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

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Basic information

Entry
Database: PDB / ID: 1gdu
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: 1.07 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: To Be Published
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 29, 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: 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 1.4Apr 4, 2018Group: Data collection / Category: diffrn_source
Item: _diffrn_source.pdbx_synchrotron_site / _diffrn_source.type
Revision 1.5Dec 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 / 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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.6Oct 30, 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)22,6003
Polymers22,5042
Non-polymers961
Water6,485360
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area750 Å2
ΔGint-9 kcal/mol
Surface area8920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)33.290, 37.050, 40.259
Angle α, β, γ (deg.)102.46, 103.81, 102.07
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.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 360 / 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: 2.01 Å3/Da / Density % sol: 38.83 %
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
1100 mMboric acid1drop
22 mM1dropCaCl2
3100 mM1dropNaCl
410 mM3,3-dimethyl glutaric acid1drop
525 mg/mlprotein1drop
61.4 M1reservoirNa2SO4
70.1 Msodium citrate1reservoir
80-5 %2-propanol1reservoir

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
12831
21
31
Diffraction source
SourceSiteBeamlineTypeIDWavelength
SYNCHROTRONEMBL/DESY, HAMBURG BW7B10.95
SYNCHROTRONEMBL/DESY, HAMBURG X3120.92
SEALED TUBEOTHER30.71
DetectorType: MARRESEARCH / Detector: AREA DETECTOR / Date: Dec 5, 1993
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.951
20.921
30.711
ReflectionResolution: 1.07→15 Å / Num. all: 297606 / Num. obs: 297606 / % possible obs: 92.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Biso Wilson estimate: 6 Å2 / Rmerge(I) obs: 0.083 / Net I/σ(I): 6.8
Reflection shellResolution: 1.07→1.09 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.083 / Num. unique all: 3279 / % possible all: 87.6
Reflection
*PLUS
Lowest resolution: 15 Å / Num. obs: 70387 / Num. measured all: 297606
Reflection shell
*PLUS
% possible obs: 87.6 %

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
SHELXL-97refinement
RefinementResolution: 1.07→15 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
Rwork0.1036 --
all0.1036 70387 -
obs0.1036 70387 -
Rfree-0 not used
Refinement stepCycle: LAST / Resolution: 1.07→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3119 0 5 360 3484
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.015
X-RAY DIFFRACTIONs_angle_d0.031
Software
*PLUS
Name: SHELXL-97 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 15 Å / σ(F): 0 / Rfactor all: 0.104
Solvent computation
*PLUS
Displacement parameters
*PLUS

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