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- PDB-1gdq: FUSARIUM OXYSPORUM TRYPSIN AT ATOMIC RESOLUTION -

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Basic information

Entry
Database: PDB / ID: 1gdq
TitleFUSARIUM OXYSPORUM TRYPSIN AT ATOMIC RESOLUTION
Components
  • GLY-ALA-ARG
  • TRYPSIN
KeywordsHYDROLASE / beta-barrel
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: 0.93 Å
AuthorsRypniewski, W.R. / Oestergaard, P. / Noerregaard-Madsen, M. / Dauter, M. / Wilson, K.S.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2001
Title: Fusarium oxysporum trypsin at atomic resolution at 100 and 283 K: a study of ligand binding.
Authors: Rypniewski, W.R. / Ostergaard, P.R. / Norregaard-Madsen, M. / Dauter, M. / Wilson, K.S.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 1995
Title: Structure of inhibited trypsin from Fusarium oxysporum at 1.55A
Authors: Rypniewski, W.R. / Dambmann, C. / von der Osten, C. / Dauter, M. / Wilson, K.S.
History
DepositionSep 28, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 7, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Jan 31, 2018Group: Advisory / Experimental preparation / Category: exptl_crystal_grow / pdbx_unobs_or_zero_occ_atoms / Item: _exptl_crystal_grow.temp
Revision 1.4Dec 27, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / 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
Revision 1.5Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TRYPSIN
B: GLY-ALA-ARG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,7885
Polymers22,5042
Non-polymers2843
Water9,422523
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)33.045, 36.974, 39.783
Angle α, β, γ (deg.)102.81, 104.56, 102.40
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: Protein/peptide GLY-ALA-ARG


Mass: 303.339 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 523 / 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: 1.95 Å3/Da / Density % sol: 37 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 6
Details: sodium sulphate, sodium citrate, pH 6, VAPOR DIFFUSION, SITTING DROP, temperature 19K
Crystal grow
*PLUS
pH: 6
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
125 Mprotein1drop
210 mM3,3-dimethyl glutaric acid1drop
32 mM1dropCaCl2
4100 mM1dropNaCl
51.4 M1reservoirNa2SO4
60.1 Msodium citrate1reservoir
70-5 %2-propanol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.87
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 23, 1994
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 0.93→12 Å / Num. all: 576525 / Num. obs: 576525 / % possible obs: 92.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.3 % / Biso Wilson estimate: 6 Å2 / Rmerge(I) obs: 0.043 / Net I/σ(I): 19
Reflection shellResolution: 0.93→0.95 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.247 / Num. unique all: 5033 / % possible all: 86.3
Reflection
*PLUS
Lowest resolution: 12 Å / Num. obs: 107781 / Num. measured all: 576525
Reflection shell
*PLUS
% possible obs: 86.3 %

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
SHELXL-97refinement
RefinementResolution: 0.93→12 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
Details: least-squares refinement against I's. Full-matrix least-squares at the end to obtain error estimates
RfactorNum. reflectionSelection details
Rwork0.0986 --
all0.0986 107781 -
obs0.0986 107781 -
Rfree-0 not used
Refinement stepCycle: LAST / Resolution: 0.93→12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1568 0 16 523 2107
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.014
X-RAY DIFFRACTIONs_angle_d0.031
Software
*PLUS
Name: SHELXL-97 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 12 Å / σ(F): 0
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: s_chiral_restr / Dev ideal: 0.112

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