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- PDB-8rzg: ZgGH129 from Zobellia galactanivorans soaked with the product of ... -

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Basic information

Entry
Database: PDB / ID: 8rzg
TitleZgGH129 from Zobellia galactanivorans soaked with the product of the reaction ADG (3,6-anhydro-D-galactose).
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: 1.81 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)308,03446
Polymers304,9124
Non-polymers3,12242
Water39,0392167
1
A: Conserved hypothetical periplasmic protein
B: Conserved hypothetical periplasmic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)154,12324
Polymers152,4562
Non-polymers1,66722
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11220 Å2
ΔGint-111 kcal/mol
Surface area43370 Å2
MethodPISA
2
C: Conserved hypothetical periplasmic protein
D: Conserved hypothetical periplasmic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)153,91122
Polymers152,4562
Non-polymers1,45520
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10240 Å2
ΔGint-121 kcal/mol
Surface area42850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)219.949, 106.825, 165.529
Angle α, β, γ (deg.)90.000, 113.932, 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, 2209 molecules

#2: Chemical
ChemComp-A1H39 / (1~{R},4~{S},5~{R},8~{S})-2,6-dioxabicyclo[3.2.1]octane-4,8-diol / ADG (3,6-anhydro-D-galactose)


Mass: 146.141 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H10O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-TLA / L(+)-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 5 / 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.: 8 / 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.: 13 / Source method: obtained synthetically / Formula: C2H6O2
#8: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2167 / 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: 2.85 Å3/Da / Density % sol: 56.85 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 2:1 ratio of 0.14M Na/K-tartrate, 14% PEG 3350 with 1.63 mg/ml of enzyme

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.9801 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jan 25, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9801 Å / Relative weight: 1
ReflectionResolution: 1.81→48.48 Å / Num. obs: 272848 / % possible obs: 86.5 % / Redundancy: 2 % / Biso Wilson estimate: 33.73 Å2 / CC1/2: 0.998 / Rrim(I) all: 0.067 / Net I/σ(I): 8.4
Reflection shellResolution: 1.81→1.91 Å / Redundancy: 2 % / Num. unique obs: 40731 / CC1/2: 0.453 / Rrim(I) all: 1.229 / % possible all: 88.5

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimlessdata scaling
Cootmodel building
MOLREPphasing
PHENIX1.16_3549refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.81→48 Å / SU ML: 0.2695 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 22.0837
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1939 13595 4.98 %
Rwork0.1656 259185 -
obs0.167 272780 86.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 35.19 Å2
Refinement stepCycle: LAST / Resolution: 1.81→48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20803 0 192 2167 23162
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005321607
X-RAY DIFFRACTIONf_angle_d0.798629241
X-RAY DIFFRACTIONf_chiral_restr0.05163089
X-RAY DIFFRACTIONf_plane_restr0.0053808
X-RAY DIFFRACTIONf_dihedral_angle_d12.132712800
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.81-1.830.36014360.3488119X-RAY DIFFRACTION81.65
1.83-1.860.37374410.34159089X-RAY DIFFRACTION90.77
1.86-1.880.35184520.33229051X-RAY DIFFRACTION90.25
1.88-1.90.34064870.32229001X-RAY DIFFRACTION90.53
1.9-1.930.32574410.29958995X-RAY DIFFRACTION90.37
1.93-1.950.32245110.29188921X-RAY DIFFRACTION89.91
1.95-1.980.31584480.28298947X-RAY DIFFRACTION89.31
1.98-2.010.29925090.26848883X-RAY DIFFRACTION89.31
2.01-2.040.28245130.25948832X-RAY DIFFRACTION89.27
2.04-2.080.29534660.24398872X-RAY DIFFRACTION88.76
2.08-2.110.27054520.23868795X-RAY DIFFRACTION88.23
2.11-2.150.26854550.22228806X-RAY DIFFRACTION88.46
2.15-2.190.24364630.20618778X-RAY DIFFRACTION87.86
2.19-2.240.23914350.19968811X-RAY DIFFRACTION87.78
2.24-2.290.23984730.19648691X-RAY DIFFRACTION87.49
2.29-2.340.21594490.17828722X-RAY DIFFRACTION87
2.34-2.40.21184820.16868468X-RAY DIFFRACTION85.22
2.4-2.460.20834260.16388299X-RAY DIFFRACTION83
2.46-2.530.19864810.15598664X-RAY DIFFRACTION87.08
2.53-2.620.19414520.1548753X-RAY DIFFRACTION87.52
2.62-2.710.17874320.15558754X-RAY DIFFRACTION87.24
2.71-2.820.19534340.15398708X-RAY DIFFRACTION86.59
2.82-2.950.19794610.15868612X-RAY DIFFRACTION86.24
2.95-3.10.20524310.16028540X-RAY DIFFRACTION85.32
3.1-3.30.18524370.15758498X-RAY DIFFRACTION84.45
3.3-3.550.1684500.14778328X-RAY DIFFRACTION83.35
3.55-3.910.15164420.13378206X-RAY DIFFRACTION81.75
3.91-4.470.13534040.11598197X-RAY DIFFRACTION80.91
4.47-5.630.13124170.11367880X-RAY DIFFRACTION77.96
5.63-480.16084150.15067965X-RAY DIFFRACTION77.61
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)
10.686137316872-0.0242981533146-0.0380353641560.5429123823190.08060527058590.499274946103-0.00112018192668-0.1358080719930.04245892689040.0964340020014-0.02627770298180.04941026124620.0488246261345-0.00809363108474-1.53442355054E-60.26462024473-0.01088353822510.03807246357390.264155713554-0.02665573521330.260584191696-70.688296434351.183492506932.8384172657
20.6972034280630.01174363694170.003894866194750.630763798727-0.07737326182850.451595515931-0.02823659307870.04862946538670.0325173340418-0.005972160521360.0172790725137-0.109874170241-0.03528585086650.122386279409-5.3230407812E-60.2448486447650.003714937537260.0162799773540.310230453282-0.003751337809790.239939972727-41.713007478455.121959018614.5560922803
30.6278316478950.01215960815670.02474309463790.672459624178-0.05455124675620.5867704444140.0356715830345-0.126550919984-0.07290488326020.08211901274440.069774167201-0.05697499591650.08045037839650.0089463464418-1.12296968413E-50.3054899319450.0260718390635-0.05015472282040.308485248122-0.02501764584640.26645000431119.382297171442.298433249158.8633019708
40.773434115957-0.038250779159-0.05610550748080.5459131964480.01194261774720.703036941378-0.01181775345010.01560833337640.0899381574735-0.0784480785850.05889807666430.0621263239106-0.113820198773-0.0843576064234-4.93467715374E-60.3109663317080.00217199975275-0.01039176768980.242703445593-0.006440191829460.3336785860293.9864301006566.137806922939.1285832892
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 36 through 693)

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