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- PDB-5yfc: Crystal structure of a new DPP III family member -

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Basic information

Entry
Database: PDB / ID: 5yfc
TitleCrystal structure of a new DPP III family member
ComponentsDipeptidyl peptidase 3
KeywordsHYDROLASE / dipeptidyl peptidase III / aflatoxin-oxidase
Function / homology
Function and homology information


dipeptidyl-peptidase III / metalloexopeptidase activity / dipeptidyl-peptidase activity / aminopeptidase activity / proteolysis / metal ion binding / cytoplasm
Similarity search - Function
Dipeptidyl-peptidase 3 / Peptidase family M49 / Peptidase family M49
Similarity search - Domain/homology
Dipeptidyl peptidase 3
Similarity search - Component
Biological speciesArmillaria tabescens (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.76 Å
AuthorsXu, T. / Liu, J.
CitationJournal: Biochem. Biophys. Res. Commun. / Year: 2017
Title: Crystal structures of Aflatoxin-oxidase from Armillariella tabescens reveal a dual activity enzyme.
Authors: Xu, T. / Xie, C. / Yao, D. / Zhou, C.Z. / Liu, J.
History
DepositionSep 20, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 3, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: Dipeptidyl peptidase 3
B: Dipeptidyl peptidase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)158,24223
Polymers156,3622
Non-polymers1,88021
Water26,3381462
1
A: Dipeptidyl peptidase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,13912
Polymers78,1811
Non-polymers95811
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area200 Å2
ΔGint-16 kcal/mol
Surface area27050 Å2
MethodPISA
2
B: Dipeptidyl peptidase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,10311
Polymers78,1811
Non-polymers92210
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area200 Å2
ΔGint-16 kcal/mol
Surface area27010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.390, 207.730, 59.010
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Dipeptidyl peptidase 3 / Dipeptidyl aminopeptidase III / Dipeptidyl peptidase III


Mass: 78181.234 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Armillaria tabescens (fungus) / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: B0S4Q0, dipeptidyl-peptidase III

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Non-polymers , 5 types, 1483 molecules

#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1462 / 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: 2.29 Å3/Da / Density % sol: 46.26 % / Mosaicity: 0.25 °
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7.5 / Details: 0.1 M Tris-HCl pH 8.5, 2.5 M Ammonium Sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9793 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 22, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.76→59.01 Å / Num. obs: 134694 / % possible obs: 98 % / Redundancy: 7.2 % / CC1/2: 0.994 / Rmerge(I) obs: 0.066 / Rpim(I) all: 0.027 / Rrim(I) all: 0.071 / Net I/σ(I): 22.6 / Num. measured all: 968571 / Scaling rejects: 5046
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.76-1.797.10.0844624764910.9940.0340.09114.895.8
9.66-59.015.20.05831136040.9910.0290.06520.168.9

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Processing

Software
NameVersionClassification
Aimless0.5.9data scaling
REFMAC5.8.0158refinement
PDB_EXTRACT3.22data extraction
iMOSFLMdata reduction
MOLREPphasing
RefinementResolution: 1.76→59.01 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.928 / SU B: 1.954 / SU ML: 0.064 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.111 / ESU R Free: 0.113
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1978 6535 4.9 %RANDOM
Rwork0.1521 ---
obs0.1543 128119 97.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 74.3 Å2 / Biso mean: 10.813 Å2 / Biso min: 2.82 Å2
Baniso -1Baniso -2Baniso -3
1--0.05 Å2-0 Å2-0.04 Å2
2---0.22 Å20 Å2
3---0.26 Å2
Refinement stepCycle: final / Resolution: 1.76→59.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10814 0 101 1462 12377
Biso mean--35.05 18.15 -
Num. residues----1380
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.01911543
X-RAY DIFFRACTIONr_bond_other_d0.0020.0210760
X-RAY DIFFRACTIONr_angle_refined_deg1.9911.9715779
X-RAY DIFFRACTIONr_angle_other_deg1.098325128
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8651519
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.45425.115524
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.942152018
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.7921549
X-RAY DIFFRACTIONr_chiral_restr0.1360.21800
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0212895
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022263
LS refinement shellResolution: 1.764→1.81 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.218 483 -
Rwork0.148 9306 -
all-9789 -
obs--96.51 %

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