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- PDB-7sa8: Crystal Structure of the periplasmic lyase AlgL K66A Mutant -

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Basic information

Entry
Database: PDB / ID: 7sa8
TitleCrystal Structure of the periplasmic lyase AlgL K66A Mutant
ComponentsAlginate lyase
KeywordsLYASE / Alginate lyase
Function / homologyalginic acid catabolic process / Alginate lyase / poly(beta-D-mannuronate) lyase activity / Alginate lyase domain / Alginate lyase / Chondroitin AC/alginate lyase / periplasmic space / Alginate lyase
Function and homology information
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsGheorghita, A.A. / Pfoh, R. / Wong, S.S.Y. / Howell, P.L.
Funding support Canada, 2items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)MOP 43998 Canada
Canadian Institutes of Health Research (CIHR)FDN154327 Canada
CitationJournal: J.Biol.Chem. / Year: 2022
Title: The Pseudomonas aeruginosa homeostasis enzyme AlgL clears the periplasmic space of accumulated alginate during polymer biosynthesis.
Authors: Gheorghita, A.A. / Wolfram, F. / Whitfield, G.B. / Jacobs, H.M. / Pfoh, R. / Wong, S.S.Y. / Guitor, A.K. / Goodyear, M.C. / Berezuk, A.M. / Khursigara, C.M. / Parsek, M.R. / Howell, P.L.
History
DepositionSep 22, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 3, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Alginate lyase


Theoretical massNumber of molelcules
Total (without water)39,8211
Polymers39,8211
Non-polymers00
Water68538
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area13090 Å2
Unit cell
Length a, b, c (Å)58.736, 67.496, 76.216
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Alginate lyase


Mass: 39820.723 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: algL / Production host: Escherichia coli (E. coli) / References: UniProt: A0A2U8U7V5
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 38 / 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: 1.9 Å3/Da / Density % sol: 35.16 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.275 M K2SO4, 19% (w/v) PEG 3350, and 0.1 M HEPES pH 6.9. Crystals were cryoprotected by soaking for 10 min with 2 mM mannuronate tetrasaccharide and 20% (v/v) PEG 4000.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SEALED TUBE / Type: BRUKER D8 QUEST / Wavelength: 1.5406 Å
DetectorType: BRUKER PHOTON 100 / Detector: CMOS / Date: May 13, 2015
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5406 Å / Relative weight: 1
ReflectionResolution: 2.5→20.305 Å / Num. obs: 10903 / % possible obs: 99.3 % / Redundancy: 10.3 % / Rmerge(I) obs: 0.098 / Net I/σ(I): 16
Reflection shellResolution: 2.5→2.6 Å / Rmerge(I) obs: 0.435 / Num. unique obs: 1196 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PROTEUM PLUSdata reduction
PROTEUM PLUSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4OZV

4ozv


Resolution: 2.5→20.305 Å / Cor.coef. Fo:Fc: 0.912 / Cor.coef. Fo:Fc free: 0.878 / SU B: 29.256 / SU ML: 0.295 / Cross valid method: THROUGHOUT / ESU R: 1.643 / ESU R Free: 0.337
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2689 571 5.237 %
Rwork0.2461 10332 -
all0.247 --
obs-10332 99.299 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 39.375 Å2
Baniso -1Baniso -2Baniso -3
1--0.699 Å20 Å2-0 Å2
2--1.296 Å2-0 Å2
3----0.597 Å2
Refinement stepCycle: LAST / Resolution: 2.5→20.305 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2432 0 0 38 2470
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0132518
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172289
X-RAY DIFFRACTIONr_angle_refined_deg1.5031.6443424
X-RAY DIFFRACTIONr_angle_other_deg1.2731.585249
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1515316
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.29321.799139
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.63815385
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.0241519
X-RAY DIFFRACTIONr_chiral_restr0.0660.2316
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022917
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02617
X-RAY DIFFRACTIONr_nbd_refined0.20.2567
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1880.22104
X-RAY DIFFRACTIONr_nbtor_refined0.1630.21243
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0810.21096
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.160.273
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0980.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1250.211
X-RAY DIFFRACTIONr_nbd_other0.2020.235
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2620.22
X-RAY DIFFRACTIONr_mcbond_it1.463.181258
X-RAY DIFFRACTIONr_mcbond_other1.4513.1771257
X-RAY DIFFRACTIONr_mcangle_it2.4944.7531570
X-RAY DIFFRACTIONr_mcangle_other2.4954.7561571
X-RAY DIFFRACTIONr_scbond_it1.3953.3441259
X-RAY DIFFRACTIONr_scbond_other1.3933.3411258
X-RAY DIFFRACTIONr_scangle_it2.4214.9311851
X-RAY DIFFRACTIONr_scangle_other2.4134.931851
X-RAY DIFFRACTIONr_lrange_it6.77158.76310818
X-RAY DIFFRACTIONr_lrange_other6.77158.73610805
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.5640.31350.327750X-RAY DIFFRACTION100
2.564-2.6340.289450.321731X-RAY DIFFRACTION100
2.634-2.710.289370.321714X-RAY DIFFRACTION100
2.71-2.7930.329350.299694X-RAY DIFFRACTION100
2.793-2.8830.381330.273657X-RAY DIFFRACTION99.5671
2.883-2.9840.224340.265661X-RAY DIFFRACTION99.8563
2.984-3.0950.243360.247641X-RAY DIFFRACTION100
3.095-3.220.295330.255588X-RAY DIFFRACTION100
3.22-3.3610.278310.249579X-RAY DIFFRACTION100
3.361-3.5230.407330.255559X-RAY DIFFRACTION99.3289
3.523-3.7110.332350.264522X-RAY DIFFRACTION98.4099
3.711-3.9320.205250.242501X-RAY DIFFRACTION97.7695
3.932-4.1990.193280.203484X-RAY DIFFRACTION99.2248
4.199-4.5280.274360.195433X-RAY DIFFRACTION99.5754
4.528-4.9490.252260.182403X-RAY DIFFRACTION99.7674
4.949-5.5140.238290.231372X-RAY DIFFRACTION99.5037
5.514-6.3320.299120.242357X-RAY DIFFRACTION100
6.332-7.670.118140.236294X-RAY DIFFRACTION100
7.67-10.5090.179100.186247X-RAY DIFFRACTION100
10.509-20.3050.30240.304143X-RAY DIFFRACTION83.5227
Refinement TLS params.Method: refined / Origin x: 9.039 Å / Origin y: 82.556 Å / Origin z: 19.965 Å
111213212223313233
T0.0054 Å20.0009 Å20.0056 Å2-0.0294 Å2-0.0304 Å2--0.1793 Å2
L1.0451 °2-0.2083 °20.1033 °2-0.187 °2-0.2679 °2--1.4904 °2
S0.033 Å °0.1573 Å °-0.2099 Å °0.0079 Å °-0.0499 Å °0.0179 Å °0.0157 Å °-0.013 Å °0.0169 Å °
Refinement TLS groupSelection: ALL

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