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- PDB-6nff: Structure of X-prolyl dipeptidyl aminopeptidase from Lactobacillu... -

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Basic information

Entry
Database: PDB / ID: 6nff
TitleStructure of X-prolyl dipeptidyl aminopeptidase from Lactobacillus helveticus
ComponentsXaa-Pro dipeptidyl-peptidase
KeywordsHYDROLASE / peptidase
Function / homology
Function and homology information


Xaa-Pro dipeptidyl-peptidase / dipeptidyl-peptidase activity / aminopeptidase activity / serine-type peptidase activity / proteolysis / cytoplasm
Similarity search - Function
Serum Albumin; Chain A, Domain 1 - #70 / Peptidase S15, X-Pro dipeptidyl-peptidase / X-Prolyl dipeptidyl aminopeptidase PepX, N-terminal domain / PepX, N-terminal domain superfamily / X-Prolyl dipeptidyl aminopeptidase PepX, N-terminal / X-Prolyl dipeptidyl aminopeptidase PepX, N-terminal / CocE/Serine esterase / Xaa-Pro dipeptidyl-peptidase, C-terminal / X-Pro dipeptidyl-peptidase C-terminal non-catalytic domain / X-Pro dipeptidyl-peptidase C-terminal non-catalytic domain ...Serum Albumin; Chain A, Domain 1 - #70 / Peptidase S15, X-Pro dipeptidyl-peptidase / X-Prolyl dipeptidyl aminopeptidase PepX, N-terminal domain / PepX, N-terminal domain superfamily / X-Prolyl dipeptidyl aminopeptidase PepX, N-terminal / X-Prolyl dipeptidyl aminopeptidase PepX, N-terminal / CocE/Serine esterase / Xaa-Pro dipeptidyl-peptidase, C-terminal / X-Pro dipeptidyl-peptidase C-terminal non-catalytic domain / X-Pro dipeptidyl-peptidase C-terminal non-catalytic domain / Xaa-Pro dipeptidyl-peptidase-like domain / X-Pro dipeptidyl-peptidase (S15 family) / Serum Albumin; Chain A, Domain 1 / Galactose-binding-like domain superfamily / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Xaa-Pro dipeptidyl-peptidase
Similarity search - Component
Biological speciesLactobacillus helveticus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsJuers, D.H. / Bratt, N.J. / Ojennus, D.D.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2019
Title: Structural characterization of a prolyl aminodipeptidase (PepX) from Lactobacillus helveticus.
Authors: Ojennus, D.D. / Bratt, N.J. / Jones, K.L. / Juers, D.H.
History
DepositionDec 20, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 2, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Oct 11, 2023Group: 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

Downloads & links

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Assembly

Deposited unit
A: Xaa-Pro dipeptidyl-peptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,11723
Polymers92,6421
Non-polymers1,47522
Water10,106561
1
A: Xaa-Pro dipeptidyl-peptidase
hetero molecules

A: Xaa-Pro dipeptidyl-peptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)188,23446
Polymers185,2842
Non-polymers2,95044
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Unit cell
Length a, b, c (Å)154.630, 154.630, 106.594
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-1411-

HOH

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Components

#1: Protein Xaa-Pro dipeptidyl-peptidase / X-Pro dipeptidyl-peptidase / X-prolyl-dipeptidyl aminopeptidase / X-PDAP


Mass: 92641.891 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactobacillus helveticus (bacteria) / Gene: pepX / Production host: Escherichia coli (E. coli) / References: UniProt: Q59485, Xaa-Pro dipeptidyl-peptidase
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 561 / 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: 3.57 Å3/Da / Density % sol: 64.23 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop
Details: 5.3 mg/mL protein against 6.8-8.2% PEG3350, 75 mM potassium phosphate, pH 6.0, 1 mM DTT
PH range: 6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SEALED TUBE / Type: OXFORD DIFFRACTION NOVA / Wavelength: 1.54 Å
DetectorType: OXFORD ONYX CCD / Detector: CCD / Date: Jul 29, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2→30.3 Å / Num. obs: 87344 / % possible obs: 100 % / Redundancy: 18.3 % / CC1/2: 0.987 / Rrim(I) all: 0.401 / Net I/σ(I): 8.1
Reflection shellResolution: 2→2.04 Å / Redundancy: 10.4 % / Mean I/σ(I) obs: 0.5 / Num. unique obs: 4411 / CC1/2: 0.249 / Rrim(I) all: 4.952 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
CrysalisProdata collection
CrysalisProdata reduction
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1LNS

1lns


Resolution: 2→30.3 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 32.95
RfactorNum. reflection% reflection
Rfree0.2729 4332 5.09 %
Rwork0.2364 --
obs0.2382 85144 97.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2→30.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6395 0 89 561 7045
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076630
X-RAY DIFFRACTIONf_angle_d0.8748954
X-RAY DIFFRACTIONf_dihedral_angle_d11.9463909
X-RAY DIFFRACTIONf_chiral_restr0.051943
X-RAY DIFFRACTIONf_plane_restr0.0051155
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.02270.44681300.47562541X-RAY DIFFRACTION94
2.0227-2.04650.42391020.44511840X-RAY DIFFRACTION67
2.0465-2.07150.43661530.41222708X-RAY DIFFRACTION100
2.0715-2.09770.4568990.40092325X-RAY DIFFRACTION85
2.0977-2.12530.37431430.34982687X-RAY DIFFRACTION98
2.1253-2.15440.34861590.34292700X-RAY DIFFRACTION99
2.1544-2.18520.36971300.3382721X-RAY DIFFRACTION99
2.1852-2.21780.38241420.39022521X-RAY DIFFRACTION93
2.2178-2.25240.37321380.33172742X-RAY DIFFRACTION100
2.2524-2.28930.32311380.31812707X-RAY DIFFRACTION99
2.2893-2.32880.35441320.2822732X-RAY DIFFRACTION100
2.3288-2.37110.30481490.27662748X-RAY DIFFRACTION100
2.3711-2.41670.33861380.28822740X-RAY DIFFRACTION100
2.4167-2.4660.32721570.28132717X-RAY DIFFRACTION100
2.466-2.51960.3191460.26692735X-RAY DIFFRACTION100
2.5196-2.57820.33511610.27092732X-RAY DIFFRACTION100
2.5782-2.64270.36871590.27812727X-RAY DIFFRACTION100
2.6427-2.71410.2751680.25282717X-RAY DIFFRACTION100
2.7141-2.79390.32131680.26012726X-RAY DIFFRACTION100
2.7939-2.8840.3291200.252803X-RAY DIFFRACTION100
2.884-2.9870.29141540.25552724X-RAY DIFFRACTION100
2.987-3.10650.32011440.25242751X-RAY DIFFRACTION100
3.1065-3.24770.29761370.25632777X-RAY DIFFRACTION99
3.2477-3.41870.2881360.23422759X-RAY DIFFRACTION99
3.4187-3.63260.26861510.22192745X-RAY DIFFRACTION99
3.6326-3.91250.23421650.18832762X-RAY DIFFRACTION99
3.9125-4.30520.20031360.15862763X-RAY DIFFRACTION98
4.3052-4.92590.15771710.13512782X-RAY DIFFRACTION100
4.9259-6.19740.15631460.14952875X-RAY DIFFRACTION100
6.1974-30.32890.19491600.1663005X-RAY DIFFRACTION100

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