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- PDB-1hj9: Atomic resolution structures of trypsin provide insight into stru... -

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Basic information

Entry
Database: PDB / ID: 1hj9
TitleAtomic resolution structures of trypsin provide insight into structural radiation damage
ComponentsBETA-TRYPSIN
KeywordsHYDROLASE / RADIATION DAMAGE / DISULPHID BOND BREAKAGE / TRYPSIN / ATOMIC RESOLUTION / SERINE PROTEINASE
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
ANILINE / Serine protease 1
Similarity search - Component
Biological speciesBOS TAURUS (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 0.95 Å
AuthorsLeiros, H.-K.S. / McSweeney, S.M. / Smalas, A.O.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2001
Title: Atomic Resolution Structure of Trypsin Provide Insight Into Structural Radiation Damage
Authors: Leiros, H.-K.S. / Mcsweeney, S.M. / Smalas, A.O.
History
DepositionJan 10, 2001Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 4, 2002Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "B" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "B" 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: BETA-TRYPSIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,8387
Polymers23,3241
Non-polymers5136
Water4,594255
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)54.055, 56.812, 66.282
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 , 1 types, 1 molecules A

#1: Protein BETA-TRYPSIN


Mass: 23324.287 Da / Num. of mol.: 1 / Fragment: RESIDUES 21-243 / Source method: isolated from a natural source / Source: (natural) BOS TAURUS (cattle) / References: UniProt: P00760, trypsin

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Non-polymers , 5 types, 261 molecules

#2: Chemical ChemComp-ANL / ANILINE


Mass: 93.126 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H7N
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-CA / CALCIUM ION


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


Mass: 18.015 Da / Num. of mol.: 255 / 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: 2.18 Å3/Da / Density % sol: 43.62 %
Crystal growpH: 8 / Details: pH 8.00
Crystal grow
*PLUS
pH: 8 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
125 %PEG80001reservoir
20.2 Mammonium sulfate1reservoir
30.1 MTris1reservoirpH8.
40.1 Maniline1reservoir
515 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM1A / Wavelength: 0.8
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jun 15, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8 Å / Relative weight: 1
ReflectionResolution: 0.95→15 Å / Num. obs: 128074 / % possible obs: 99.5 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.048 / Net I/σ(I): 7.3
Reflection shellResolution: 0.95→1 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.472 / Mean I/σ(I) obs: 1.6 / % possible all: 99.5
Reflection
*PLUS
Lowest resolution: 15 Å / Num. measured all: 886215
Reflection shell
*PLUS
% possible obs: 99.6 %

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Processing

Software
NameClassification
SHELXL-97refinement
DENZOdata reduction
SCALAdata scaling
RefinementMethod to determine structure: OTHER / Resolution: 0.95→8 Å / Num. parameters: 17690 / Num. restraintsaints: 22136 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
RfactorNum. reflection% reflection
Rfree0.1399 6402 5 %
obs0.1171 -99.5 %
all-127765 -
Solvent computationSolvent model: MOEWS & KRETSINGER
Refine analyzeNum. disordered residues: 8 / Occupancy sum hydrogen: 1495.52 / Occupancy sum non hydrogen: 1872.21
Refinement stepCycle: LAST / Resolution: 0.95→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1629 0 29 255 1913
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.018
X-RAY DIFFRACTIONs_angle_d0.035
X-RAY DIFFRACTIONs_similar_dist
X-RAY DIFFRACTIONs_from_restr_planes
X-RAY DIFFRACTIONs_zero_chiral_vol0.093
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.102
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.093
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt
X-RAY DIFFRACTIONs_similar_adp_cmpnt
X-RAY DIFFRACTIONs_approx_iso_adps
Software
*PLUS
Name: SHELXL-97 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 8 Å / Rfactor Rwork: 0.1171
Solvent computation
*PLUS
Displacement parameters
*PLUS

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