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- PDB-5l8s: The crystal structure of a cold-adapted acylaminoacyl peptidase r... -

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Basic information

Entry
Database: PDB / ID: 5l8s
TitleThe crystal structure of a cold-adapted acylaminoacyl peptidase reveals a novel quaternary architecture based on the arm-exchange mechanism
ComponentsAmino acyl peptidase
KeywordsHYDROLASE / acyl aminoacyl peptidase / alpha/beta hydrolase domain / arm exchange / beta-propeller domain / cold adaptation / dimerization / proline hinge / Sporosarcina psychrophila
Function / homology
Function and homology information


serine-type endopeptidase activity / proteolysis
Similarity search - Function
Peptidase S9, prolyl oligopeptidase, catalytic domain / Prolyl oligopeptidase family / Six-bladed beta-propeller, TolB-like / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Amino acyl peptidase
Similarity search - Component
Biological speciesSporosarcina psychrophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsBrocca, S. / Ferrari, C. / Barbiroli, A. / Pesce, A. / Lotti, M. / Nardini, M.
Funding support Italy, 1items
OrganizationGrant numberCountry
Fondo di Ateneo of the University of Milano-Milano Bicocca Italy
CitationJournal: FEBS J. / Year: 2016
Title: A bacterial acyl aminoacyl peptidase couples flexibility and stability as a result of cold adaptation.
Authors: Brocca, S. / Ferrari, C. / Barbiroli, A. / Pesce, A. / Lotti, M. / Nardini, M.
History
DepositionJun 8, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 16, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 14, 2016Group: Database references
Revision 1.2Jan 10, 2024Group: 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: Amino acyl peptidase
B: Amino acyl peptidase
C: Amino acyl peptidase
D: Amino acyl peptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)277,1278
Polymers276,7434
Non-polymers3844
Water8,575476
1
A: Amino acyl peptidase
C: Amino acyl peptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)138,5644
Polymers138,3712
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4190 Å2
ΔGint-62 kcal/mol
Surface area45900 Å2
MethodPISA
2
B: Amino acyl peptidase
D: Amino acyl peptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)138,5644
Polymers138,3712
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4150 Å2
ΔGint-63 kcal/mol
Surface area46140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)148.080, 151.100, 191.230
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Amino acyl peptidase / Peptidase S9


Mass: 69185.695 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sporosarcina psychrophila (bacteria) / Gene: aph, AZE41_09720 / Production host: Escherichia coli (E. coli) / References: UniProt: E1VFE0
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 476 / 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: 3.9 Å3/Da / Density % sol: 69 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 30% PEG 400, 0.1 M Na-Hepes (pH 7.5), and 0.2 M MgCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.93929 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 11, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.93929 Å / Relative weight: 1
ReflectionResolution: 2.5→63.74 Å / Num. obs: 148344 / % possible obs: 100 % / Redundancy: 5.6 % / Rmerge(I) obs: 0.128 / Net I/σ(I): 10.8
Reflection shellResolution: 2.5→2.64 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.399 / Mean I/σ(I) obs: 4.5 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1VE6

1ve6


Resolution: 2.5→63.48 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.934 / SU B: 7.858 / SU ML: 0.174 / Cross valid method: THROUGHOUT / ESU R: 0.311 / ESU R Free: 0.238 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24776 7433 5 %RANDOM
Rwork0.21209 ---
obs0.21386 140806 99.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 43.962 Å2
Baniso -1Baniso -2Baniso -3
1-0.37 Å2-0 Å20 Å2
2--0.36 Å2-0 Å2
3----0.73 Å2
Refinement stepCycle: 1 / Resolution: 2.5→63.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19524 0 20 476 20020
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01920113
X-RAY DIFFRACTIONr_bond_other_d0.0010.0218451
X-RAY DIFFRACTIONr_angle_refined_deg1.2821.9527265
X-RAY DIFFRACTIONr_angle_other_deg0.727342610
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.17552426
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.12324.431027
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.325153358
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.6531596
X-RAY DIFFRACTIONr_chiral_restr0.0750.22871
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02122893
X-RAY DIFFRACTIONr_gen_planes_other0.0010.024783
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.2824.2199674
X-RAY DIFFRACTIONr_mcbond_other2.284.2199673
X-RAY DIFFRACTIONr_mcangle_it3.6586.32312089
X-RAY DIFFRACTIONr_mcangle_other3.6596.32312090
X-RAY DIFFRACTIONr_scbond_it2.7024.55510439
X-RAY DIFFRACTIONr_scbond_other2.6894.55510436
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.4156.68515164
X-RAY DIFFRACTIONr_long_range_B_refined6.37433.42422014
X-RAY DIFFRACTIONr_long_range_B_other6.36533.41921975
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.368 545 -
Rwork0.306 10301 -
obs--100 %

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