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- PDB-9ywn: Protein Structure of the First Glycoside Hydrolase Family 30, Sub... -

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Basic information

Entry
Database: PDB / ID: 9ywn
TitleProtein Structure of the First Glycoside Hydrolase Family 30, Subfamily 12 Endoxylanase
ComponentsGlucuronoarabinoxylan endo-1,4-beta-xylanase
KeywordsHYDROLASE / glycoside hydrolase / Xylanase / Endoxylanase
Function / homology
Function and homology information


glucosylceramidase activity / sphingolipid metabolic process / xylan catabolic process / carbohydrate binding / membrane
Similarity search - Function
Glycosyl hydrolase family 30, TIM-barrel domain / Glycosyl hydrolase family 30 TIM-barrel 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. ...Glycosyl hydrolase family 30, TIM-barrel domain / Glycosyl hydrolase family 30 TIM-barrel 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
ACETIC ACID / FORMIC ACID / DI(HYDROXYETHYL)ETHER / Glucuronoarabinoxylan endo-1,4-beta-xylanase
Similarity search - Component
Biological speciesAnaerobacterium chartisolvens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.916 Å
AuthorsSt John, F.J. / Tan, K.
Funding support United States, 1items
OrganizationGrant numberCountry
Department of Energy (DOE, United States)DE-AC02-06CH11357 United States
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2026
Title: Protein structure of a glycoside hydrolase family 30, subfamily 12 endo-1,4-beta-xylanase.
Authors: St John, F.J. / Crooks, C. / Endres, M. / Pakdaman, L. / Koch, L. / Bynum, L. / Kuch, N. / Joachimiak, A. / Tan, K.
History
DepositionOct 24, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 15, 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: Glucuronoarabinoxylan endo-1,4-beta-xylanase
B: Glucuronoarabinoxylan endo-1,4-beta-xylanase
C: Glucuronoarabinoxylan endo-1,4-beta-xylanase
D: Glucuronoarabinoxylan endo-1,4-beta-xylanase
E: Glucuronoarabinoxylan endo-1,4-beta-xylanase
F: Glucuronoarabinoxylan endo-1,4-beta-xylanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)302,38167
Polymers298,2416
Non-polymers4,14061
Water29,3641630
1
A: Glucuronoarabinoxylan endo-1,4-beta-xylanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,32610
Polymers49,7071
Non-polymers6209
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Glucuronoarabinoxylan endo-1,4-beta-xylanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,59113
Polymers49,7071
Non-polymers88412
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Glucuronoarabinoxylan endo-1,4-beta-xylanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,55713
Polymers49,7071
Non-polymers85012
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Glucuronoarabinoxylan endo-1,4-beta-xylanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,35811
Polymers49,7071
Non-polymers65210
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Glucuronoarabinoxylan endo-1,4-beta-xylanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,2209
Polymers49,7071
Non-polymers5138
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Glucuronoarabinoxylan endo-1,4-beta-xylanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,32811
Polymers49,7071
Non-polymers62210
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)89.307, 133.392, 137.700
Angle α, β, γ (deg.)90.000, 101.544, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 6 molecules ABCDEF

#1: Protein
Glucuronoarabinoxylan endo-1,4-beta-xylanase


Mass: 49706.887 Da / Num. of mol.: 6
Fragment: The C-terminal was truncated by removing two non-catalytic domains. These removed domains inlcude a carbohydrate binding module family 6 and dockerin domains.
Source method: isolated from a genetically manipulated source
Details: DSM 27016
Source: (gene. exp.) Anaerobacterium chartisolvens (bacteria)
Gene: DFR58_1374 / Plasmid: pMCSG53 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A369AIV8

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Non-polymers , 7 types, 1691 molecules

#2: Chemical...
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 22 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: CH2O2
#4: Chemical
ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H4O2
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Na
#7: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1630 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
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: 2.86 Å3/Da / Density % sol: 56.99 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 0.17 M ammonium acetate, 0.085 M sodium acetate HCl pH 4.6, 25.5 percent PEG 4000 and 15 percent glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 19-ID / Wavelength: 0.9857 Å
DetectorType: DECTRIS EIGER2 XE 9M / Detector: PIXEL / Date: Mar 16, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9857 Å / Relative weight: 1
ReflectionResolution: 1.92→50.21 Å / Num. obs: 239756 / % possible obs: 99.6 % / Redundancy: 3.3 % / Biso Wilson estimate: 32.3 Å2 / CC1/2: 0.994 / CC star: 0.998 / Rpim(I) all: 0.072 / Rrim(I) all: 0.131 / Χ2: 0.744 / Net I/av σ(I): 9.4 / Net I/σ(I): 9.4
Reflection shellResolution: 1.92→1.95 Å / Redundancy: 2.9 % / Mean I/σ(I) obs: 0.89 / Num. unique obs: 11542 / CC1/2: 0.403 / CC star: 0.758 / Rpim(I) all: 0.649 / Rrim(I) all: 1.157 / Χ2: 0.535 / % possible all: 96.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0431refinement
HKL-3000data reduction
HKL-3000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.916→48.949 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.947 / SU B: 4.1 / SU ML: 0.109 / Cross valid method: THROUGHOUT / ESU R: 0.132 / ESU R Free: 0.125
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.205 11805 4.928 %RANDOM
Rwork0.1686 227733 --
all0.17 ---
obs-239538 98.983 %-
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: 25.988 Å2
Baniso -1Baniso -2Baniso -3
1-0.063 Å20 Å20.787 Å2
2---0.577 Å2-0 Å2
3---0.178 Å2
Refinement stepCycle: LAST / Resolution: 1.916→48.949 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19950 0 267 1630 21847
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01221171
X-RAY DIFFRACTIONr_bond_other_d0.0010.01619023
X-RAY DIFFRACTIONr_angle_refined_deg1.5971.78428865
X-RAY DIFFRACTIONr_angle_other_deg0.5461.7343916
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.96952652
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.418560
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.115103184
X-RAY DIFFRACTIONr_dihedral_angle_6_deg14.50410979
X-RAY DIFFRACTIONr_chiral_restr0.0760.23118
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0225253
X-RAY DIFFRACTIONr_gen_planes_other0.0010.025055
X-RAY DIFFRACTIONr_nbd_refined0.2170.24117
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1970.217814
X-RAY DIFFRACTIONr_nbtor_refined0.1870.210539
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0840.210883
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.170.21402
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1230.23
X-RAY DIFFRACTIONr_metal_ion_refined0.1510.219
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2110.229
X-RAY DIFFRACTIONr_nbd_other0.2230.2110
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2960.231
X-RAY DIFFRACTIONr_mcbond_it2.4352.60210434
X-RAY DIFFRACTIONr_mcbond_other2.4342.60210435
X-RAY DIFFRACTIONr_mcangle_it3.6514.66213107
X-RAY DIFFRACTIONr_mcangle_other3.6514.66213108
X-RAY DIFFRACTIONr_scbond_it3.142.91410737
X-RAY DIFFRACTIONr_scbond_other3.142.91410738
X-RAY DIFFRACTIONr_scangle_it4.8955.17915747
X-RAY DIFFRACTIONr_scangle_other4.8955.17915748
X-RAY DIFFRACTIONr_lrange_it6.81127.06824190
X-RAY DIFFRACTIONr_lrange_other6.7426.22323904
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
1.916-1.9650.3137770.3149480.301177980.9320.93688.35260.286
1.965-2.0190.2868730.274163640.275174150.9390.94698.97790.254
2.019-2.0780.2678550.248160280.249169270.950.95699.74010.223
2.078-2.1410.2668190.238155600.239163930.9510.96199.91460.21
2.141-2.2110.2647480.22151380.222158910.9540.96799.96850.192
2.211-2.2890.2397780.204146660.206154470.9610.97299.98060.174
2.289-2.3750.2347490.189140850.191148550.9660.97699.85860.159
2.375-2.4720.2157010.174136100.176143160.970.9899.96510.146
2.472-2.5810.2256700.17130050.172136760.9670.98299.99270.144
2.581-2.7070.2226860.159124950.163131810.9680.9841000.137
2.707-2.8530.2145800.153118800.156124610.970.98599.9920.134
2.853-3.0250.25820.15112800.153118630.9750.98699.99160.133
3.025-3.2330.2015450.151105360.154110860.9740.98699.95490.139
3.233-3.4910.1984770.14998750.152103620.9780.98799.90350.143
3.491-3.8230.1654460.13891130.13995620.9830.9999.96860.137
3.823-4.2710.1584450.12481750.12686320.9850.99199.8610.127
4.271-4.9250.1363880.11272420.11376690.9890.99399.49150.12
4.925-6.0170.1693230.14561530.14664830.9870.99199.8920.15
6.017-8.4450.1672310.15448110.15550450.9840.98999.94050.162
8.445-48.9490.1491320.13327690.13429200.9880.99199.34930.149

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