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- PDB-8rzj: ZgGH129 from Zobellia galactanivorans in complex with the inhibit... -

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Basic information

Entry
Database: PDB / ID: 8rzj
TitleZgGH129 from Zobellia galactanivorans in complex with the inhibitor ADG-IF (3,6-anhydro-D-galacto-isofagomine).
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) / : / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / L(+)-TARTARIC ACID / Conserved hypothetical periplasmic protein
Function and homology information
Biological speciesZobellia galactanivorans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.99 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)309,35456
Polymers304,9124
Non-polymers4,44252
Water40,8222266
1
A: Conserved hypothetical periplasmic protein
B: Conserved hypothetical periplasmic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)154,77930
Polymers152,4562
Non-polymers2,32328
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13260 Å2
ΔGint-63 kcal/mol
Surface area42170 Å2
MethodPISA
2
C: Conserved hypothetical periplasmic protein
D: Conserved hypothetical periplasmic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)154,57526
Polymers152,4562
Non-polymers2,11924
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11920 Å2
ΔGint-84 kcal/mol
Surface area42200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)218.781, 106.120, 164.695
Angle α, β, γ (deg.)90.000, 113.924, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Conserved hypothetical periplasmic protein


Mass: 76228.109 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zobellia galactanivorans (bacteria) / Gene: zobellia_3152 / Production host: Escherichia coli (E. coli) / References: UniProt: G0L004

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Non-polymers , 8 types, 2318 molecules

#2: Chemical
ChemComp-A1H36 / (1~{R},5~{R},8~{S})-6-oxa-3-azabicyclo[3.2.1]octan-8-ol / ADG-IF (3,6-anhydro-D-galacto-isofagomine)


Mass: 129.157 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H11NO2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-CL / CHLORIDE ION


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


Mass: 62.068 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical
ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C6H14O4
#6: Chemical
ChemComp-TLA / L(+)-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C4H6O6
#7: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Na
#8: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2266 / 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: 2.8 Å3/Da / Density % sol: 56.12 %
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: Feb 1, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9801 Å / Relative weight: 1
ReflectionResolution: 1.99→48.22 Å / Num. obs: 232909 / % possible obs: 98.3 % / Redundancy: 7 % / Biso Wilson estimate: 33.35 Å2 / CC1/2: 0.995 / Rrim(I) all: 0.155 / Net I/σ(I): 8.3
Reflection shellResolution: 1.99→2.09 Å / Redundancy: 7 % / Mean I/σ(I) obs: 1.6 / Num. unique obs: 32888 / CC1/2: 0.689 / Rrim(I) all: 1.168 / % possible all: 95.3

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimlessdata scaling
Cootmodel building
MOLREPphasing
PHENIX1.16-3549refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.99→47.38 Å / SU ML: 0.2283 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.8249
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1851 11665 5.01 %
Rwork0.1539 221121 -
obs0.1555 232786 98.17 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 34.74 Å2
Refinement stepCycle: LAST / Resolution: 1.99→47.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20787 0 285 2266 23338
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011221656
X-RAY DIFFRACTIONf_angle_d1.183529268
X-RAY DIFFRACTIONf_chiral_restr0.08813085
X-RAY DIFFRACTIONf_plane_restr0.00513806
X-RAY DIFFRACTIONf_dihedral_angle_d12.430712802
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.99-2.010.30573740.29366438X-RAY DIFFRACTION86.17
2.01-2.030.28643820.2497313X-RAY DIFFRACTION97.66
2.03-2.060.27713540.23747318X-RAY DIFFRACTION97.71
2.06-2.080.26024010.22447323X-RAY DIFFRACTION97.65
2.08-2.110.253560.22217297X-RAY DIFFRACTION97.76
2.11-2.140.28163900.22287290X-RAY DIFFRACTION97.97
2.14-2.170.23843860.21437397X-RAY DIFFRACTION97.87
2.17-2.20.24923760.21417318X-RAY DIFFRACTION97.84
2.2-2.240.26874010.21617250X-RAY DIFFRACTION97.98
2.24-2.270.23653840.20277370X-RAY DIFFRACTION98.19
2.27-2.310.23943910.20437332X-RAY DIFFRACTION98.21
2.31-2.350.23043910.20187425X-RAY DIFFRACTION98.29
2.35-2.40.22894050.19227272X-RAY DIFFRACTION98.3
2.4-2.450.22643860.19097390X-RAY DIFFRACTION98.43
2.45-2.50.23243620.1847404X-RAY DIFFRACTION98.49
2.5-2.560.21114290.17327301X-RAY DIFFRACTION98.53
2.56-2.620.20444080.1567410X-RAY DIFFRACTION98.65
2.62-2.690.1793520.15037437X-RAY DIFFRACTION98.72
2.69-2.770.19824200.15337374X-RAY DIFFRACTION98.85
2.77-2.860.19713730.1547450X-RAY DIFFRACTION98.9
2.86-2.970.18153920.15357456X-RAY DIFFRACTION98.99
2.97-3.080.1984090.15567380X-RAY DIFFRACTION99.06
3.08-3.220.17953760.15117501X-RAY DIFFRACTION99.14
3.22-3.390.18483690.14417490X-RAY DIFFRACTION99.36
3.39-3.610.15633960.13317437X-RAY DIFFRACTION99.2
3.61-3.890.1573740.12787484X-RAY DIFFRACTION99.34
3.89-4.280.13524320.11327492X-RAY DIFFRACTION99.42
4.28-4.890.13654060.10487520X-RAY DIFFRACTION99.5
4.89-6.170.14794040.12827543X-RAY DIFFRACTION99.54
6.17-47.380.16753860.15217709X-RAY DIFFRACTION99.37
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)
10.69824114526-0.0257594199819-0.003713959517090.526999395910.03680848566090.525721206832-0.000139388039827-0.1291267178910.02937082879850.0792561323986-0.02191715398660.05348724489450.0338624169659-0.01108120580146.83984210997E-60.225480996733-0.01066499660980.03691816536570.219665813616-0.02043209050180.232700717384-70.464980158250.565479851232.5977724142
20.6184608786750.009623343425270.005269572335370.549974203183-0.07780070446880.409172250724-0.01975421381710.05358568062710.01283812564050.001296394143450.00940686990063-0.0956409958675-0.04055770403350.127149321766-3.96794076518E-60.22120650263-0.007986834208020.01664391875190.2724425887960.003797140607040.21565104072-41.535708049154.385267249614.5787072736
30.660898991702-0.03785682458480.1302834992620.594212931493-0.08259225477030.6170969163990.0402537547255-0.190692854307-0.0959112219190.08692211639620.0713071070812-0.01592631156090.102413096268-0.0131963276255-3.28721078175E-60.2841628812020.0126176059482-0.04376177803380.2964321295440.002446924624080.24290321738919.185601391341.809463612258.485759926
40.788530358957-0.0123720652316-0.01660040930790.4524883232530.01965231123660.7325123311330.00713784860936-0.0138225465650.0735800949126-0.0394805131750.0398999214330.0694143932184-0.11222205305-0.0948450500771-6.32242470432E-60.261653890350.00372688747466-0.008232759668090.2121324090860.0001192537710380.2912244918953.7988874653865.473740182938.8327888313
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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