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- PDB-7r2x: Paradendryphiella salina PL8 mannuronate-specific alginate lyase -

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Basic information

Entry
Database: PDB / ID: 7r2x
TitleParadendryphiella salina PL8 mannuronate-specific alginate lyase
ComponentsMannuronic acid specific lyase
KeywordsLYASE / Alginate lyase / polysaccharide lyase / (alpha/alpha)6 barrel + anti-parallel beta-sheet / secreated
Function / homology
Function and homology information


carbohydrate binding / carbohydrate metabolic process / lyase activity / extracellular region
Similarity search - Function
Polysaccharide lyase 8 / Polysaccharide lyase 8, N-terminal alpha-helical / Polysaccharide lyase family 8, N terminal alpha-helical domain / Polysaccharide lyase family 8, central domain / Polysaccharide lyase family 8, super-sandwich domain / Chondroitin AC/alginate lyase / Chondroitin AC/alginate lyase / Beta-galactosidase; Chain A, domain 5 - #10 / Glycoside hydrolase-type carbohydrate-binding / Beta-galactosidase; Chain A, domain 5 ...Polysaccharide lyase 8 / Polysaccharide lyase 8, N-terminal alpha-helical / Polysaccharide lyase family 8, N terminal alpha-helical domain / Polysaccharide lyase family 8, central domain / Polysaccharide lyase family 8, super-sandwich domain / Chondroitin AC/alginate lyase / Chondroitin AC/alginate lyase / Beta-galactosidase; Chain A, domain 5 - #10 / Glycoside hydrolase-type carbohydrate-binding / Beta-galactosidase; Chain A, domain 5 / Galactose mutarotase-like domain superfamily / Glycosyltransferase / Alpha/alpha barrel / Distorted Sandwich / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Mannuronic acid specific lyase
Similarity search - Component
Biological speciesParadendryphiella salina (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.35 Å
AuthorsFredslung, F. / Welner, D.H. / Wilkens, C.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Commission9082-00021BEuropean Union
CitationJournal: To Be Published
Title: Paradendryphiella salina PL8 mannuronate-specific alginate lyase
Authors: Fredslung, F. / Welner, D.H. / Wilkens, C.
History
DepositionFeb 6, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 15, 2023Provider: repository / Type: Initial release
Revision 1.1May 1, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Nov 6, 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

Downloads & links

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Assembly

Deposited unit
A: Mannuronic acid specific lyase
B: Mannuronic acid specific lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)172,2949
Polymers170,7452
Non-polymers1,5487
Water362
1
A: Mannuronic acid specific lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,0364
Polymers85,3731
Non-polymers6643
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Mannuronic acid specific lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,2575
Polymers85,3731
Non-polymers8854
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)108.890, 108.890, 150.490
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number144
Space group name H-MP31
Space group name HallP31
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1chain "A"
d_2ens_1(chain "B" and (resid 25 through 786 or resid 787 through 789))

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1ASPSERA1 - 762
d_12ens_1NAGNAGB
d_13ens_1NAGNAGC
d_14ens_1NAGNAGD
d_21ens_1ASPSERE1 - 762
d_22ens_1NAGNAGF
d_23ens_1NAGNAGG
d_24ens_1NAGNAGH

NCS oper: (Code: givenMatrix: (0.3750982172, -0.926444488576, -0.0316533890861), (-0.447202344056, -0.210762113178, 0.869246452463), (-0.811979920271, -0.31189732483, -0.493364639836)Vector: 83. ...NCS oper: (Code: given
Matrix: (0.3750982172, -0.926444488576, -0.0316533890861), (-0.447202344056, -0.210762113178, 0.869246452463), (-0.811979920271, -0.31189732483, -0.493364639836)
Vector: 83.1380252589, 61.0823720108, 3.21923132749)

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Components

#1: Protein Mannuronic acid specific lyase


Mass: 85372.648 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: N-terminal EFQ and C-teminal VDHHHHHH are from the vector.
Source: (gene. exp.) Paradendryphiella salina (fungus) / Gene: PsMan8A / Production host: Komagataella pastoris (fungus) / References: UniProt: A0A5Q5AD67
#2: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 3.02 Å3/Da / Density % sol: 59.27 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 25% PEG3350 and 0.1 M Bis-Tris pH 5.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 7, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 3.35→47.15 Å / Num. obs: 28559 / % possible obs: 99.4 % / Redundancy: 3.5 % / Biso Wilson estimate: 133.66 Å2 / CC1/2: 0.99 / Net I/σ(I): 0.99
Reflection shellResolution: 3.35→3.47 Å / Num. unique obs: 2833 / CC1/2: 0.42

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Processing

Software
NameVersionClassification
ISOLDErefinement
PHENIX1.19.2_4158refinement
MxCuBE3data collection
XDSdata reduction
XDSdata scaling
Cootmodel building
PHASERphasing
REFMAC5refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Alpha Fold model

Resolution: 3.35→47.15 Å / SU ML: 0.5298 / Cross valid method: FREE R-VALUE / σ(F): 1.93 / Phase error: 32.1865
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2453 1429 5 %
Rwork0.2072 27126 -
obs0.2092 28555 99.11 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 133.64 Å2
Refinement stepCycle: LAST / Resolution: 3.35→47.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11830 0 98 2 11930
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.001612210
X-RAY DIFFRACTIONf_angle_d0.431516647
X-RAY DIFFRACTIONf_chiral_restr0.04181839
X-RAY DIFFRACTIONf_plane_restr0.00362185
X-RAY DIFFRACTIONf_dihedral_angle_d11.04354282
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 4.01856586199 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.35-3.470.3911370.36212603X-RAY DIFFRACTION95.54
3.47-3.60.3921450.33442745X-RAY DIFFRACTION99.93
3.6-3.770.34991440.2962746X-RAY DIFFRACTION99.72
3.77-3.970.27791440.25862733X-RAY DIFFRACTION99.86
3.97-4.210.28031440.21952716X-RAY DIFFRACTION99.76
4.22-4.540.22831440.19782731X-RAY DIFFRACTION99.72
4.54-50.2331440.16812744X-RAY DIFFRACTION99.65
5-5.720.22741440.19172723X-RAY DIFFRACTION99.72
5.72-7.190.28341420.22842697X-RAY DIFFRACTION98.95
7.2-47.150.19411410.16932688X-RAY DIFFRACTION98.33
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.714748128270.3718787175360.9319467112971.83020604937-0.4917334999064.8001589310.17441110547-0.288306191461-0.199707511314-0.1979104385640.1918440699810.2816776320240.728485618492-0.37839336045-0.328814815450.933006683664-0.0135351682144-0.1749061239111.04421832870.1397533780451.18501701818-1.796630792836.406670769810.6354484549
23.782817940521.71939512281-0.7593759746453.97298929001-1.521786415626.726534894970.1250429563630.951358664459-0.174158209917-1.334574317780.2768847299580.1260727263341.834353806140.148528014906-0.3268869475261.617475749230.215448614937-0.2801391168031.41034978709-0.1802648075831.06957523921.3784188295935.6165106838-23.6737117737
32.75660452529-3.82620729034.178153236165.43464416643-5.562660255276.625737988550.7985903871930.9547428434380.188832779246-0.151292654477-0.496047537814-0.317700127183-1.803504338593.24040191743-0.3308110935431.43548031980.1328337166880.09588937369492.3111277987-0.09146909466241.6782953309517.196053333749.6103509631-26.251406569
43.096079210160.4182903025620.5391145370634.36132147288-0.9712027030843.90774642812-0.3519071363550.142434999861-0.108099488028-1.046509445770.09546899782920.3131131791780.819874774856-0.4126893902230.2458120737881.342652237610.03241668141710.1804635847591.2179621486-0.05021444716431.0265970904448.78220216857.8821877174-9.42965757624
50.4920606139630.934880554313-0.7179922936983.70623151538-3.148240579392.67182581974-0.03388336688790.933185856664-1.23147057631-2.592112950350.08213010262950.1587867689970.3687072141030.4233716504130.1115350621433.66640970772-0.402613571410.01587465396771.0777765615-0.1929218130461.9596737761644.40907347220.1993424535-13.6287190253
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 26 through 602 )AA26 - 6022 - 578
22chain 'A' and (resid 603 through 739 )AA603 - 739579 - 715
33chain 'A' and (resid 740 through 786 )AA740 - 786716 - 762
44chain 'B' and (resid 26 through 739 )BE26 - 7392 - 715
55chain 'B' and (resid 740 through 786 )BE740 - 786716 - 762

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