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- PDB-1pq5: Trypsin at pH 5, 0.85 A -

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Basic information

Entry
Database: PDB / ID: 1pq5
TitleTrypsin at pH 5, 0.85 A
ComponentsTrypsin
KeywordsHYDROLASE / trypsin / serine protease / catalysis
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 / 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
Biological speciesFusarium oxysporum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 0.85 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 18, 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: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software / Item: _software.name
Revision 1.4Nov 20, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_entry_details / pdbx_modification_feature / pdbx_unobs_or_zero_occ_atoms / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)22,6645
Polymers22,2001
Non-polymers4634
Water8,611478
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)32.890, 36.958, 39.781
Angle α, β, γ (deg.)102.84, 104.54, 102.39
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Trypsin


Mass: 22200.490 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


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-ARG / ARGININE


Type: L-peptide linking / Mass: 175.209 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H15N4O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 478 / Source method: isolated from a natural source / Formula: H2O
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: 1.97 Å3/Da / Density % sol: 37.52 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5
Details: Na sulphate, Na citrate, pH 5, 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: Jun 20, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.811 Å / Relative weight: 1
ReflectionResolution: 0.83→35 Å / Num. all: 146915 / Num. obs: 146915 / % possible obs: 91.6 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 2 % / Biso Wilson estimate: 4.99 Å2 / Rsym value: 0.033 / Net I/σ(I): 34
Reflection shellResolution: 0.83→0.84 Å / Redundancy: 2 % / Mean I/σ(I) obs: 7.22 / Num. unique all: 3215 / Rsym value: 0.101 / % possible all: 80.6
Reflection
*PLUS
Lowest resolution: 30 Å / Num. obs: 146839 / Rmerge(I) obs: 0.033
Reflection shell
*PLUS
Mean I/σ(I) obs: 7.2

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Processing

Software
NameClassification
SHELXLrefinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementResolution: 0.85→30 Å / Num. parameters: 20006 / Num. restraintsaints: 25358 / Stereochemistry target values: ENGH AND HUBER
Details: initially Rfree (building stage) was used (10% of data at random), later Rfree was not used.
RfactorNum. reflection% reflection
Rwork0.0984 --
all0.0984 137323 -
obs-137323 92.1 %
Refine analyzeNum. disordered residues: 43 / Occupancy sum hydrogen: 1500.73 / Occupancy sum non hydrogen: 1998.19
Refinement stepCycle: LAST / Resolution: 0.85→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3371 0 38 479 3888
Software
*PLUS
Name: SHELXL / Version: 96 / Classification: refinement
Refinement
*PLUS
Highest resolution: 0.83 Å / Rfactor Rwork: 0.098
Solvent computation
*PLUS
Displacement parameters
*PLUS

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