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

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Basic information

Entry
Database: PDB / ID: 5yfb
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: 2.2 Å
AuthorsXu, T. / Sun, Z. / 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 / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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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)157,32615
Polymers156,3622
Non-polymers96413
Water5,062281
1
A: Dipeptidyl peptidase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,6477
Polymers78,1811
Non-polymers4666
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area400 Å2
ΔGint-39 kcal/mol
Surface area26930 Å2
MethodPISA
2
B: Dipeptidyl peptidase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,6798
Polymers78,1811
Non-polymers4987
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area100 Å2
ΔGint-37 kcal/mol
Surface area27150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)207.208, 84.630, 90.220
Angle α, β, γ (deg.)90.000, 108.460, 90.000
Int Tables number5
Space group name H-MC121

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Components

#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
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 281 / 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: 2.44 Å3/Da / Density % sol: 49.68 % / Mosaicity: 0.29 °
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7.5 / Details: 0.2 M Sodium formate pH 7.0, 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9785 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 22, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 2.2→98.27 Å / Num. obs: 73866 / % possible obs: 98.4 % / Redundancy: 6.4 % / CC1/2: 0.998 / Rmerge(I) obs: 0.057 / Rpim(I) all: 0.024 / Rrim(I) all: 0.062 / Net I/σ(I): 14.6 / Num. measured all: 472137 / Scaling rejects: 904
Reflection shell

Diffraction-ID: 1 / Redundancy: 6.6 %

Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.2-2.250.12944220.990.0530.1498.8
11-98.270.0486500.9980.0190.05299.9

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Processing

Software
NameVersionClassification
Aimless0.5.9data scaling
REFMAC5.8.0158refinement
PDB_EXTRACT3.22data extraction
MOSFLMdata reduction
MOLREPphasing
RefinementResolution: 2.2→98.27 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.889 / SU B: 5.895 / SU ML: 0.151 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.28 / ESU R Free: 0.223 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2484 3734 5.1 %RANDOM
Rwork0.1872 ---
obs0.1903 70130 98.16 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 88.54 Å2 / Biso mean: 24.031 Å2 / Biso min: 3.75 Å2
Baniso -1Baniso -2Baniso -3
1-0.11 Å2-0 Å2-0.37 Å2
2--1.35 Å2-0 Å2
3----0.99 Å2
Refinement stepCycle: final / Resolution: 2.2→98.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10825 0 56 281 11162
Biso mean--33.03 17.1 -
Num. residues----1381
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.01911115
X-RAY DIFFRACTIONr_bond_other_d0.0020.0210380
X-RAY DIFFRACTIONr_angle_refined_deg1.8271.96415060
X-RAY DIFFRACTIONr_angle_other_deg1.085324133
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.32351387
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.31924.94498
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.21151908
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0991548
X-RAY DIFFRACTIONr_chiral_restr0.1210.21697
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02112317
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022187
LS refinement shellResolution: 2.2→2.257 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.282 282 -
Rwork0.222 5170 -
all-5452 -
obs--98.68 %

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