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- PDB-2o9q: The crystal structure of Bovine Trypsin complexed with a small in... -

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Basic information

Entry
Database: PDB / ID: 2o9q
TitleThe crystal structure of Bovine Trypsin complexed with a small inhibition peptide ORB2K
Components
  • Cationic trypsin
  • ORB2K
KeywordsHYDROLASE / trypsin / inhibitor
Function / homology
Function and homology information


trypsin / serpin family protein binding / serine protease inhibitor complex / digestion / endopeptidase activity / 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 speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsLi, J. / Zhang, C. / Xu, X. / Wang, J. / Gong, W. / Lai, R.
CitationJournal: To be Published
Title: From protease inhibitor to antibiotics: single point mutation makes tremendous functional shift
Authors: Li, J. / Zhang, C. / Xu, X. / Wang, J. / Yang, H. / Xu, C. / Ma, D. / Wang, Y. / Gong, W. / Lai, R.
History
DepositionDec 14, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 25, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 18, 2017Group: Refinement description / Category: software
Revision 1.3Oct 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_atom_id / _pdbx_struct_conn_angle.ptnr1_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.value / _struct_conn.pdbx_dist_value / _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: Cationic trypsin
C: ORB2K
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,5476
Polymers25,2192
Non-polymers3284
Water5,585310
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.016, 63.451, 69.684
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Cationic trypsin / Beta-trypsin


Mass: 23324.287 Da / Num. of mol.: 1 / Fragment: Cationic trypsin / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Organ: pancreas / References: UniProt: P00760, trypsin
#2: Protein/peptide ORB2K


Mass: 1894.349 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: The small peptide ORB2K was synthesized by AC SCIENTIFIC (XI AN) INC. (Xi An, China), and confirmed purity higher than 95% by HPLC and MALDI-TOF mass spectrometry.
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 310 / 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: 2.02 Å3/Da / Density % sol: 38.99 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.5MCaCl2, 0.5M (NH4)2SO4, 0.1M HEPEs-Na, 25% PEG 4000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Apr 22, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.7→16 Å / Num. obs: 20777 / % possible obs: 90.1 % / Redundancy: 12.9 % / Rmerge(I) obs: 0.04 / Χ2: 1.067 / Net I/σ(I): 21.5
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 10.6 % / Rmerge(I) obs: 0.125 / Num. unique all: 1930 / Χ2: 0.655 / % possible all: 86.1

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.2.0005refinement
PDB_EXTRACT2data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1SFI

1sfi


Resolution: 1.7→16 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.954 / SU B: 1.884 / SU ML: 0.064 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.119 / ESU R Free: 0.113 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.195 1080 5.2 %RANDOM
Rwork0.155 ---
obs0.157 20743 90.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 18.697 Å2
Baniso -1Baniso -2Baniso -3
1-0.83 Å20 Å20 Å2
2---0.51 Å20 Å2
3----0.32 Å2
Refinement stepCycle: LAST / Resolution: 1.7→16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1752 0 16 310 2078
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0221812
X-RAY DIFFRACTIONr_angle_refined_deg1.1211.9562471
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1685245
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.17325.66760
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.80815293
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.513152
X-RAY DIFFRACTIONr_chiral_restr0.080.2273
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021338
X-RAY DIFFRACTIONr_nbd_refined0.1870.2862
X-RAY DIFFRACTIONr_nbtor_refined0.30.21247
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1120.2257
X-RAY DIFFRACTIONr_metal_ion_refined0.0960.24
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1190.238
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1060.250
X-RAY DIFFRACTIONr_mcbond_it0.78121208
X-RAY DIFFRACTIONr_mcangle_it1.35331904
X-RAY DIFFRACTIONr_scbond_it2.0064700
X-RAY DIFFRACTIONr_scangle_it2.7916562
LS refinement shellResolution: 1.701→1.745 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.284 73 -
Rwork0.212 1325 -
obs-1398 83.91 %

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