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- PDB-9rdg: Glucuronoxylan-specific GH30_8 family xylanase CtXyn30A from Clos... -

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Basic information

Entry
Database: PDB / ID: 9rdg
TitleGlucuronoxylan-specific GH30_8 family xylanase CtXyn30A from Clostridium thermocellum complex with glucuronic acid epoxide inhibitor
ComponentsCarbohydrate binding family 6
KeywordsHYDROLASE / activity-based probes / glucuronoxylan-specific xylanases / GH30_8 / covalent labelling
Function / homology
Function and homology information


glucosylceramidase activity / sphingolipid metabolic process / cellulose catabolic process / carbohydrate binding / membrane
Similarity search - Function
Cellulose binding, type IV / Cellulose Binding Domain Type IV / Glycosyl hydrolase family 30, beta sandwich domain / Glycosyl hydrolase family 30 beta sandwich domain / Glycoside hydrolase family 30 / Carbohydrate binding module (family 6) / Clostridium cellulosome enzymes repeated domain signature. / CBM6 (carbohydrate binding type-6) domain profile. / Carbohydrate binding module family 6 / Dockerin domain ...Cellulose binding, type IV / Cellulose Binding Domain Type IV / Glycosyl hydrolase family 30, beta sandwich domain / Glycosyl hydrolase family 30 beta sandwich domain / Glycoside hydrolase family 30 / Carbohydrate binding module (family 6) / Clostridium cellulosome enzymes repeated domain signature. / CBM6 (carbohydrate binding type-6) domain profile. / Carbohydrate binding module family 6 / Dockerin domain / Dockerin domain profile. / Dockerin type I domain / Dockerin type I repeat / Dockerin domain superfamily / Glycosyl hydrolase, all-beta / Galactose-binding-like domain superfamily / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / Glycoside hydrolase superfamily
Similarity search - Domain/homology
Chem-HQ8 / Carbohydrate binding family 6
Similarity search - Component
Biological speciesAcetivibrio thermocellus DSM 2360 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsCorrea, T.L.R. / Li, Z. / Moroz, O.V. / Pickles, I.B. / Lebedev, A.A. / Akkad, S. / Willems, L. / Overkleeft, H.S. / Davies, G.J.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Research Council (ERC)European Union
CitationJournal: To Be Published
Title: A Chemoproteomic Biotechnological Toolkit for Resolving Xylanase Specificity in Decorated Xylan
Authors: Correa, T.L.R. / Li, Z. / Moroz, O.V. / Pickles, I.B. / Lebedev, A.A. / Akkad, S. / Willems, L. / Overkleeft, H.S. / Davies, G.J.
History
DepositionJun 2, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 24, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Carbohydrate binding family 6
B: Carbohydrate binding family 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,7606
Polymers93,7512
Non-polymers1,0094
Water16,159897
1
A: Carbohydrate binding family 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,3803
Polymers46,8751
Non-polymers5042
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Carbohydrate binding family 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,3803
Polymers46,8751
Non-polymers5042
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.071, 60.514, 83.88
Angle α, β, γ (deg.)98.395, 97.404, 105.501
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails (eV)
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: VAL / End label comp-ID: VAL / Auth seq-ID: -2 - 386 / Label seq-ID: 24 - 412

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

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Components

#1: Protein Carbohydrate binding family 6


Mass: 46875.488 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: MGSSHHHHHHSSGLVPRGSHMAS is the expression tag
Source: (gene. exp.) Acetivibrio thermocellus DSM 2360 (bacteria)
Gene: Cthe_3012 / Production host: Escherichia coli (E. coli) / References: UniProt: A3DJS9
#2: Polysaccharide 4-O-methyl-alpha-D-glucopyranuronic acid-(1-2)-beta-D-xylopyranose


Type: oligosaccharide / Mass: 340.281 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
WURCS=2.0/2,2,1/[a212h-1b_1-5][a2122A-1a_1-5_4*OC]/1-2/a2-b1WURCSPDB2Glycan 1.1.0
[][<C5O3>]{[(1+1)][a-D-GlcpA4Me]{}}LINUCSPDB-CARE
#3: Chemical ChemComp-HQ8 / (1~{R},2~{S},4~{S},5~{R})-cyclohexane-1,2,3,4,5-pentol


Mass: 164.156 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H12O5 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 897 / Source method: isolated from a natural source / Formula: H2O
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: 2.59 Å3/Da / Density % sol: 52.6 %
Crystal growTemperature: 292 K / Method: vapor diffusion / Details: 100 mM Tris-HCl pH 8.5, 12% PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: May 6, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.5→48.44 Å / Num. obs: 147933 / % possible obs: 98 % / Redundancy: 3.6 % / CC1/2: 0.991 / Rmerge(I) obs: 0.071 / Rpim(I) all: 0.071 / Rrim(I) all: 0.1 / Χ2: 0.76 / Net I/σ(I): 7.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
8.22-48.443.30.02417.69200.9620.0240.0330.4199.1
1.5-1.533.70.6461.372340.6310.6460.9130.6496.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0430 (refmacat 0.4.105)refinement
REFMAC5.8.0430 (refmacat 0.4.105)refinement
Aimless0.7.9data scaling
DIALS3.14.1-ge7f638df6-releasedata reduction
gemmi0.7.1data extraction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→48.44 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.937 / WRfactor Rfree: 0.208 / WRfactor Rwork: 0.183 / SU B: 1.517 / SU ML: 0.056 / Average fsc free: 0.9661 / Average fsc work: 0.973 / Cross valid method: FREE R-VALUE / ESU R: 0.075 / ESU R Free: 0.075
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2147 7296 4.935 %
Rwork0.189 140548 -
all0.19 --
obs-147844 97.935 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 15.224 Å2
Baniso -1Baniso -2Baniso -3
1-0.176 Å2-0.047 Å20.729 Å2
2--0.113 Å2-0.184 Å2
3----0.403 Å2
Refinement stepCycle: LAST / Resolution: 1.5→48.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6252 0 64 897 7213
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0126618
X-RAY DIFFRACTIONr_bond_other_d0.0050.0166014
X-RAY DIFFRACTIONr_angle_refined_deg1.951.8119037
X-RAY DIFFRACTIONr_angle_other_deg0.9951.76113822
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2825806
X-RAY DIFFRACTIONr_dihedral_angle_2_deg9.333544
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.808101060
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.65410333
X-RAY DIFFRACTIONr_chiral_restr0.2380.2965
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.028050
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021646
X-RAY DIFFRACTIONr_nbd_refined0.1950.21042
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1430.25241
X-RAY DIFFRACTIONr_nbtor_refined0.1620.23158
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0640.23182
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1080.2570
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1070.28
X-RAY DIFFRACTIONr_nbd_other0.1550.236
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.0980.225
X-RAY DIFFRACTIONr_mcbond_it1.3461.3653173
X-RAY DIFFRACTIONr_mcbond_other1.3441.3653173
X-RAY DIFFRACTIONr_mcangle_it1.8352.4713984
X-RAY DIFFRACTIONr_mcangle_other1.8342.4713985
X-RAY DIFFRACTIONr_scbond_it1.9541.5033445
X-RAY DIFFRACTIONr_scbond_other1.9541.5033444
X-RAY DIFFRACTIONr_scangle_it2.8492.6965049
X-RAY DIFFRACTIONr_scangle_other2.8492.6965050
X-RAY DIFFRACTIONr_lrange_it4.04915.5787407
X-RAY DIFFRACTIONr_lrange_other3.81514.187189
X-RAY DIFFRACTIONr_ncsr_local_group_10.0540.0513473
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.053560.05009
12BX-RAY DIFFRACTIONLocal ncs0.053560.05009
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.5-1.5390.275480.258102470.258111610.9470.94996.72070.248
1.539-1.5810.2615070.234100200.236108690.9530.95896.85340.223
1.581-1.6270.2535210.22197500.223105750.9510.96497.12530.208
1.627-1.6770.2444890.20895210.209102920.9590.9797.260.192
1.677-1.7320.2184680.19292450.19399640.9680.97497.48090.175
1.732-1.7920.2214760.18589170.18796240.9670.97797.59980.168
1.792-1.860.2014550.17485920.17692660.9740.9897.63650.157
1.86-1.9360.2344270.20983500.2189700.9660.9797.84840.19
1.936-2.0220.1984210.17979970.1885960.9740.97997.92930.163
2.022-2.120.213770.17477170.17582370.9720.9898.26390.16
2.12-2.2350.1833460.17172850.17177630.9780.98198.29960.156
2.235-2.370.223520.19968690.273430.9680.97598.33860.19
2.37-2.5330.1823370.15765420.15869710.9790.98398.68020.153
2.533-2.7360.1963070.16860520.16964390.9750.98198.75760.165
2.736-2.9960.1933220.16755790.16959590.9740.98199.02670.168
2.996-3.3480.2242810.19150470.19353730.9650.97599.16250.193
3.348-3.8630.2322440.20944410.2147210.9680.97599.23740.215
3.863-4.7230.211840.18138130.18240190.9690.97899.45260.195
4.723-6.6480.2191580.18829110.18930820.9750.98299.57820.205
6.648-48.440.17750.18616530.18617340.9880.98399.6540.2

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