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- PDB-7fhz: Crystal structure of Multi-functional Polysaccharide lyase Smlt14... -

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Basic information

Entry
Database: PDB / ID: 7fhz
TitleCrystal structure of Multi-functional Polysaccharide lyase Smlt1473 (WT) from Stenotrophomonas maltophilia (strain K279a) in apo form at pH 9.0
ComponentsPolysaccharide lyase
KeywordsLYASE / Anionic Polysaccharide lyase
Function / homology
Function and homology information


glucuronan lyase / glucuronan lyase activity / mannuronate-specific alginate lyase / poly(beta-D-mannuronate) lyase activity / Lyases; Carbon-oxygen lyases; Acting on polysaccharides / hyaluronate lyase / hyaluronate lyase activity / polysaccharide catabolic process / cell outer membrane / periplasmic space
Similarity search - Function
Alginate lyase domain / Alginate lyase / Chondroitin AC/alginate lyase / Chondroitin AC/alginate lyase / Glycosyltransferase / Alpha/alpha barrel / Prokaryotic membrane lipoprotein lipid attachment site profile. / Mainly Alpha
Similarity search - Domain/homology
Polysaccharide lyase
Similarity search - Component
Biological speciesStenotrophomonas maltophilia K279a (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsPandey, S. / Berger, B.W. / Acharya, R.
Funding support India, United States, 2items
OrganizationGrant numberCountry
Department of Biotechnology (DBT, India)BT/PR15324/BRB/10/1482/2016 India
National Science Foundation (NSF, United States)CBET 1452855 United States
CitationJournal: J.Biol.Chem. / Year: 2021
Title: Structural insights into the mechanism of pH-selective substrate specificity of the polysaccharide lyase Smlt1473.
Authors: Pandey, S. / Mahanta, P. / Berger, B.W. / Acharya, R.
History
DepositionJul 30, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 27, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Polysaccharide lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,6353
Polymers34,4431
Non-polymers1922
Water72140
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area290 Å2
ΔGint-18 kcal/mol
Surface area13200 Å2
Unit cell
Length a, b, c (Å)47.983, 160.579, 46.942
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z

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Components

#1: Protein Polysaccharide lyase / PL / Alginate lyase / Endolytic polysaccharide lyase / Hyaluronate lyase / Multifunctional ...PL / Alginate lyase / Endolytic polysaccharide lyase / Hyaluronate lyase / Multifunctional polysaccharide lyase / Poly-beta-D-glucuronate lyase


Mass: 34442.637 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Stenotrophomonas maltophilia K279a (bacteria)
Strain: K279a / Gene: Smlt1473 / Plasmid: pET28a(+) / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21
References: UniProt: B2FHL8, Lyases; Carbon-oxygen lyases; Acting on polysaccharides
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 40 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 2.63 Å3/Da / Density % sol: 53.15 %
Description: rod-shaped THE ENTRY CONTAINS FRIEDEL PAIRS IN I/F_PLUS/MINUS COLUMNS.
Crystal growTemperature: 298.15 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 0.2 Ammonium Sulfate, 0.1M Tris-HCl, pH 9.0, 30% (w/v) PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR-H / Wavelength: 1.54178 Å
DetectorType: BRUKER PHOTON 100 / Detector: CMOS / Date: Feb 28, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.45→41.19 Å / Num. obs: 13694 / % possible obs: 97.4 % / Redundancy: 6.94 % / Biso Wilson estimate: 12.11 Å2 / CC1/2: 0.971 / Rmerge(I) obs: 0.1368 / Net I/σ(I): 10.52
Reflection shellResolution: 2.45→2.55 Å / Redundancy: 1.69 % / Rmerge(I) obs: 0.3897 / Mean I/σ(I) obs: 1.87 / Num. unique obs: 1338 / CC1/2: 0.545 / % possible all: 86.1

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
PROTEUM PLUSdata reduction
PROTEUM PLUSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7FHU

7fhu


Resolution: 2.5→35.73 Å / SU ML: 0.3791 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.6686
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.286 588 4.53 %
Rwork0.2549 12380 -
obs0.2563 12968 98.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 14.73 Å2
Refinement stepCycle: LAST / Resolution: 2.5→35.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2385 0 10 40 2435
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00422460
X-RAY DIFFRACTIONf_angle_d0.78193352
X-RAY DIFFRACTIONf_chiral_restr0.0493340
X-RAY DIFFRACTIONf_plane_restr0.0057448
X-RAY DIFFRACTIONf_dihedral_angle_d14.6862343
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.750.35611380.31492902X-RAY DIFFRACTION94.29
2.75-3.150.31311330.29033088X-RAY DIFFRACTION99.6
3.15-3.970.26061320.24763142X-RAY DIFFRACTION99.6
3.97-35.730.25751850.20713248X-RAY DIFFRACTION99.54

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