27, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Nov 6, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_DOI ..._citation.journal_abbrev / _citation.pdbx_database_id_DOI / _citation.title / _citation_author.name
Revision 1.5Oct 25, 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_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_asym_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.6Nov 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: Trypsin
B: Trypsin
P: 9-mer peptide from Trypsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,5085
Polymers24,4083
Non-polymers992
Water2,648147
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6800 Å2
ΔGint-55 kcal/mol
Surface area9400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.945, 53.921, 77.245
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein Trypsin


Mass: 13303.996 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: P00761, trypsin
#2: Protein Trypsin


Mass: 10207.492 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: P00761, trypsin

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Protein/peptide , 1 types, 1 molecules P

#3: Protein/peptide 9-mer peptide from Trypsin


Mass: 896.901 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: It is an oligopeptide fragment from native trypsin by auto catalysis of trypsin produced during preparation of trypsin.
Source: (natural) Sus scrofa (pig) / References: UniProt: P00761, trypsin

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Non-polymers , 3 types, 149 molecules

#4: Chemical ChemComp-CA / CALCIUM ION


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


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 147 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 1.89 Å3/Da / Density % sol: 34.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.7
Details: 1.5M ammonium sulphate, pH 6.70, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.15→76.7 Å / Num. all: 11187 / Num. obs: 9847 / Redundancy: 3.5 % / Rmerge(I) obs: 0.14
Reflection shellResolution: 2.15→2.23 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.14 / Num. unique all: 9847

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Processing

Software
NameVersionClassification
MAR345data collection
DENZOdata reduction
CNSrefinement
REFMAC5refinement
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb code 1qqu

1qqu


Resolution: 2.15→19.31 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.917 / SU B: 8.915 / SU ML: 0.236 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.378 / ESU R Free: 0.229 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.22787 467 4.7 %RANDOM
Rwork0.193 ---
all0.193 11187 --
obs0.193 9425 88.44 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 17.896 Å2
Baniso -1Baniso -2Baniso -3
1--1.61 Å20 Å20 Å2
2--0.37 Å20 Å2
3---1.24 Å2
Refinement stepCycle: LAST / Resolution: 2.15→19.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1704 0 5 147 1856
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.040.0211727
X-RAY DIFFRACTIONr_bond_other_d0.0050.021496
X-RAY DIFFRACTIONr_angle_refined_deg2.5971.9442342
X-RAY DIFFRACTIONr_angle_other_deg1.47433513
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.6763226
X-RAY DIFFRACTIONr_dihedral_angle_2_deg19.01615293
X-RAY DIFFRACTIONr_chiral_restr0.1810.2264
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.021943
X-RAY DIFFRACTIONr_gen_planes_other0.0080.02313
X-RAY DIFFRACTIONr_nbd_refined0.3910.3460
X-RAY DIFFRACTIONr_nbd_other0.2560.31612
X-RAY DIFFRACTIONr_nbtor_other0.0220.51
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.7470.5197
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.010.51
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.4960.361
X-RAY DIFFRACTIONr_symmetry_vdw_other0.5490.392
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2340.522
X-RAY DIFFRACTIONr_mcbond_it2.1371.51134
X-RAY DIFFRACTIONr_mcangle_it3.31621809
X-RAY DIFFRACTIONr_scbond_it5.2423593
X-RAY DIFFRACTIONr_scangle_it7.3584.5533
LS refinement shellResolution: 2.15→2.206 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.234 487
Rwork0.2 637

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