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- PDB-1rxp: STRUCTURE OF TRYPSIN (ORTHORHOMBIC) WITH 1-(4-TERT-BUTYLCARBAMOYL... -

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Basic information

Entry
Database: PDB / ID: 1rxp
TitleSTRUCTURE OF TRYPSIN (ORTHORHOMBIC) WITH 1-(4-TERT-BUTYLCARBAMOYL- PIPERAZINE-1-CARBONYL)-3-(3-GUANIDINO-PROPYL)-4-OXO-AZETIDINE-2-CARBOXYLIC ACID
ComponentsTRYPSIN
KeywordsHYDROLASE / TRYPTASE INHIBITOR / SERINE PROTEASE / AZETIDINONE
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
Chem-169 / Serine protease 1
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / molecular replacement / Resolution: 1.7 Å
AuthorsBisacchi, G.S. / Jacobson, B.
Citation
Journal: Bioorg.Med.Chem.Lett. / Year: 2004
Title: Solid-phase synthesis and SAR of 4-carboxy-2-azetidinone mechanism-based tryptase inhibitors
Authors: Sutton, J.C. / Bolton, S.A. / Davis, M.E. / Hartl, K.S. / Jacobson, B. / Mathur, A. / Ogletree, M.L. / Slusarchyk, W.A. / Zahler, R. / Seiler, S.M. / Bisacchi, G.S.
#1: Journal: Acta Crystallogr.,Sect.B / Year: 1982
Title: On the Disordered Activation Domain in Trypsinogen. Chemical Labelling and Low-Temperature Crystallography
Authors: Walter, J. / Steigemann, W. / Singh, T.P. / Bartunik, H. / Bode, W. / Huber, R.
History
DepositionDec 18, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 8, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TRYPSIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,8884
Polymers23,3241
Non-polymers5643
Water4,071226
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.290, 58.250, 66.680
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Cell settingorthorhombic
Space group name H-MP212121

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Components

#1: Protein TRYPSIN / / E.C.3.4.21.4


Mass: 23324.287 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Organ: PANCREAS / References: UniProt: P00760, trypsin
#2: Chemical ChemComp-CA / CALCIUM ION


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


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-169 / 1-(4-TERT-BUTYLCARBAMOYL-PIPERAZINE-1-CARBONYL)-3-(3-GUANIDINO-PROPYL)-4-OXO-AZETIDINE-2-CARBOXYLIC ACID


Mass: 427.499 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H33N7O5
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 226 / 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: 1.99 Å3/Da / Density % sol: 37.8 %

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 1.540,1.080
DetectorType: MARRESEARCH / Detector: CCD / Date: Jun 21, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.541
21.081
ReflectionResolution: 1.7→50 Å / Num. all: 25226 / Num. obs: 23883 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 7.6 % / Biso Wilson estimate: 9.2 Å2 / Rmerge(I) obs: 0.056 / Net I/σ(I): 23.9
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.184 / Mean I/σ(I) obs: 7.3 / % possible all: 99.3

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
X-PLOR98.1refinement
RefinementMethod to determine structure: molecular replacement / Resolution: 1.7→8 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 1
RfactorNum. reflection% reflectionSelection details
Rfree0.222 2309 10.1 %RANDOM
Rwork0.195 ---
all0.197 25226 --
obs0.195 22917 97.1 %-
Displacement parametersBiso mean: 10.5 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.19 Å0.17 Å
Luzzati d res low-5 Å
Luzzati sigma a0.09 Å0.1 Å
Refinement stepCycle: LAST / Resolution: 1.7→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1629 0 36 226 1891
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.009
X-RAY DIFFRACTIONx_angle_deg1.6
X-RAY DIFFRACTIONx_dihedral_angle_d26.2
X-RAY DIFFRACTIONx_improper_angle_d1.37
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 1.7→1.81 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.233 330 9.4 %
Rwork0.211 3186 -
obs--91.1 %

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