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- PDB-1lns: Crystal Structure Analysis of the X-Prolyl Dipeptidyl Aminopeptid... -

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Basic information

Entry
Database: PDB / ID: 1lns
TitleCrystal Structure Analysis of the X-Prolyl Dipeptidyl Aminopeptidase From Lactococcus lactis
ComponentsX-PROLYL DIPEPTIDYL AMINOPEPTIDASE
KeywordsHYDROLASE / ALPHA BETA HYDROLASE FOLD
Function / homology
Function and homology information


Xaa-Pro dipeptidyl-peptidase / dipeptidyl-peptidase activity / serine-type peptidase activity / 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 / 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 ...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 / 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 domain-like / Galactose-binding-like domain superfamily / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Jelly Rolls / Sandwich / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Xaa-Pro dipeptidyl-peptidase
Similarity search - Component
Biological speciesLactococcus lactis (lactic acid bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.2 Å
AuthorsRigolet, P. / Mechin, I. / Delage, M.M. / Chich, J.F.
CitationJournal: Structure / Year: 2002
Title: The Structural Basis for Catalysis and Specificity of the X-prolyl dipepdidyl aminopeptidase from Lactococcus lactis
Authors: Rigolet, P. / Mechin, I. / Delage, M.M. / Chich, J.F.
History
DepositionMay 3, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 6, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Feb 14, 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: X-PROLYL DIPEPTIDYL AMINOPEPTIDASE


Theoretical massNumber of molelcules
Total (without water)87,8001
Polymers87,8001
Non-polymers00
Water5,495305
1
A: X-PROLYL DIPEPTIDYL AMINOPEPTIDASE

A: X-PROLYL DIPEPTIDYL AMINOPEPTIDASE


Theoretical massNumber of molelcules
Total (without water)175,6002
Polymers175,6002
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Unit cell
Length a, b, c (Å)92.500, 102.500, 101.500
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
DetailsThe second part of the biological assembly is generated by the two fold axis: -X,-Y,Z.

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Components

#1: Protein X-PROLYL DIPEPTIDYL AMINOPEPTIDASE / X-Pro dipeptidyl-peptidase / Xaa-Pro dipeptidyl-peptidase


Mass: 87800.109 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactococcus lactis (lactic acid bacteria)
Gene: pepX (ORF2) / Plasmid: pTIL1 / Production host: Escherichia coli (E. coli) / Strain (production host): NCDO 763 / References: UniProt: P22346, Xaa-Pro dipeptidyl-peptidase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 305 / 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: 2.74 Å3/Da / Density % sol: 55.1 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.2
Details: PEG 4000, pH 5.2, VAPOR DIFFUSION, HANGING DROP, temperature 291.0K
Crystal grow
*PLUS
Temperature: 18 ℃ / pH: 8 / Details: Chich, J.F., (1995) Proteins., 23. 278.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
110 mg/mlprotein1drop
250 mMTris-HCl1droppH8.0
30.1 M1dropNaCl
410 %glycerol1drop
550 mMMES1reservoirpH5.0
67 %PEG40001reservoir

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: LURE / Beamline: DW32 / Wavelength: 0.9376 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 26, 1998
RadiationMonochromator: monochromator crystal Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9376 Å / Relative weight: 1
ReflectionResolution: 2.2→23 Å / Num. all: 46255 / Num. obs: 46103 / % possible obs: 93.8 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 3.3 % / Biso Wilson estimate: 12.4 Å2 / Rsym value: 0.065
Reflection shellResolution: 2.2→2.34 Å / % possible all: 92.8
Reflection
*PLUS
Lowest resolution: 25 Å / Num. obs: 46073 / % possible obs: 95.8 % / Num. measured all: 153738 / Rmerge(I) obs: 0.057
Reflection shell
*PLUS
% possible obs: 95.3 % / Rmerge(I) obs: 0.17

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
ROTAVATAdata reduction
MLPHAREphasing
CNS1.1refinement
CCP4(AGROVATAdata scaling
ROTAVATAdata scaling
RefinementMethod to determine structure: MIR / Resolution: 2.2→22.88 Å / Rfactor Rfree error: 0.005 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 1.5 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.223 2310 5 %RANDOM
Rwork0.184 ---
all-46103 --
obs-45808 92.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 26.4162 Å2 / ksol: 0.304795 e/Å3
Displacement parametersBiso mean: 21.2 Å2
Baniso -1Baniso -2Baniso -3
1-0.98 Å20 Å20 Å2
2--1.26 Å20 Å2
3----2.24 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.29 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.28 Å0.22 Å
Refinement stepCycle: LAST / Resolution: 2.2→22.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6200 0 0 308 6508
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d24.4
X-RAY DIFFRACTIONc_improper_angle_d0.76
X-RAY DIFFRACTIONc_mcbond_it1.251.5
X-RAY DIFFRACTIONc_mcangle_it1.922
X-RAY DIFFRACTIONc_scbond_it2.162
X-RAY DIFFRACTIONc_scangle_it3.192.5
LS refinement shellResolution: 2.2→2.34 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.271 374 5 %
Rwork0.227 7179 -
obs-7179 92.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
Refinement
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 20 Å / Num. reflection obs: 45043 / % reflection Rfree: 5 % / Rfactor Rfree: 0.223 / Rfactor Rwork: 0.184
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24.4
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.74
LS refinement shell
*PLUS
Rfactor Rfree: 0.271 / Rfactor Rwork: 0.227

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