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- PDB-8qrz: Microbacterium testaceum C-glucosyl deglycosidase (CGD), wild type -

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Basic information

Entry
Database: PDB / ID: 8qrz
TitleMicrobacterium testaceum C-glucosyl deglycosidase (CGD), wild type
ComponentsSugar phosphate isomerase
KeywordsLYASE / bacterial C-glucosyl deglycosidase / C-C bond cleavage / C-glucosyl flavonoids / Microbacterium testaceum NS220 / plant endosymbiont / N-terminal DUF6379 beta-sandwich domain / C-terminal TIM barrel domain / homodimer
Function / homology
Function and homology information


isomerase activity / lyase activity
Similarity search - Function
Domain of unknown function DUF6379 / C-glycoside deglycosidase beta subunit / : / Xylose isomerase-like, TIM barrel domain / Xylose isomerase-like TIM barrel / Xylose isomerase-like superfamily
Similarity search - Domain/homology
RUBIDIUM ION / C-deglycosylation enzyme beta subunit
Similarity search - Component
Biological speciesMicrobacterium testaceum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsFurlanetto, V. / Kalyani, D.C. / Divne, C.
Funding support Sweden, 3items
OrganizationGrant numberCountry
Other governmentFormas 2017-00983 Sweden
Other privateOscar and Lili Lamm Memorial Foundation DO2017-0020 Sweden
Other governmentVR 2017-03877 Sweden
CitationJournal: To Be Published
Title: Microbacterium testaceum C-glucosyl deglycosidase (CGD), wild type
Authors: Furlanetto, V. / Kalyani, D.C. / Srivastava, V. / Hallberg, B.M. / Ezcurra, I. / Divne, C.
History
DepositionOct 9, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 23, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Sugar phosphate isomerase
B: Sugar phosphate isomerase
C: Sugar phosphate isomerase
D: Sugar phosphate isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)195,4148
Polymers195,0734
Non-polymers3424
Water6,738374
1
A: Sugar phosphate isomerase
B: Sugar phosphate isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,7074
Polymers97,5362
Non-polymers1712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6010 Å2
ΔGint-32 kcal/mol
Surface area32820 Å2
MethodPISA
2
C: Sugar phosphate isomerase
D: Sugar phosphate isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,7074
Polymers97,5362
Non-polymers1712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5960 Å2
ΔGint-38 kcal/mol
Surface area32960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.220, 80.410, 82.960
Angle α, β, γ (deg.)90.17, 94.39, 106.58
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Sugar phosphate isomerase


Mass: 48768.133 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Microbacterium testaceum (bacteria) / Gene: NS220_14145 / Variant: NS220 / Plasmid: pNIC-CTHO / Production host: Escherichia coli B (bacteria) / Strain (production host): (DE3)-T1 / References: UniProt: A0A147EV52
#2: Chemical
ChemComp-RB / RUBIDIUM ION


Mass: 85.468 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Rb / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 374 / 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: 2.59 Å3/Da / Density % sol: 52.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1 M PIPES pH 7.0, 25% (w/v) PEGSH (PEG SMEAR HIGH), 0.1 M rubidium(I) chloride, 0.1 M magnesium(II) formate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.61992 Å
DetectorType: DECTRIS EIGER2 XE CdTe 9M / Detector: PIXEL / Date: Aug 16, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.61992 Å / Relative weight: 1
ReflectionResolution: 2→47.29 Å / Num. obs: 128896 / % possible obs: 98.8 % / Redundancy: 4.1 % / Biso Wilson estimate: 31.55 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.111 / Net I/σ(I): 8.4
Reflection shellResolution: 2→2.1 Å / Redundancy: 3.9 % / Rmerge(I) obs: 1.034 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 17550 / CC1/2: 0.458 / % possible all: 98.7

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
XDSdata scaling
PHENIX1.19.2_4158phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→39.91 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.95 / Phase error: 33.21 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2899 2011 1.56 %Random selection
Rwork0.2365 ---
obs0.2373 128873 98.77 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→39.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13760 0 4 374 14138
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00814159
X-RAY DIFFRACTIONf_angle_d0.98419300
X-RAY DIFFRACTIONf_dihedral_angle_d6.1771920
X-RAY DIFFRACTIONf_chiral_restr0.0562108
X-RAY DIFFRACTIONf_plane_restr0.0112541
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.050.38681540.34839015X-RAY DIFFRACTION99
2.05-2.110.39231410.33319120X-RAY DIFFRACTION99
2.11-2.170.35651400.31279037X-RAY DIFFRACTION99
2.17-2.240.38491400.30619143X-RAY DIFFRACTION99
2.24-2.320.33141450.29189027X-RAY DIFFRACTION99
2.32-2.410.35381470.28049052X-RAY DIFFRACTION99
2.41-2.520.32811440.27119129X-RAY DIFFRACTION99
2.52-2.650.33341230.26459037X-RAY DIFFRACTION99
2.65-2.820.3191560.26259093X-RAY DIFFRACTION99
2.82-3.040.30631350.26099080X-RAY DIFFRACTION99
3.04-3.340.31781440.24239078X-RAY DIFFRACTION99
3.34-3.820.27821470.21628994X-RAY DIFFRACTION98
3.82-4.820.21911530.17439048X-RAY DIFFRACTION99
4.82-39.910.22481420.19299009X-RAY DIFFRACTION98

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