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- PDB-5egw: 2.70 A crystal structure of the Amb a 11 cysteine protease, a maj... -

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Basic information

Entry
Database: PDB / ID: 5egw
Title2.70 A crystal structure of the Amb a 11 cysteine protease, a major ragweed pollen allergen, in its proform
ComponentsCysteine protease
KeywordsALLERGEN / ragweed / cysteine protease / propeptide
Function / homology
Function and homology information


Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / cysteine-type endopeptidase activity / protein homodimerization activity / proteolysis
Similarity search - Function
Cathepsin propeptide inhibitor domain (I29) / Cathepsin propeptide inhibitor domain (I29) / Cathepsin propeptide inhibitor domain (I29) / Papain-like cysteine endopeptidase / : / Cysteine peptidase, asparagine active site / Eukaryotic thiol (cysteine) proteases asparagine active site. / Peptidase C1A, papain C-terminal / Papain family cysteine protease / Papain family cysteine protease ...Cathepsin propeptide inhibitor domain (I29) / Cathepsin propeptide inhibitor domain (I29) / Cathepsin propeptide inhibitor domain (I29) / Papain-like cysteine endopeptidase / : / Cysteine peptidase, asparagine active site / Eukaryotic thiol (cysteine) proteases asparagine active site. / Peptidase C1A, papain C-terminal / Papain family cysteine protease / Papain family cysteine protease / Cysteine proteinases / Cysteine peptidase, cysteine active site / Eukaryotic thiol (cysteine) proteases cysteine active site. / Cathepsin B; Chain A / Papain-like cysteine peptidase superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Cysteine protease Amb a 11.0101
Similarity search - Component
Biological speciesAmbrosia artemisiifolia (common ragweed)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsBriozzo, P. / Kopecny, D.
CitationJournal: J.Biol.Chem. / Year: 2016
Title: Structural and Functional Characterization of the Major Allergen Amb a 11 from Short Ragweed Pollen.
Authors: Groeme, R. / Airouche, S. / Kopecny, D. / Jaekel, J. / Savko, M. / Berjont, N. / Bussieres, L. / Le Mignon, M. / Jagic, F. / Zieglmayer, P. / Baron-Bodo, V. / Bordas-Le Floch, V. / ...Authors: Groeme, R. / Airouche, S. / Kopecny, D. / Jaekel, J. / Savko, M. / Berjont, N. / Bussieres, L. / Le Mignon, M. / Jagic, F. / Zieglmayer, P. / Baron-Bodo, V. / Bordas-Le Floch, V. / Mascarell, L. / Briozzo, P. / Moingeon, P.
History
DepositionOct 27, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Apr 27, 2016Provider: repository / Type: Initial release
Revision 1.1May 11, 2016Group: Database references
Revision 1.2Jun 29, 2016Group: Database references
Revision 1.3Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cysteine protease
B: Cysteine protease


Theoretical massNumber of molelcules
Total (without water)86,1632
Polymers86,1632
Non-polymers00
Water1086
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2970 Å2
ΔGint-11 kcal/mol
Surface area30430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.450, 89.550, 104.060
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Cysteine protease


Mass: 43081.473 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ambrosia artemisiifolia (common ragweed)
Plasmid: pET-15b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: V5LU01
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / 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: 2.26 Å3/Da / Density % sol: 45.49 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: protein buffer:20 mM Tris HCl pH 8.5, 150 mM NaCl, 5% (v/v) glycerol; precipitant solution: 100 mM trisodium citrate, 20% PEG 4000, 20% isopropanol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.9801 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 16, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9801 Å / Relative weight: 1
ReflectionResolution: 2.7→65 Å / Num. obs: 21824 / % possible obs: 99 % / Redundancy: 7.44 % / Rsym value: 0.113 / Net I/σ(I): 12.9
Reflection shellResolution: 2.7→2.85 Å / Mean I/σ(I) obs: 1.25 / % possible all: 93.7

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Processing

Software
NameVersionClassification
HKL-2000data scaling
BUSTER-TNTBUSTER 2.10.0refinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1S4V

1s4v


Resolution: 2.7→44.78 Å / Cor.coef. Fo:Fc: 0.9363 / Cor.coef. Fo:Fc free: 0.9106 / SU R Cruickshank DPI: 3.134 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 2.573 / SU Rfree Blow DPI: 0.288 / SU Rfree Cruickshank DPI: 0.293
RfactorNum. reflection% reflectionSelection details
Rfree0.2179 1153 5.28 %RANDOM
Rwork0.179 ---
obs0.181 21821 99.02 %-
Displacement parametersBiso max: 158.54 Å2 / Biso mean: 76.68 Å2 / Biso min: 32.62 Å2
Baniso -1Baniso -2Baniso -3
1-0.8333 Å20 Å20 Å2
2--17.9543 Å20 Å2
3----18.7876 Å2
Refine analyzeLuzzati coordinate error obs: 0.412 Å
Refinement stepCycle: final / Resolution: 2.7→44.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5417 0 0 6 5423
Biso mean---59.12 -
Num. residues----688
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1937SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes151HARMONIC2
X-RAY DIFFRACTIONt_gen_planes806HARMONIC5
X-RAY DIFFRACTIONt_it5554HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion679SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact6245SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d5554HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg7492HARMONIC21.23
X-RAY DIFFRACTIONt_omega_torsion2.87
X-RAY DIFFRACTIONt_other_torsion21.72
LS refinement shellResolution: 2.7→2.83 Å / Total num. of bins used: 11
RfactorNum. reflection% reflection
Rfree0.273 125 4.66 %
Rwork0.2474 2556 -
all0.2485 2681 -
obs--99.02 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.57030.4478-0.66050.8623-0.14540.8366-0.07840.18880.2035-0.11030.03740.2444-0.1204-0.17920.041-0.67530.0687-0.0842-0.74790.0478-0.648922.9795-4.4895-11.8839
23.1198-0.48220.09391.2868-0.15920.9611-0.1832-0.04460.3986-0.0206-0.0291-0.4873-0.34890.28540.2124-0.677-0.1069-0.0397-0.82170.0899-0.577465.0366-2.6238-9.225
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A21 - 385
2X-RAY DIFFRACTION2{ B|* }B20 - 349

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