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- PDB-7q0x: Bovine Trypsin co-crystallized with V(IV)OSO4 and pic -

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Basic information

Entry
Database: PDB / ID: 7q0x
TitleBovine Trypsin co-crystallized with V(IV)OSO4 and pic
ComponentsCationic trypsin
KeywordsHYDROLASE / Protein-metal binding
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 / 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
PYRIDINE-2-CARBOXYLIC ACID / OXYGEN ATOM / VANADIUM ION / Serine protease 1
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.09 Å
AuthorsSantos, M.F.A. / Fernandes, A.C.P. / Correia, I. / Sciortino, G. / Garribba, E. / Santos-Silva, T. / Pessoa, J.C.
Funding support Portugal, 1items
OrganizationGrant numberCountry
Fundacao para a Ciencia e a Tecnologia Portugal
CitationJournal: Chemistry / Year: 2022
Title: Binding of V IV O 2+ , V IV OL, V IV OL 2 and V V O 2 L Moieties to Proteins: X-ray/Theoretical Characterization and Biological Implications.
Authors: Santos, M.F.A. / Sciortino, G. / Correia, I. / Fernandes, A.C.P. / Santos-Silva, T. / Pisanu, F. / Garribba, E. / Costa Pessoa, J.
History
DepositionOct 16, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 25, 2022Provider: repository / Type: Initial release
Revision 1.1Jun 1, 2022Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jun 15, 2022Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.3Jul 27, 2022Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.4Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cationic trypsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,23412
Polymers23,3241
Non-polymers91011
Water5,224290
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2430 Å2
ΔGint-21 kcal/mol
Surface area8820 Å2
Unit cell
Length a, b, c (Å)54.522, 54.522, 108.199
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-626-

HOH

21A-669-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Cationic trypsin / Beta-trypsin


Mass: 23324.287 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / Production host: Escherichia coli (E. coli) / References: UniProt: P00760, trypsin

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Non-polymers , 7 types, 301 molecules

#2: Chemical ChemComp-V / VANADIUM ION


Mass: 50.941 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: V / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-O / OXYGEN ATOM


Mass: 15.999 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: O
#4: Chemical ChemComp-6PC / PYRIDINE-2-CARBOXYLIC ACID / PICOLINIC ACID


Mass: 123.109 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H5NO2 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#7: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 290 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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: 1.99 Å3/Da / Density % sol: 38.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion / Details: 30% PEG4K; 0.2 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 1.04 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 15, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.04 Å / Relative weight: 1
ReflectionResolution: 1.09→41.22 Å / Num. obs: 78462 / % possible obs: 100 % / Redundancy: 5.4 % / CC1/2: 0.995 / Net I/σ(I): 8.2
Reflection shellResolution: 1.09→1.11 Å / Mean I/σ(I) obs: 2.2 / Num. unique obs: 3802 / CC1/2: 0.761

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1C1P

1c1p


Resolution: 1.09→41.22 Å / Cor.coef. Fo:Fc: 0.986 / Cor.coef. Fo:Fc free: 0.982 / SU B: 0.835 / SU ML: 0.018 / Cross valid method: THROUGHOUT / ESU R: 0.023 / ESU R Free: 0.025 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1362 3945 5 %RANDOM
Rwork0.11141 ---
obs0.11262 74447 99.95 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.1 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.741 Å2
Baniso -1Baniso -2Baniso -3
1--0.05 Å2-0.02 Å20 Å2
2---0.05 Å20 Å2
3---0.15 Å2
Refinement stepCycle: 1 / Resolution: 1.09→41.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1629 0 56 290 1975
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.021733
X-RAY DIFFRACTIONr_bond_other_d0.0020.021627
X-RAY DIFFRACTIONr_angle_refined_deg1.8131.9752333
X-RAY DIFFRACTIONr_angle_other_deg0.89733763
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6895217
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.83825.86258
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.38815284
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.916152
X-RAY DIFFRACTIONr_chiral_restr0.1120.2270
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0211904
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02366
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2551.275888
X-RAY DIFFRACTIONr_mcbond_other1.2561.275885
X-RAY DIFFRACTIONr_mcangle_it1.5821.9231093
X-RAY DIFFRACTIONr_mcangle_other1.5821.9231092
X-RAY DIFFRACTIONr_scbond_it2.1641.491845
X-RAY DIFFRACTIONr_scbond_other2.1491.485841
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.5482.1171233
X-RAY DIFFRACTIONr_long_range_B_refined4.69612.9552266
X-RAY DIFFRACTIONr_long_range_B_other4.71912.9652267
X-RAY DIFFRACTIONr_rigid_bond_restr4.43733360
X-RAY DIFFRACTIONr_sphericity_free39.937575
X-RAY DIFFRACTIONr_sphericity_bonded11.4153564
LS refinement shellResolution: 1.09→1.118 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.209 272 -
Rwork0.198 5429 -
obs--99.98 %

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