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- PDB-8rzi: ZgGH129 from Zobellia galactanivorans soaked with 1,2-diF-ADG (3,... -

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Basic information

Entry
Database: PDB / ID: 8rzi
TitleZgGH129 from Zobellia galactanivorans soaked with 1,2-diF-ADG (3,6-Anhydro-2-deoxy-2-fluoro-a-D-galactopyranosyl fluoride) resulting in a trapped glycosyl-enzyme intermediate.
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 / L(+)-TARTARIC ACID / Conserved hypothetical periplasmic protein
Function and homology information
Biological speciesZobellia galactanivorans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.96 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 ...citation / citation_author / pdbx_entry_details / pdbx_modification_feature
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)308,12149
Polymers304,9124
Non-polymers3,20845
Water40,5162249
1
A: Conserved hypothetical periplasmic protein
B: Conserved hypothetical periplasmic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)154,01123
Polymers152,4562
Non-polymers1,55521
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10990 Å2
ΔGint-95 kcal/mol
Surface area42590 Å2
MethodPISA
2
C: Conserved hypothetical periplasmic protein
D: Conserved hypothetical periplasmic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)154,10926
Polymers152,4562
Non-polymers1,65324
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11100 Å2
ΔGint-89 kcal/mol
Surface area42630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)219.695, 106.554, 164.442
Angle α, β, γ (deg.)90.000, 114.012, 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 , 7 types, 2294 molecules

#2: Chemical
ChemComp-A1H37 / (1~{R},4~{S},5~{S},8~{S})-4-fluoranyl-2,6-dioxabicyclo[3.2.1]octan-8-ol / 1,2-diF-ADG / 3,6-Anhydro-2-deoxy-2-fluoro-a-D-galactopyranosyl fluoride


Mass: 148.132 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H9FO3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-TLA / L(+)-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H6O6
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical
ChemComp-NA / SODIUM ION


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


Mass: 35.453 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Cl
#7: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 23 / Source method: obtained synthetically / Formula: C2H6O2
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2249 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.82 Å3/Da / Density % sol: 56.38 %
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: 0.9786 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: 0.9786 Å / Relative weight: 1
ReflectionResolution: 1.96→48.18 Å / Num. obs: 245610 / % possible obs: 99.4 % / Redundancy: 3.4 % / Biso Wilson estimate: 36.49 Å2 / CC1/2: 0.998 / Rrim(I) all: 0.083 / Net I/σ(I): 10.9
Reflection shellResolution: 1.96→2.07 Å / Redundancy: 3.4 % / Mean I/σ(I) obs: 1 / Num. unique obs: 35024 / CC1/2: 0.468 / Rrim(I) all: 1.214 / % possible all: 97.4

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
XDSdata reduction
Aimlessdata scaling
Cootmodel building
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.96→34.97 Å / SU ML: 0.2246 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.7794
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1835 12163 4.95 %
Rwork0.1544 233389 -
obs0.1558 245552 99.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 38.28 Å2
Refinement stepCycle: LAST / Resolution: 1.96→34.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20806 0 198 2249 23253
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.009321593
X-RAY DIFFRACTIONf_angle_d1.164429208
X-RAY DIFFRACTIONf_chiral_restr0.06773082
X-RAY DIFFRACTIONf_plane_restr0.0063806
X-RAY DIFFRACTIONf_dihedral_angle_d13.16112779
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.96-1.980.34463370.31486897X-RAY DIFFRACTION89.02
1.98-2.010.31694170.29697798X-RAY DIFFRACTION99.94
2.01-2.030.29194180.28467797X-RAY DIFFRACTION99.89
2.03-2.060.29733930.26637796X-RAY DIFFRACTION99.84
2.06-2.080.27994560.26247736X-RAY DIFFRACTION99.65
2.08-2.110.29834310.24797732X-RAY DIFFRACTION99.85
2.11-2.140.26033960.23447832X-RAY DIFFRACTION99.91
2.14-2.180.24533870.22717832X-RAY DIFFRACTION99.85
2.18-2.210.25443860.2197743X-RAY DIFFRACTION99.84
2.21-2.250.24634110.21087735X-RAY DIFFRACTION99.71
2.25-2.280.23824020.20087832X-RAY DIFFRACTION99.7
2.28-2.330.21744110.19337761X-RAY DIFFRACTION99.82
2.33-2.370.21194500.17927740X-RAY DIFFRACTION99.79
2.37-2.420.21043850.17257857X-RAY DIFFRACTION99.77
2.42-2.470.20653870.16577784X-RAY DIFFRACTION99.82
2.47-2.530.1823880.16527799X-RAY DIFFRACTION99.72
2.53-2.590.20313890.16597831X-RAY DIFFRACTION99.85
2.59-2.660.19694010.16747857X-RAY DIFFRACTION99.82
2.66-2.740.2134140.16837746X-RAY DIFFRACTION99.68
2.74-2.830.20263930.16637848X-RAY DIFFRACTION99.83
2.83-2.930.19584200.16047765X-RAY DIFFRACTION99.89
2.93-3.050.19254250.15727828X-RAY DIFFRACTION99.81
3.05-3.190.19224040.15547787X-RAY DIFFRACTION99.67
3.19-3.350.18393930.14977855X-RAY DIFFRACTION99.76
3.35-3.560.17043940.13757865X-RAY DIFFRACTION99.72
3.56-3.840.14774650.12397766X-RAY DIFFRACTION99.61
3.84-4.220.13733870.11297853X-RAY DIFFRACTION99.66
4.22-4.830.12863920.10417860X-RAY DIFFRACTION99.6
4.83-6.090.1493980.12417903X-RAY DIFFRACTION99.64
6.09-34.970.16224330.14167954X-RAY DIFFRACTION99.16
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)
10.8073915951970.0368039661169-0.06959950689940.527891731226-0.07004645573870.490535712127-0.03329024442430.169162297668-0.0266270539643-0.0822913058650.000236338186647-0.05933310527070.04372128566010.00472459856113-4.30029743848E-60.28491401516-0.0125201526620.03394836451640.284353790794-0.001626996338030.26966276323170.7089437623-55.7248228636-32.4301664822
20.7436227370540.0197416748128-0.0264700315480.5286859454640.07925093204740.450880317481-0.0345489498638-0.01946634224190.006908469706470.01627099553230.02476216164460.108774110665-0.019679844237-0.113539314985-1.54915343571E-50.267845361235-0.004838277657710.01816486248450.3027322378110.006053588838740.26443285881841.7398489399-51.8402368001-14.4849254541
30.7605583941980.05657490194310.08842109855010.6312318450240.07332992307360.6336971721610.03227392408140.246642376714-0.0424884121197-0.1042580444660.07781326538340.03611369172490.0580321145187-0.0208897341498-5.58709913323E-60.339330996542-0.0297247240276-0.05149444039590.381138002720.04133011731230.274772576368-19.426625807-64.5063377002-58.3597939632
40.8218078141850.0472947990754-0.03265800533870.4941790747290.0615865026570.74281337680.008955781718560.03423434445030.1873901611250.03519784646440.0556088373415-0.0470745591016-0.1359962376630.0974479834608-1.59922742306E-50.339800815736-0.0144792562008-0.003191542329620.2699569816780.02444391008560.399876804343-3.90645420832-40.7091300499-38.9853523204
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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