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- PDB-4uq9: X-ray structure of glucuronoxylan-xylanohydrolase (Xyn30A) from C... -

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Basic information

Entry
Database: PDB / ID: 4uq9
TitleX-ray structure of glucuronoxylan-xylanohydrolase (Xyn30A) from Clostridium thermocellum at 1.77 A resolution
ComponentsCARBOHYDRATE BINDING FAMILY 6
KeywordsHYDROLASE
Function / homology
Function and homology information


glucosylceramidase activity / sphingolipid metabolic process / polysaccharide catabolic process / carbohydrate binding
Similarity search - Function
Glycosyl hydrolase family 30, beta sandwich domain / Glycosyl hydrolase family 30 beta sandwich domain / Glycoside hydrolase family 30 / Cellulose binding, type IV / Cellulose Binding Domain Type IV / 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 ...Glycosyl hydrolase family 30, beta sandwich domain / Glycosyl hydrolase family 30 beta sandwich domain / Glycoside hydrolase family 30 / Cellulose binding, type IV / Cellulose Binding Domain Type IV / 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 / Golgi alpha-mannosidase II / Glycosyl hydrolase, all-beta / Galactose-binding-like domain superfamily / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Carbohydrate binding family 6 / :
Similarity search - Component
Biological speciesRUMINICLOSTRIDIUM THERMOCELLUM (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.77 Å
AuthorsFreire, F. / Verma, A.K. / Goyal, A. / Fontes, C.M.G.A. / Najmudin, S.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2016
Title: Conservation in the Mechanism of Glucuronoxylan Hydrolysis Revealed by the Structure of Glucuronoxylan Xylano-Hydrolase (Ctxyn30A) from Clostridium Thermocellum
Authors: Freire, F. / Verma, A.K. / Bule, P. / Alves, V.D. / Fontes, C.M.G.A. / Goyal, A. / Najmudin, S.
History
DepositionJun 22, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 24, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 23, 2016Group: Database references
Revision 1.2Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CARBOHYDRATE BINDING FAMILY 6


Theoretical massNumber of molelcules
Total (without water)46,4541
Polymers46,4541
Non-polymers00
Water4,125229
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)46.620, 50.330, 58.710
Angle α, β, γ (deg.)65.16, 67.56, 76.99
Int Tables number1
Space group name H-MP1

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Components

#1: Protein CARBOHYDRATE BINDING FAMILY 6 / XYN30A


Mass: 46454.062 Da / Num. of mol.: 1 / Fragment: N-TERMINAL CATALYTIC MODULE, RESIDUES 34-419 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) RUMINICLOSTRIDIUM THERMOCELLUM (bacteria)
Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21
References: UniProt: E6UTM3, UniProt: A3DJS9*PLUS, endo-1,4-beta-xylanase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 229 / Source method: isolated from a natural source / Formula: H2O

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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: 2.48 Å3/Da / Density % sol: 50.49 % / Description: NONE
Crystal growpH: 8.5 / Details: 0.1 M TRIS-HCL 8.5, 8 % PEG 8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9537
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 13, 2014
Details: KIRKPATRICK-BAEZ PAIR OF BI-MORPH MIRRORS PLUS CHANNEL CUT CRYOGENICALLY COOLED MONOCHROMATOR CRYSTAL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.77→45.53 Å / Num. obs: 40534 / % possible obs: 93.4 % / Observed criterion σ(I): 1.91 / Redundancy: 4.1 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 14.15
Reflection shellResolution: 1.77→1.84 Å / Redundancy: 4 % / Rmerge(I) obs: 0.95 / Mean I/σ(I) obs: 1.91 / % possible all: 79.5

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Processing

Software
NameVersionClassification
REFMAC5refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4CKQ

4ckq


Resolution: 1.77→45.53 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.931 / SU B: 7.685 / SU ML: 0.114 / Cross valid method: THROUGHOUT / ESU R: 0.14 / ESU R Free: 0.129 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.237 1937 4.8 %RANDOM
Rwork0.207 ---
obs0.208 38598 93.44 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.07 Å2
Baniso -1Baniso -2Baniso -3
1-1.02 Å20.65 Å20.32 Å2
2---0.26 Å20.3 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.77→45.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3128 0 0 229 3357
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0193237
X-RAY DIFFRACTIONr_bond_other_d0.0010.022976
X-RAY DIFFRACTIONr_angle_refined_deg1.8381.9254411
X-RAY DIFFRACTIONr_angle_other_deg0.89836834
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3255399
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.45624.172163
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.15815527
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.5361521
X-RAY DIFFRACTIONr_chiral_restr0.1210.2466
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0213756
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02803
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7430.6711569
X-RAY DIFFRACTIONr_mcbond_other0.7430.6711568
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.77→1.82 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.41 110 -
Rwork0.39 2329 -
obs--76.31 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.8395-1.22170.2932.9378-0.81891.0806-0.0313-0.06130.06920.1830.0248-0.1342-0.00960.0320.00660.07190.08530.03870.16480.05960.14458.9461-3.254820.5918
20.2723-0.44790.31081.1874-0.46910.53160.0184-0.0189-0.0731-0.06940.06020.0996-0.0103-0.0693-0.07860.02350.04650.0370.17340.07580.197741.85879.2074-1.2512
30.4548-0.61430.60491.2892-0.30031.38610.0002-0.0322-0.06820.15510.11740.0640.18010.0472-0.11750.07460.06110.05590.13720.08680.225556.9012-10.788813.9846
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-3 - 10
2X-RAY DIFFRACTION2A11 - 295
3X-RAY DIFFRACTION3A296 - 386

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