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

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Basic information

Entry
Database: PDB / ID: 8rzh
TitleZgGH129 from Zobellia galactanivorans in complex with the inhibitor AD-DGJ (3,6-anhydro-D-1-deoxygalactonojirimycin).
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) / 3,6,9,12,15,18-HEXAOXAICOSANE / : / L(+)-TARTARIC ACID / Conserved hypothetical periplasmic protein
Function and homology information
Biological speciesZobellia galactanivorans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.83 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)308,63345
Polymers304,9124
Non-polymers3,72141
Water52,6222921
1
A: Conserved hypothetical periplasmic protein
B: Conserved hypothetical periplasmic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)154,45424
Polymers152,4562
Non-polymers1,99822
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11530 Å2
ΔGint-104 kcal/mol
Surface area43670 Å2
MethodPISA
2
C: Conserved hypothetical periplasmic protein
D: Conserved hypothetical periplasmic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)154,18021
Polymers152,4562
Non-polymers1,72319
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10180 Å2
ΔGint-125 kcal/mol
Surface area43780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)219.204, 106.492, 165.341
Angle α, β, γ (deg.)90.000, 113.797, 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, 2962 molecules

#2: Chemical
ChemComp-A1H38 / (1~{R},4~{S},5~{R},8~{S})-6-oxa-2-azabicyclo[3.2.1]octane-4,8-diol / AD-DGJ / 3,6-anhydro-D-1-deoxygalactonojirimycin


Mass: 145.156 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H11NO3 / 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-16P / 3,6,9,12,15,18-HEXAOXAICOSANE


Mass: 294.384 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C14H30O6
#5: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Cl
#6: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Na
#7: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C2H6O2
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2921 / 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: 2.83 Å3/Da / Density % sol: 56.57 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 2:1 ratio 0.14M Na/K-tartrate, 14% PEG 3350 1.63 mg/ml

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.9786 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jun 22, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 1.83→48.42 Å / Num. obs: 303236 / % possible obs: 99.3 % / Redundancy: 2.9 % / Biso Wilson estimate: 23.34 Å2 / CC1/2: 0.998 / Rrim(I) all: 0.064 / Net I/σ(I): 10.9
Reflection shellResolution: 1.83→1.93 Å / Redundancy: 2.9 % / Mean I/σ(I) obs: 3 / Num. unique obs: 44194 / CC1/2: 0.848 / Rrim(I) all: 0.433 / % possible all: 99.3

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimlessdata scaling
Cootmodel building
MOLREPphasing
PHENIX1.16refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.83→41.32 Å / SU ML: 0.1648 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 15.4806
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1624 15098 4.98 %
Rwork0.1361 287956 -
obs0.1374 303054 99.17 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 27.81 Å2
Refinement stepCycle: LAST / Resolution: 1.83→41.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20922 0 201 2921 24044
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013421780
X-RAY DIFFRACTIONf_angle_d1.169629441
X-RAY DIFFRACTIONf_chiral_restr0.07873092
X-RAY DIFFRACTIONf_plane_restr0.00823828
X-RAY DIFFRACTIONf_dihedral_angle_d13.09712947
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.83-1.850.23285310.19919448X-RAY DIFFRACTION98.41
1.85-1.870.23754980.18989577X-RAY DIFFRACTION99
1.87-1.90.2394940.1879554X-RAY DIFFRACTION99.66
1.9-1.920.22575300.20099574X-RAY DIFFRACTION99.44
1.92-1.940.21325090.18679590X-RAY DIFFRACTION99.39
1.94-1.970.21794900.1719660X-RAY DIFFRACTION99.63
1.97-20.19624910.16049665X-RAY DIFFRACTION99.75
2-2.030.2075000.15039623X-RAY DIFFRACTION99.78
2.03-2.060.18545040.14599552X-RAY DIFFRACTION99.64
2.06-2.090.17234960.14989643X-RAY DIFFRACTION99.54
2.09-2.130.16844630.13719640X-RAY DIFFRACTION99.48
2.13-2.170.18224890.13969588X-RAY DIFFRACTION99.13
2.17-2.210.16315000.13549503X-RAY DIFFRACTION98.44
2.21-2.260.17214790.13959583X-RAY DIFFRACTION99.01
2.26-2.310.19444800.14039672X-RAY DIFFRACTION99.72
2.31-2.360.18535270.13849590X-RAY DIFFRACTION99.8
2.36-2.420.16035030.13419623X-RAY DIFFRACTION99.72
2.42-2.480.16725330.13459638X-RAY DIFFRACTION99.56
2.48-2.560.16255290.13539543X-RAY DIFFRACTION99.53
2.56-2.640.16175050.13039620X-RAY DIFFRACTION99.38
2.64-2.730.17015160.13749576X-RAY DIFFRACTION99.09
2.73-2.840.17524650.14199551X-RAY DIFFRACTION98.34
2.84-2.970.17615100.14299688X-RAY DIFFRACTION99.65
2.97-3.130.16285200.14329647X-RAY DIFFRACTION99.55
3.13-3.320.16424970.13739608X-RAY DIFFRACTION99.38
3.32-3.580.15684960.12979621X-RAY DIFFRACTION98.85
3.58-3.940.14155250.11769557X-RAY DIFFRACTION98.51
3.94-4.510.11474900.10389610X-RAY DIFFRACTION98.59
4.51-5.680.12815430.11149589X-RAY DIFFRACTION98.48
5.68-41.320.14754850.14649623X-RAY DIFFRACTION96.65
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)
10.570922103793-0.03017020940080.07945907352930.5530011878530.07110866425930.429295364016-0.0167072450048-0.06699222653190.01648435236350.0023879841694-0.004972987033710.101953274107-0.040976027839-0.116600595086-2.51523836814E-50.1450924185610.005490922418830.02321954960680.19829792165-0.006044277280860.144189588168.35070503983-0.058520897656961.0403464063
20.7336821744680.0480742517685-0.006934927359650.554499819376-0.04740842572430.4595995238880.000965827973470.1424648873080.0505590221472-0.0765843218967-0.0185748150628-0.04163984977250.001376043580140.01510442451290.0007882166753610.1513449346050.01369142496510.03537960902920.1576079067850.02626209784330.14887383767437.2212798799-3.7995133263742.7690442355
30.73111870952-0.008645262713110.009269317198840.4839685154080.01168496455820.611434257304-0.00455831325566-0.009944821363020.0396054233050.04680023921360.0428654536095-0.0808217301094-0.050068892280.0644020068153-1.44544074254E-50.1719042316060.00407121682443-0.009608010903230.130148927457-0.006658277279560.194032584041-37.195342190210.920651147836.8312842905
40.5596817208650.04592512545330.06618907683430.5969088994890.1026307713280.5276215830250.03746674712160.113369239056-0.108377846005-0.0550194328560.06125206824670.002534652781090.08408750754020.004708964084950.0007062501729070.196544957902-0.00802844538982-0.03900372156950.182578304977-0.005774557307750.168810925238-52.4933117855-12.807711891816.9020839366
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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