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- PDB-9rhv: GH10 family xylanase XynA from Bacillus sp. KW1 complex with xylo... -

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Basic information

Entry
Database: PDB / ID: 9rhv
TitleGH10 family xylanase XynA from Bacillus sp. KW1 complex with xylobiosyl-configured cyclophellitol probe bearing an alpha-1,3 - Araf decoration
ComponentsBeta-1,4-xylanase
KeywordsHYDROLASE / activity-based probes / GH10 family xylanase / arabinoxylan-specific xylanase / covalent labelling
Function / homology: / :
Function and homology information
Biological speciesBacillus sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.02 Å
AuthorsCorrea, T.L.R. / Li, Z. / Moroz, O.V. / Pickles, I.B. / Lebedev, 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. / Akkad, S. / Willems, L. / Overkleeft, H.S. / Davies, G.J.
History
DepositionJun 10, 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: Beta-1,4-xylanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,3513
Polymers49,9231
Non-polymers4282
Water1,13563
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area970 Å2
ΔGint2 kcal/mol
Surface area16450 Å2
Unit cell
Length a, b, c (Å)109.065, 109.065, 84.791
Angle α, β, γ (deg.)90, 90, 90
Int Tables number91
Space group name H-MP4122

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Components

#1: Protein Beta-1,4-xylanase


Mass: 49922.984 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: 1. The visible portion of the ligand covalently bound to GLU A280 is represented by three monomers (A1J01, XYP, and AHR), which are covalently linked to each other. In the complete compound, ...Details: 1. The visible portion of the ligand covalently bound to GLU A280 is represented by three monomers (A1J01, XYP, and AHR), which are covalently linked to each other. In the complete compound, the OH group at C4 of AHR is replaced by an extended substituent attached via a nitrogen atom. Accordingly, the O4 atom has been removed, and a short, contiguous fragment of residual electron density extending from C4, consistent with only 2-3 atoms, remains unmodelled. 2. The beta-sheet on one side of the CBM domain adopts two conformations. Only one conformation is modelled, and the alternative (unmodelled) conformation gives rise to difference density between strands. The affected residue ranges are A40-A56, A358-A366, and A399-A405.
Source: (gene. exp.) Bacillus sp. (in: firmicutes) (bacteria)
Gene: xyn10A / Production host: Escherichia coli (E. coli) / References: UniProt: A0ACD6BAA5, endo-1,4-beta-xylanase
#2: Polysaccharide alpha-L-arabinofuranose-(1-3)-beta-D-xylopyranose


Type: oligosaccharide / Mass: 282.245 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LArafa1-3DXylpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a212h-1b_1-5][a211h-1a_1-4]/1-2/a3-b1WURCSPDB2Glycan 1.1.0
[][<C5O2>]{[(1+1)][a-L-Araf]{}}LINUCSPDB-CARE
#3: Chemical ChemComp-A1J01 / (1~{S},2~{R},3~{S},4~{R},6~{R})-7-oxabicyclo[4.1.0]heptane-2,3,4-triol


Mass: 146.141 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H10O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 63 / 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: 2.53 Å3/Da / Density % sol: 51.29 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / Details: 20% PEG3350, 0.2M KSCN

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.976 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Sep 19, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 2.02→57.05 Å / Num. obs: 34175 / % possible obs: 100 % / Redundancy: 17.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.11 / Rpim(I) all: 0.037 / Rrim(I) all: 0.116 / Χ2: 0.93 / Net I/σ(I): 14.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
9.03-57.0515.50.02763.846810.0090.0280.6499.7
2.02-2.0718.13.9490.724540.3091.3544.1770.8799.6

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Processing

Software
NameVersionClassification
DIALS3.21.1.1-g807743295-releasedata reduction
Aimless0.8.2data scaling
REFMAC5.8.0431 (refmacat 0.4.126)refinement
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.02→54.592 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.945 / SU B: 10.482 / SU ML: 0.132 / Cross valid method: FREE R-VALUE / ESU R: 0.168 / ESU R Free: 0.152
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.2345 1705 4.998 %RANDOM
Rwork0.2014 32406 --
all0.203 ---
obs-34111 99.962 %-
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: 65.249 Å2
Baniso -1Baniso -2Baniso -3
1-0.605 Å20 Å2-0 Å2
2--0.605 Å2-0 Å2
3----1.211 Å2
Refinement stepCycle: LAST / Resolution: 2.02→54.592 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3104 0 27 63 3194
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0123242
X-RAY DIFFRACTIONr_bond_other_d0.0040.0162897
X-RAY DIFFRACTIONr_angle_refined_deg1.9481.8234411
X-RAY DIFFRACTIONr_angle_other_deg0.9671.7836655
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.6295381
X-RAY DIFFRACTIONr_dihedral_angle_2_deg10.025522
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.56110508
X-RAY DIFFRACTIONr_dihedral_angle_6_deg16.20410178
X-RAY DIFFRACTIONr_chiral_restr0.1070.2461
X-RAY DIFFRACTIONr_gen_planes_refined0.010.023935
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02821
X-RAY DIFFRACTIONr_nbd_refined0.1610.2529
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1260.22586
X-RAY DIFFRACTIONr_nbtor_refined0.1530.21481
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0650.21676
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.120.296
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.0760.212
X-RAY DIFFRACTIONr_nbd_other0.0890.267
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.0740.210
X-RAY DIFFRACTIONr_mcbond_it2.7093.6421527
X-RAY DIFFRACTIONr_mcbond_other2.7073.6421527
X-RAY DIFFRACTIONr_mcangle_it3.716.571907
X-RAY DIFFRACTIONr_mcangle_other3.716.571908
X-RAY DIFFRACTIONr_scbond_it3.7873.9341715
X-RAY DIFFRACTIONr_scbond_other3.7873.9371716
X-RAY DIFFRACTIONr_scangle_it5.4767.1052501
X-RAY DIFFRACTIONr_scangle_other5.4757.1092502
X-RAY DIFFRACTIONr_lrange_it6.73633.9133438
X-RAY DIFFRACTIONr_lrange_other6.73633.9293439
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
2.02-2.0720.341170.3423450.3424630.9040.89199.95940.34
2.072-2.1290.3391270.30722770.30924050.9180.92699.95840.303
2.129-2.1910.2961140.27822380.27923520.9440.9421000.269
2.191-2.2580.309990.2621760.26222770.9310.95199.91220.242
2.258-2.3320.2391180.22420910.22522100.9650.96999.95480.2
2.332-2.4140.2511190.20120650.20321840.9640.9741000.173
2.414-2.5050.245980.19219550.19420530.9670.9781000.164
2.505-2.6070.229960.18319120.18520080.9710.981000.151
2.607-2.7220.2021140.16318120.16619280.9760.98499.89630.135
2.722-2.8550.193970.15917380.16118350.9770.9851000.135
2.855-3.0090.232760.18116910.18317680.9710.9899.94340.154
3.009-3.1910.238820.17815820.18116640.9670.9811000.155
3.191-3.410.185860.15814900.1615760.9840.9861000.14
3.41-3.6820.161840.16913930.16914770.9840.9841000.155
3.682-4.0320.265600.19313020.19613620.9640.9791000.181
4.032-4.5050.181570.19211890.19212460.9790.9781000.183
4.505-5.1950.273560.20810580.21111140.9610.9731000.198
5.195-6.3490.382480.2589070.2639550.9290.9631000.242
6.349-8.9180.244320.2237310.2247630.9630.9711000.214
8.918-54.5920.178250.2124510.214770.9740.96599.79040.206
Refinement TLS params.Method: refined / Origin x: 31.0586 Å / Origin y: 29.8135 Å / Origin z: 10.1779 Å
111213212223313233
T0.0649 Å20.0185 Å20.0015 Å2-0.2984 Å2-0.0423 Å2--0.0656 Å2
L3.7182 °2-0.411 °20.6227 °2-1.4701 °20.0957 °2--1.7836 °2
S-0.1079 Å °-0.7843 Å °0.1331 Å °0.2662 Å °0.1096 Å °-0.1181 Å °0.1024 Å °-0.1121 Å °-0.0017 Å °
Refinement TLS groupSelection: ALL

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