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

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Basic information

Entry
Database: PDB / ID: 4uqb
TitleX-ray structure of glucuronoxylan-xylanohydrolase (Xyn30A) from Clostridium thermocellum at 1.68 A resolution
ComponentsCARBOHYDRATE BINDING FAMILY 6
KeywordsHYDROLASE
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 / 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: 1.68 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 / Derived calculations / 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,1235
Polymers46,4541
Non-polymers6694
Water7,476415
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)46.980, 50.590, 59.310
Angle α, β, γ (deg.)114.77, 101.43, 103.85
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: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 415 / 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: 2.52 Å3/Da / Density % sol: 51.23 % / Description: NONE
Crystal growpH: 7.5
Details: 0.1 M HEPES 7.5, 10 % (V/V)PEG 8000, 8 % (V/V)ETHILE GLYCOL

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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: 1.68→50.68 Å / Num. obs: 47651 / % possible obs: 92.3 % / Observed criterion σ(I): 1.77 / Redundancy: 4.3 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 13.63
Reflection shellResolution: 1.68→1.74 Å / Redundancy: 4 % / Rmerge(I) obs: 0.83 / Mean I/σ(I) obs: 1.77 / % possible all: 77.2

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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: 1.68→45.49 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.953 / SU B: 2.952 / SU ML: 0.09 / Cross valid method: THROUGHOUT / ESU R: 0.107 / ESU R Free: 0.102 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.206 1945 4.1 %RANDOM
Rwork0.179 ---
obs0.181 45706 92.31 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.8 Å2
Baniso -1Baniso -2Baniso -3
1--2.34 Å2-1.32 Å2-0.49 Å2
2--0.72 Å22.13 Å2
3----0.21 Å2
Refinement stepCycle: LAST / Resolution: 1.68→45.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3128 0 40 415 3583
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0193294
X-RAY DIFFRACTIONr_bond_other_d0.0010.023030
X-RAY DIFFRACTIONr_angle_refined_deg1.2121.9384494
X-RAY DIFFRACTIONr_angle_other_deg0.74636970
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3165405
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.01524.207164
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.46315533
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.46315533
X-RAY DIFFRACTIONr_chiral_restr0.0710.2479
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0213781
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02806
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_it0.792.6611575
X-RAY DIFFRACTIONr_mcbond_other0.7892.661574
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: 1.68→1.72 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.307 123 -
Rwork0.344 2681 -
obs--74.52 %

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