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- PDB-4ab8: Fragments bound to bovine trypsin for the SAMPL challenge -

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Basic information

Entry
Database: PDB / ID: 4ab8
TitleFragments bound to bovine trypsin for the SAMPL challenge
ComponentsCATIONIC TRYPSIN
KeywordsHYDROLASE / FRAGMENT SCREENING / MODELLING
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 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 / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, histidine active site. / 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
3,4-dihydro-2H-1,5-benzodioxepin-6-ylmethanamine / Serine protease 1
Similarity search - Component
Biological speciesBOS TAURUS (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsNewman, J. / Peat, T.S.
Citation
Journal: J.Comput.Aided Mol.Des. / Year: 2012
Title: The Dingo Dataset: A Comprehensive Set of Data for the Sampl Challenge.
Authors: Newman, J. / Dolezal, O. / Fazio, V. / Caradoc-Davies, T. / Peat, T.S.
#1: Journal: J.Biomol.Screen / Year: 2009
Title: Practical Aspects of the Sampl Challenge: Providing an Extensive Experimental Data Set for the Modeling Community.
Authors: Newman, J. / Fazio, V.J. / Caradoc-Davies, T.T. / Branson, K. / Peat, T.S.
#2: Journal: Aust.J.Chem. / Year: 2013
Title: Fragment Screening for the Modelling Community: Spr, Itc, and Crystallography
Authors: Dolezal, O. / Doughty, L. / Hattarki, M.K. / Fazio, V.J. / Caradoc-Davies, T.T. / Newman, J. / Peat, T.S.
History
DepositionDec 8, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 8, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 5, 2014Group: Database references
Revision 1.2Dec 20, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_validate_polymer_linkage / struct_site
Item: _citation.country / _database_2.pdbx_DOI ..._citation.country / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_validate_polymer_linkage.dist / _pdbx_validate_polymer_linkage.label_alt_id_2 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CATIONIC TRYPSIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,9509
Polymers23,3241
Non-polymers6268
Water2,846158
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)54.323, 54.323, 105.320
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-2017-

HOH

21A-2101-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein CATIONIC TRYPSIN / BETA-TRYPSIN / ALPHA-TRYPSIN CHAIN 1 / ALPHA-TRYPSIN CHAIN 2


Mass: 23324.287 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: SIGMA / Source: (natural) BOS TAURUS (cattle) / Organ: PANCREAS / References: UniProt: P00760, trypsin

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Non-polymers , 5 types, 166 molecules

#2: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-VXU / 3,4-dihydro-2H-1,5-benzodioxepin-6-ylmethanamine / CC00413


Mass: 179.216 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H13NO2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 158 / Source method: isolated from a natural source / Formula: H2O

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Details

Nonpolymer detailsVXU: FRAGMENT CC00413 FROM MAYBRIDGE

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1000

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Sample preparation

CrystalDensity Matthews: 1.92 Å3/Da / Density % sol: 36.1 % / Description: NONE
Crystal growpH: 5.8
Details: 22.5% PEG 3350, 0.18 M AMMONIUM SULFATE, 0.12 M SODIUM THIOCYANATE, 0.09 M BIS-TRIS PH 5.5, 0.01 M TRIS PH 8.5 (FINAL MEASURED PH=5.82). THE PROTEIN WAS AT 2 MM (47 MG/ML), WITH 4 MM ...Details: 22.5% PEG 3350, 0.18 M AMMONIUM SULFATE, 0.12 M SODIUM THIOCYANATE, 0.09 M BIS-TRIS PH 5.5, 0.01 M TRIS PH 8.5 (FINAL MEASURED PH=5.82). THE PROTEIN WAS AT 2 MM (47 MG/ML), WITH 4 MM BENZYLAMINE AND 10 MM CALCIUM CHLORIDE ADDED TO STABILIZE IT. THE CRYSTALLIZATIONS WERE SET UP WITH A PHOENITO PROTOCOL (NEWMAN ET AL. 2008), WHERE A PHOENIX ROBOT (ART ROBBINS INSTRUMENTS, SUNNYSIDE, CA) WAS USED TO DISPENSE THE PROTEIN INTO AN SD2 CRYSTALLIZATION PLATE (PRE-FILLED WITH 50 ML RESERVOIR SOLUTION) AND A MOSQUITO ROBOT (TTP LABTECH, MELBOURN, UK) WAS USED TO DISPENSE THE RESERVOIR SOLUTION AND SEED STOCK OVER THE PROTEIN DROPLET.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.95369
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Oct 25, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95369 Å / Relative weight: 1
ReflectionResolution: 1.6→52.7 Å / Num. obs: 24461 / % possible obs: 99.9 % / Observed criterion σ(I): 1 / Redundancy: 10 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 22.6
Reflection shellResolution: 1.6→1.69 Å / Redundancy: 8.7 % / Rmerge(I) obs: 0.66 / Mean I/σ(I) obs: 3.4 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1K1M

1k1m


Resolution: 1.6→47.05 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.947 / SU B: 1.636 / SU ML: 0.059 / Cross valid method: THROUGHOUT / ESU R: 0.1 / ESU R Free: 0.098 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT. U VALUES REFINED INDIVIDUALLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.2047 1242 5.1 %RANDOM
Rwork0.16878 ---
obs0.17059 23176 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.709 Å2
Baniso -1Baniso -2Baniso -3
1--0.34 Å2-0.17 Å20 Å2
2---0.34 Å20 Å2
3---0.51 Å2
Refinement stepCycle: LAST / Resolution: 1.6→47.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1629 0 39 158 1826
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0191879
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.2531.972542
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5025249
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.85126.06661
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.17315311
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.195152
X-RAY DIFFRACTIONr_chiral_restr0.1620.2280
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.0211405
X-RAY DIFFRACTIONr_gen_planes_other
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.307 82 -
Rwork0.233 1510 -
obs--99.87 %

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