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

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Basic information

Entry
Database: PDB / ID: 7fhx
TitleCrystal structure of Multi-functional Polysaccharide lyase Smlt1473 (WT) from Stenotrophomonas maltophilia (strain K279a) in apo form at pH 5.0
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
DI(HYDROXYETHYL)ETHER / Polysaccharide lyase
Similarity search - Component
Biological speciesStenotrophomonas maltophilia K279a (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.63 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 / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z
Revision 1.2Nov 13, 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
B: Polysaccharide lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,1665
Polymers70,8572
Non-polymers3083
Water1,27971
1
A: Polysaccharide lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,5252
Polymers35,4291
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area180 Å2
ΔGint-12 kcal/mol
Surface area13040 Å2
MethodPISA
2
B: Polysaccharide lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,6413
Polymers35,4291
Non-polymers2122
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area13150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.131, 94.737, 160.499
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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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: 35428.699 Da / Num. of mol.: 2
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.: 1 / Source method: isolated from a natural source / Formula: SO4
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C4H10O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 71 / 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: 2.71 Å3/Da / Density % sol: 54.63 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN I/F_PLUS/MINUS COLUMNS.
Crystal growTemperature: 298.15 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 0.2M LiSo4 Monohydrate, 0.1M sodium acetate trihydrate pH 5.0, 30% (w/v) PEG 3350

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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: Dec 26, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.63→47.36 Å / Num. obs: 21068 / % possible obs: 91.2 % / Redundancy: 10.35 % / CC1/2: 0.988 / Rmerge(I) obs: 0.1598 / Net I/σ(I): 14.36
Reflection shellResolution: 2.63→2.73 Å / Redundancy: 3.86 % / Rmerge(I) obs: 0.5177 / Mean I/σ(I) obs: 2.62 / Num. unique obs: 1737 / CC1/2: 0.635 / % possible all: 71.3

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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: 7FHU

7fhu


Resolution: 2.63→47.304 Å / Cor.coef. Fo:Fc: 0.884 / Cor.coef. Fo:Fc free: 0.82 / SU B: 13.257 / SU ML: 0.271 / Cross valid method: FREE R-VALUE / ESU R: 2.633 / ESU R Free: 0.372
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2719 1031 4.904 %
Rwork0.2247 19993 -
all0.227 --
obs-21024 91.175 %
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: 13.07 Å2
Baniso -1Baniso -2Baniso -3
1--0.513 Å20 Å20 Å2
2--1.716 Å2-0 Å2
3----1.203 Å2
Refinement stepCycle: LAST / Resolution: 2.63→47.304 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4840 0 19 71 4930
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0134992
X-RAY DIFFRACTIONr_bond_other_d0.0050.0174560
X-RAY DIFFRACTIONr_angle_refined_deg1.4121.646793
X-RAY DIFFRACTIONr_angle_other_deg1.2631.58610416
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6965616
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.77921.046306
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.28615735
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.2891549
X-RAY DIFFRACTIONr_chiral_restr0.0650.2606
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.025851
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021271
X-RAY DIFFRACTIONr_nbd_refined0.1990.21156
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2010.24298
X-RAY DIFFRACTIONr_nbtor_refined0.1580.22393
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0770.22259
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1410.2103
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.2560.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1660.24
X-RAY DIFFRACTIONr_nbd_other0.1530.229
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.140.24
X-RAY DIFFRACTIONr_mcbond_it0.771.3472470
X-RAY DIFFRACTIONr_mcbond_other0.7671.3452469
X-RAY DIFFRACTIONr_mcangle_it1.3582.0163084
X-RAY DIFFRACTIONr_mcangle_other1.3582.0173085
X-RAY DIFFRACTIONr_scbond_it0.741.4352522
X-RAY DIFFRACTIONr_scbond_other0.741.4332519
X-RAY DIFFRACTIONr_scangle_it1.3052.1183709
X-RAY DIFFRACTIONr_scangle_other1.3052.1163704
X-RAY DIFFRACTIONr_lrange_it2.71515.2385679
X-RAY DIFFRACTIONr_lrange_other2.71515.2455679
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.63-2.6980.4560.35511410.35716790.7370.77471.29240.318
2.698-2.7720.347790.28213560.28516210.8080.86188.52560.251
2.772-2.8520.312770.27513160.27715700.8550.87688.72610.248
2.852-2.940.287600.25913110.26115480.8320.86288.56590.235
2.94-3.0360.318580.24513120.24815080.830.88290.84880.218
3.036-3.1420.258760.24612740.24614410.8860.88693.68490.217
3.142-3.260.271610.23712920.23814090.8770.9196.02560.209
3.26-3.3920.296570.2312020.23313170.9050.92395.59610.205
3.392-3.5420.309480.22712050.2313090.8830.91495.72190.2
3.542-3.7140.244560.22311350.22412510.9060.9295.20380.203
3.714-3.9140.269590.19410480.19911720.9260.93594.45390.175
3.914-4.1490.237550.18110330.18311410.9390.9595.35490.162
4.149-4.4330.209460.179610.17210660.9480.9694.46530.153
4.433-4.7850.232410.1798940.1829930.9460.95194.15910.161
4.785-5.2360.253500.1868130.199200.9320.95493.80430.17
5.236-5.8460.236390.2017470.2028410.9340.95493.46020.175
5.846-6.7330.232310.2066700.2087590.9430.93992.35840.182
6.733-8.2040.239430.1795640.1836560.9250.95292.53050.166
8.204-11.4320.187190.1714470.1725130.9690.96590.83820.158
11.432-47.3040.39200.3462720.3483360.820.90786.90480.319

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