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- PDB-8rzk: The Michaelis complex of ZgGH129 D486N from Zobellia galactanivor... -

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Basic information

Entry
Database: PDB / ID: 8rzk
TitleThe Michaelis complex of ZgGH129 D486N from Zobellia galactanivorans with neo-b/k-oligo-carrageenan tetrasaccharide (beta-kappa neo-oligo-carrageenan DP4).
ComponentsConserved hypothetical periplasmic protein
KeywordsHYDROLASE / 3 / 6-anhydro-D-galactosidase Zobellia galactanivorans carrageenan oligosaccharide 3 / 6-anhydro-D-galactose
Function / homologyProtein of unknown function DUF5696 / Family of unknown function (DUF5696) / L(+)-TARTARIC ACID / Conserved hypothetical periplasmic protein
Function and homology information
Biological speciesZobellia galactanivorans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.29 Å
AuthorsRoret, T. / Czjzek, M. / Ficko-Blean, E.
Funding support France, 1items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)ANR Mirror Mirror (ANR-22-CE11-0025-01) France
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2024
Title: Constrained Catalytic Itinerary of a Retaining 3,6-Anhydro-D-Galactosidase, a Key Enzyme in Red Algal Cell Wall Degradation.
Authors: Wallace, M.D. / Cuxart, I. / Roret, T. / Guee, L. / Debowski, A.W. / Czjzek, M. / Rovira, C. / Stubbs, K.A. / Ficko-Blean, E.
History
DepositionFeb 12, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 31, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2024Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.journal_volume / _citation_author.identifier_ORCID / _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: Conserved hypothetical periplasmic protein
B: Conserved hypothetical periplasmic protein
C: Conserved hypothetical periplasmic protein
D: Conserved hypothetical periplasmic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)308,79722
Polymers304,9094
Non-polymers3,88918
Water20,6451146
1
A: Conserved hypothetical periplasmic protein
B: Conserved hypothetical periplasmic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)154,50512
Polymers152,4542
Non-polymers2,05010
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Conserved hypothetical periplasmic protein
D: Conserved hypothetical periplasmic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)154,29310
Polymers152,4542
Non-polymers1,8388
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)162.734, 105.943, 213.664
Angle α, β, γ (deg.)90.000, 111.233, 90.000
Int Tables number5
Space group name H-MI121
Space group name HallC2y(x,y,-x+z)
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z+1/2
#4: -x+1/2,y+1/2,-z+1/2

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Components

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Protein / Sugars , 2 types, 8 molecules ABCD

#1: Protein
Conserved hypothetical periplasmic protein


Mass: 76227.125 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: D486N variant / Source: (gene. exp.) Zobellia galactanivorans (bacteria) / Gene: zobellia_3152 / Production host: Escherichia coli (E. coli) / References: UniProt: G0L004
#2: Polysaccharide
3,6-anhydro-alpha-D-galactopyranose-(1-3)-beta-D-galactopyranose-(1-4)-3,6-anhydro-alpha-D- ...3,6-anhydro-alpha-D-galactopyranose-(1-3)-beta-D-galactopyranose-(1-4)-3,6-anhydro-alpha-D-galactopyranose-(1-3)-4-O-sulfo-beta-D-galactopyranose


Type: oligosaccharide / Mass: 710.611 Da / Num. of mol.: 4 / Source method: obtained synthetically
DescriptorTypeProgram
WURCS=2.0/3,4,3/[a2112h-1b_1-5_4*OSO/3=O/3=O][a2112h-1a_1-5_3-6][a2112h-1b_1-5]/1-2-3-2/a3-b1_b4-c1_c3-d1WURCSPDB2Glycan 1.1.0

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Non-polymers , 5 types, 1160 molecules

#3: Chemical
ChemComp-TLA / L(+)-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C4H6O6
#4: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#5: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1146 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: 2.75 Å3/Da / Density % sol: 55.33 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 1.63 mg/ml 2:1 ratio 0.14M Na/K-tartrate, 14% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9801 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 25, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9801 Å / Relative weight: 1
ReflectionResolution: 2.29→47.89 Å / Num. obs: 152074 / % possible obs: 100 % / Redundancy: 6.9 % / Biso Wilson estimate: 42.15 Å2 / CC1/2: 0.996 / Rrim(I) all: 0.161 / Net I/σ(I): 9.2
Reflection shellResolution: 2.29→2.33 Å / Redundancy: 7.1 % / Mean I/σ(I) obs: 1.5 / Num. unique obs: 7468 / CC1/2: 0.551 / Rrim(I) all: 1.5 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
XDSdata reduction
Aimlessdata scaling
Cootmodel building
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.29→47.82 Å / SU ML: 0.2731 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.756
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2016 7610 5 %
Rwork0.1688 144454 -
obs0.1705 152064 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 44.91 Å2
Refinement stepCycle: LAST / Resolution: 2.29→47.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20951 0 250 1146 22347
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005221742
X-RAY DIFFRACTIONf_angle_d0.810329435
X-RAY DIFFRACTIONf_chiral_restr0.05123138
X-RAY DIFFRACTIONf_plane_restr0.00473790
X-RAY DIFFRACTIONf_dihedral_angle_d16.004412910
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.29-2.320.29992470.26324825X-RAY DIFFRACTION99.96
2.32-2.340.28772480.25764779X-RAY DIFFRACTION100
2.34-2.370.29072630.25064742X-RAY DIFFRACTION100
2.37-2.40.28462360.24834833X-RAY DIFFRACTION100
2.4-2.430.3012630.24584755X-RAY DIFFRACTION99.98
2.43-2.470.26532470.23334867X-RAY DIFFRACTION99.98
2.47-2.50.28492460.22724766X-RAY DIFFRACTION100
2.5-2.540.29722540.22684766X-RAY DIFFRACTION99.98
2.54-2.580.26432720.22094813X-RAY DIFFRACTION100
2.58-2.620.25332540.21644812X-RAY DIFFRACTION99.98
2.62-2.670.27582600.2354740X-RAY DIFFRACTION100
2.67-2.710.2832510.2364826X-RAY DIFFRACTION100
2.71-2.770.28272490.2224781X-RAY DIFFRACTION100
2.77-2.820.24382610.2114791X-RAY DIFFRACTION99.92
2.82-2.890.25122680.19974784X-RAY DIFFRACTION99.8
2.89-2.950.25042570.19864830X-RAY DIFFRACTION99.9
2.95-3.030.222580.18594782X-RAY DIFFRACTION99.98
3.03-3.110.22372270.18444858X-RAY DIFFRACTION100
3.11-3.20.20922750.18884767X-RAY DIFFRACTION99.98
3.2-3.30.19692500.17244814X-RAY DIFFRACTION100
3.3-3.420.19372730.16034813X-RAY DIFFRACTION100
3.42-3.560.16752540.14984811X-RAY DIFFRACTION100
3.56-3.720.18432260.14474838X-RAY DIFFRACTION100
3.72-3.920.16172620.14534833X-RAY DIFFRACTION100
3.92-4.160.15882630.12754813X-RAY DIFFRACTION100
4.16-4.480.14932660.11824822X-RAY DIFFRACTION99.96
4.48-4.930.14082570.11794840X-RAY DIFFRACTION100
4.93-5.640.16522240.13554888X-RAY DIFFRACTION100
5.64-7.110.18692490.15884899X-RAY DIFFRACTION99.84
7.11-47.820.1972500.17114966X-RAY DIFFRACTION99.81
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)
10.764289968011-0.102025902751-0.05035621228510.6431126995680.05677833516680.747766812966-0.004356317623860.001730907604550.02877790396650.0471931834213-0.0133758842697-0.0599200022062-0.04278449914860.0641469683518-4.65257261376E-60.365174083476-0.00946831902864-0.04158480000470.338384159050.01393251174440.39685092503657.529138578-2.4947789437751.6336260139
20.570487570318-0.2121095997470.07995086726650.6758325051350.02959591444590.5586304270630.003235248303020.1156864009380.0303807135332-0.1068977844720.01168154326690.0730751635396-0.0183306611416-0.109808653731-4.87006342948E-70.35792149123-0.000455581569818-0.01737839844470.4641827243660.004751146340170.40182546019129.54516223171.0857657507931.8360919925
30.907534591968-0.07513302061280.05014672727390.563547142264-0.05639115967250.858314382884-0.032343116425-0.1299140673040.06633530738110.1073738020850.0323323835383-0.00253113961466-0.03734955409080.02455657724625.87552942839E-60.4600383068030.0215469251102-0.002183484561810.3629664584630.004827515308860.38700340242633.951502886312.3766971138-18.2861459911
40.844157511425-0.107019674930.09387557770310.64961601691-0.04729994257430.586157477325-0.02311614792270.0844374194469-0.0869234725278-0.03949399369850.00126129145365-0.01983296529290.1339554422640.0977252500252-6.21084165841E-60.4483232668670.01248153255530.05031074883870.440786324587-0.02138079207290.40305444420345.8464721279-11.0837548125-40.7148772511
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid 35 through 693)
2X-RAY DIFFRACTION2(chain 'B' and resid 35 through 693)
3X-RAY DIFFRACTION3(chain 'C' and resid 35 through 693)
4X-RAY DIFFRACTION4(chain 'D' and resid 35 through 693)

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