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- PDB-1ppz: Trypsin complexes at atomic and ultra-high resolution -

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Basic information

Entry
Database: PDB / ID: 1ppz
TitleTrypsin complexes at atomic and ultra-high resolution
ComponentsTrypsin
KeywordsHYDROLASE / trypsin / serine protease / atomic and ultra-high resolution / complex / DFP
Function / homology
Function and homology information


trypsin / serine-type endopeptidase activity / proteolysis / extracellular region
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 speciesFusarium oxysporum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.23 Å
AuthorsSchmidt, A. / Jelsch, C. / Rypniewski, W. / Lamzin, V.S.
CitationJournal: J.Biol.Chem. / Year: 2003
Title: Trypsin Revisited: CRYSTALLOGRAPHY AT (SUB) ATOMIC RESOLUTION AND QUANTUM CHEMISTRY REVEALING DETAILS OF CATALYSIS.
Authors: Schmidt, A. / Jelsch, C. / Ostergaard, P. / Rypniewski, W. / Lamzin, V.S.
History
DepositionJun 17, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 11, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.name
Remark 600HETEROGEN DFP REACTED WITH SER 195 RESULTING IN MONOISOPROPYLPHOSPHORYLSERINE.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Trypsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,4192
Polymers22,3231
Non-polymers961
Water4,756264
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)32.999, 66.505, 39.244
Angle α, β, γ (deg.)90.00, 108.67, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Trypsin /


Mass: 22322.549 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Fusarium oxysporum (fungus) / References: UniProt: P35049, trypsin
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 264 / 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: 1.83 Å3/Da / Density % sol: 32.67 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5
Details: Na-sulfate, Na-citrate, pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop / Details: Rypniewski, W.R., (1993) Protein Eng., 6, 341. / PH range low: 5.5 / PH range high: 5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
112.5 mg/mlprotein1drop
20.7 Mammonium sulfate1drop
350 mMcitrate1drop
41.4 Mammonium sulfate1reservoir
50.1 Msodium citrate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, Hamburg / Beamline: X11 / Wavelength: 0.811 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Apr 8, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.811 Å / Relative weight: 1
ReflectionResolution: 1.22→35 Å / Num. all: 46357 / Num. obs: 46357 / % possible obs: 99.6 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 4 % / Biso Wilson estimate: 11.3 Å2 / Rsym value: 0.045 / Net I/σ(I): 28
Reflection shellResolution: 1.22→1.24 Å / Redundancy: 4 % / Mean I/σ(I) obs: 5.5 / Rsym value: 0.21 / % possible all: 97.7
Reflection
*PLUS
Lowest resolution: 31 Å / Num. obs: 47457 / Rmerge(I) obs: 0.045

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Processing

Software
NameClassification
SHELXLrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.23→35 Å / Num. parameters: 17799 / Num. restraintsaints: 23171 / Stereochemistry target values: Engh & Huber / Details: ANISOTROPIC REFINEMENT
RfactorNum. reflection% reflectionSelection details
Rwork0.1405 ---
all-46357 --
obs-46357 99.6 %-
Rfree---only initially 10% data at random
Refine analyzeNum. disordered residues: 31 / Occupancy sum hydrogen: 1485.5 / Occupancy sum non hydrogen: 1792.27
Refinement stepCycle: LAST / Resolution: 1.23→35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3322 0 5 264 3591
Software
*PLUS
Name: SHELXL / Version: 96 / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.22 Å / Rfactor Rwork: 0.14
Solvent computation
*PLUS
Displacement parameters
*PLUS

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