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- PDB-1xvm: Trypsin from Fusarium oxysporum- room temperature to atomic resolution -

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Basic information

Entry
Database: PDB / ID: 1xvm
TitleTrypsin from Fusarium oxysporum- room temperature to atomic resolution
Components
  • Trypsin
  • substrate tripeptide GLY-ALA-ARG
KeywordsHYDROLASE / atomic resolution / mobility / room temperature
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 / MOLECULAR REPLACEMENT / Resolution: 1.1 Å
AuthorsSchmidt, A. / Lamzin, V.S.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2005
Title: Extraction of functional motion in trypsin crystal structures.
Authors: Schmidt, A. / Lamzin, V.S.
History
DepositionOct 28, 2004Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 26, 2005Provider: repository / Type: Initial release
Revision 1.1Oct 21, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 25, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site
Revision 1.4Oct 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: substrate tripeptide GLY-ALA-ARG


Theoretical massNumber of molelcules
Total (without water)22,5042
Polymers22,5042
Non-polymers00
Water2,360131
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)33.277, 37.037, 40.100
Angle α, β, γ (deg.)102.22, 103.93, 102.59
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 substrate tripeptide GLY-ALA-ARG


Mass: 303.339 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: THE PEPTIDE IS CHEMICALLY SYNTHESIZED.
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 131 / 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 Å3/Da / Density % sol: 38.43 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5
Details: ammonium sulfate, sodium citrate, pH 5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.803 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Oct 2, 2003 / Details: mirrors
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.803 Å / Relative weight: 1
ReflectionHighest resolution: 1.1 Å / Num. all: 65556 / Num. obs: 65556 / % possible obs: 93 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 2 % / Biso Wilson estimate: 9 Å2 / Rsym value: 0.094 / Net I/σ(I): 6.9
Reflection shellResolution: 1.1→1.11 Å / Redundancy: 2 % / Mean I/σ(I) obs: 2.6 / Num. unique all: 2271 / Rsym value: 0.361 / % possible all: 92.4

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Processing

Software
NameClassification
SHELXmodel building
SHELXL-97refinement
DENZOdata reduction
SCALEPACKdata scaling
CCP4phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1PQ5

1pq5


Resolution: 1.1→10 Å / Num. parameters: 15420 / Num. restraintsaints: 19268 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ENGH & HUBER
Details: ANISOTROPIC REFINEMENT, Hydrogens included, refinement against diffraction intensities
RfactorNum. reflection% reflection
Rwork0.1439 --
obs0.1439 65556 91.9 %
all-65556 -
Displacement parametersBiso mean: 15.1 Å2
Refine analyzeNum. disordered residues: 11 / Occupancy sum hydrogen: 1475.2 / Occupancy sum non hydrogen: 1696.6
Refinement stepCycle: LAST / Resolution: 1.1→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3063 0 0 131 3194
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.022
X-RAY DIFFRACTIONs_angle_d0.03
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.029
X-RAY DIFFRACTIONs_zero_chiral_vol0.081
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.085
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.078
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.005
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.041
X-RAY DIFFRACTIONs_approx_iso_adps0.067

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