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- PDB-7eox: Protease structure from Euphorbia resinifera -

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Basic information

Entry
Database: PDB / ID: 7eox
TitleProtease structure from Euphorbia resinifera
ComponentsProtease
KeywordsPLANT PROTEIN / Euphorbia resinifera / plant latex / serine protease
Function / homologyIODIDE ION
Function and homology information
Biological speciesEuphorbia resinifera (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.7 Å
AuthorsSiritapetawee, J. / Attarataya, J. / Charoenwattanasatien, R.
Funding support Thailand, 1items
OrganizationGrant numberCountry
The Thailand Research Fund (TRF)RSA6280012 Thailand
CitationJournal: Biotechnol Appl Biochem / Year: 2022
Title: Sequence analysis and crystal structure of a glycosylated protease from Euphorbia resinifera latex for its proteolytic activity aspect.
Authors: Siritapetawee, J. / Attarataya, J. / Charoenwattanasatien, R.
History
DepositionApr 24, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 12, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 4, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Oct 23, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protease
B: Protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)140,37310
Polymers138,0122
Non-polymers2,3608
Water12,592699
1
A: Protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,4814
Polymers69,0061
Non-polymers4753
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area310 Å2
ΔGint3 kcal/mol
Surface area23710 Å2
MethodPISA
2
B: Protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,8916
Polymers69,0061
Non-polymers1,8855
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1880 Å2
ΔGint24 kcal/mol
Surface area24490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.673, 112.880, 201.801
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Protease


Mass: 69006.125 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Euphorbia resinifera (plant)
#2: Polysaccharide beta-D-xylopyranose-(1-2)-[alpha-D-mannopyranose-(1-3)][alpha-D-mannopyranose-(1-6)]beta-D- ...beta-D-xylopyranose-(1-2)-[alpha-D-mannopyranose-(1-3)][alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1189.079 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DXylpb1-2[DManpa1-3][DManpa1-6]DManpb1-4DGlcpNAcb1-4[LFucpa1-3]DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/5,7,6/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5][a1122h-1b_1-5][a212h-1b_1-5][a1122h-1a_1-5]/1-2-1-3-4-5-5/a3-b1_a4-c1_c4-d1_d2-e1_d3-f1_d6-g1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(3+1)][a-L-Fucp]{}[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(2+1)][b-D-Xylp]{}[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}LINUCSPDB-CARE
#3: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Chemical
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: I
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 699 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.87 Å3/Da / Density % sol: 57.21 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2M sodium idodide (0.2 M), 0.1M Bis-Tris propane pH 8.5, 20% W/V PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 28, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.7→64.16 Å / Num. obs: 168106 / % possible obs: 99 % / Redundancy: 5.8 % / CC1/2: 0.995 / Rmerge(I) obs: 0.116 / Rpim(I) all: 0.08 / Rrim(I) all: 0.141 / Net I/σ(I): 9.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all
1.7-1.7362.68380270.521.8533.278
9.31-64.165.80.03110290.9720.0210.038

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
DIALSdata reduction
DIALSdata scaling
HKL2Mapphasing
RefinementMethod to determine structure: SAD / Resolution: 1.7→60.01 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.94 / SU B: 3.197 / SU ML: 0.096 / Cross valid method: THROUGHOUT / ESU R: 0.104 / ESU R Free: 0.104 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23667 8569 5.1 %RANDOM
Rwork0.20258 ---
obs0.20434 159344 98.63 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.667 Å2
Baniso -1Baniso -2Baniso -3
1--0.33 Å20 Å20 Å2
2--1.98 Å2-0 Å2
3----1.65 Å2
Refinement stepCycle: 1 / Resolution: 1.7→60.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9438 0 126 701 10265
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0139812
X-RAY DIFFRACTIONr_bond_other_d0.0020.0178772
X-RAY DIFFRACTIONr_angle_refined_deg1.6211.65313396
X-RAY DIFFRACTIONr_angle_other_deg1.3761.5920336
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.80851262
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.67823.333426
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.99151408
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.5281536
X-RAY DIFFRACTIONr_chiral_restr0.0760.21353
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0211223
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022130
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.2662.695066
X-RAY DIFFRACTIONr_mcbond_other2.2662.695065
X-RAY DIFFRACTIONr_mcangle_it3.14.0246322
X-RAY DIFFRACTIONr_mcangle_other3.14.0246323
X-RAY DIFFRACTIONr_scbond_it2.9973.0014746
X-RAY DIFFRACTIONr_scbond_other2.9973.0014747
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.4614.3897075
X-RAY DIFFRACTIONr_long_range_B_refined5.42932.52710752
X-RAY DIFFRACTIONr_long_range_B_other5.39232.31310613
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.362 658 -
Rwork0.346 11635 -
obs--98.42 %

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