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- PDB-9bey: Structure of a lambda-carrageenan active GH2 A in complex with in... -

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Basic information

Entry
Database: PDB / ID: 9bey
TitleStructure of a lambda-carrageenan active GH2 A in complex with inhibitor
ComponentsGH2 beta-galactosidase
KeywordsSUGAR BINDING PROTEIN / Sulfatase / carrageenan
Function / homologyD-galacto-isofagomine
Function and homology information
Biological speciesPseudoalteromonas distincta (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.386 Å
AuthorsHettle, J.A. / Vickers, C. / Boraston, A.B.
Funding support Canada, 1items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada) Canada
CitationJournal: To Be Published
Title: Structure of a lambda-carrageenan active GH2 A in complex with inhibitor
Authors: Hettle, J.A. / Vickers, C. / Boraston, A.B.
History
DepositionApr 16, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 27, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GH2 beta-galactosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,60614
Polymers93,7151
Non-polymers89213
Water7,080393
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)86.450, 70.274, 89.186
Angle α, β, γ (deg.)90.00, 113.48, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein GH2 beta-galactosidase


Mass: 93714.508 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudoalteromonas distincta (bacteria) / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-GIF / D-galacto-isofagomine


Mass: 147.172 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


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


Mass: 18.015 Da / Num. of mol.: 393 / Source method: isolated from a natural source / Formula: H2O
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: 2.65 Å3/Da / Density % sol: 53.61 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 15% PEG 8000, 0.1 M sodium cacodylate, 0.2 M calcium acetate, 0.2 M LiCl, 5% glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.541 Å
DetectorType: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Apr 14, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.541 Å / Relative weight: 1
ReflectionResolution: 2.386→30 Å / Num. obs: 38258 / % possible obs: 97.9 % / Redundancy: 3.7 % / CC1/2: 0.987 / Rmerge(I) obs: 0.121 / Rpim(I) all: 0.058 / Net I/σ(I): 11.3
Reflection shellResolution: 2.386→2.44 Å / Rmerge(I) obs: 0.318 / Num. unique obs: 1529 / CC1/2: 0.821 / Rpim(I) all: 0.231

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
HKL-2000data scaling
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.386→29.676 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2311 2012 5.28 %
Rwork0.1891 --
obs0.1912 38072 96.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.386→29.676 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6386 0 58 393 6837
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0026634
X-RAY DIFFRACTIONf_angle_d0.549001
X-RAY DIFFRACTIONf_dihedral_angle_d4.8895431
X-RAY DIFFRACTIONf_chiral_restr0.046964
X-RAY DIFFRACTIONf_plane_restr0.0031162
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3864-2.4460.28061270.23791921X-RAY DIFFRACTION74
2.446-2.51210.29041430.23542425X-RAY DIFFRACTION92
2.5121-2.5860.29341480.24072618X-RAY DIFFRACTION99
2.586-2.66940.30621460.23372619X-RAY DIFFRACTION99
2.6694-2.76480.3111660.22972616X-RAY DIFFRACTION100
2.7648-2.87540.24921470.22562638X-RAY DIFFRACTION100
2.8754-3.00610.30291570.22442637X-RAY DIFFRACTION99
3.0061-3.16450.28371220.22082630X-RAY DIFFRACTION100
3.1645-3.36250.22541550.19922637X-RAY DIFFRACTION100
3.3625-3.62170.23421510.18962649X-RAY DIFFRACTION100
3.6217-3.98540.21321360.17572655X-RAY DIFFRACTION99
3.9854-4.56030.20491230.16392644X-RAY DIFFRACTION98
4.5603-5.73860.16541490.14942635X-RAY DIFFRACTION99
5.7386-29.6760.18831420.15842736X-RAY DIFFRACTION99

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