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

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Basic information

Entry
Database: PDB / ID: 5yfd
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
COPPER (II) ION / 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 ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / refine_hist / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.d_res_low / _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

Downloads & links

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Assembly

Deposited unit
A: Dipeptidyl peptidase 3
B: Dipeptidyl peptidase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)157,47614
Polymers156,3622
Non-polymers1,11412
Water14,520806
1
A: Dipeptidyl peptidase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,7257
Polymers78,1811
Non-polymers5446
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area400 Å2
ΔGint-31 kcal/mol
Surface area27040 Å2
MethodPISA
2
B: Dipeptidyl peptidase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,7517
Polymers78,1811
Non-polymers5706
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area130 Å2
ΔGint-12 kcal/mol
Surface area27090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.460, 207.140, 58.990
Angle α, β, γ (deg.)90.000, 90.020, 90.000
Int Tables number4
Space group name H-MP1211

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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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu
#4: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 806 / 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: 2.28 Å3/Da / Density % sol: 46.15 % / Mosaicity: 0.4 °
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→69.05 Å / Num. obs: 126351 / % possible obs: 92.3 % / Redundancy: 5.5 % / CC1/2: 0.995 / Rmerge(I) obs: 0.053 / Rpim(I) all: 0.025 / Rrim(I) all: 0.059 / Net I/σ(I): 23.6 / Num. measured all: 695574 / Scaling rejects: 4566
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.76-1.795.40.09763100.9770.0460.10893.1
9.66-69.054.80.0347630.9960.0180.03988.3

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Processing

Software
NameVersionClassification
Aimless0.5.32data scaling
REFMAC5.8.0158refinement
PDB_EXTRACT3.22data extraction
iMOSFLMdata reduction
MOLREPphasing
RefinementResolution: 1.76→58.99 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.909 / SU B: 2.187 / SU ML: 0.072 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.133 / ESU R Free: 0.125 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2171 6274 5 %RANDOM
Rwork0.1801 ---
obs0.1819 119996 92.07 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 54.62 Å2 / Biso mean: 10.284 Å2 / Biso min: 2.53 Å2
Baniso -1Baniso -2Baniso -3
1--0.08 Å2-0 Å20.16 Å2
2---0.27 Å2-0 Å2
3---0.35 Å2
Refinement stepCycle: final / Resolution: 1.76→58.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10800 0 55 806 11661
Biso mean--31.49 12.7 -
Num. residues----1378
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.01911163
X-RAY DIFFRACTIONr_bond_other_d0.0020.0210402
X-RAY DIFFRACTIONr_angle_refined_deg1.9541.96615175
X-RAY DIFFRACTIONr_angle_other_deg1.1324198
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.01651410
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.46524.91499
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.407151922
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0061549
X-RAY DIFFRACTIONr_chiral_restr0.1410.21719
X-RAY DIFFRACTIONr_gen_planes_refined0.010.02112392
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022201
LS refinement shellResolution: 1.764→1.81 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.231 426 -
Rwork0.163 8951 -
all-9377 -
obs--92.94 %

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