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

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Basic information

Entry
Database: PDB / ID: 4ckq
TitleX-ray structure of glucuronoxylan-xylanohydrolase (Xyn30A) from Clostridium thermocellum
Components
  • 4 HISTIDINES FROM PROTEOLYSED HIS-TAG
  • CARBOHYDRATE 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
MALONIC ACID / Carbohydrate binding family 6 / :
Similarity search - Component
Biological speciesCLOSTRIDIUM THERMOCELLUM (bacteria)
SYNTHETIC CONSTRUCT (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 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
DepositionJan 7, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 21, 2015Provider: repository / Type: Initial release
Revision 1.1Apr 22, 2015Group: Non-polymer description
Revision 1.2Nov 23, 2016Group: Database references
Revision 1.3Dec 20, 2023Group: 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
C: 4 HISTIDINES FROM PROTEOLYSED HIS-TAG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,1293
Polymers47,0252
Non-polymers1041
Water11,656647
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area950 Å2
ΔGint-9.9 kcal/mol
Surface area15410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.090, 47.463, 53.620
Angle α, β, γ (deg.)83.15, 73.41, 65.87
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.) CLOSTRIDIUM THERMOCELLUM (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21
References: UniProt: C7HEF6, UniProt: A3DJS9*PLUS, endo-1,4-beta-xylanase
#2: Protein/peptide 4 HISTIDINES FROM PROTEOLYSED HIS-TAG


Mass: 570.602 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SYNTHETIC CONSTRUCT (others) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21
#3: Chemical ChemComp-MLA / MALONIC ACID / DICARBOXYLIC ACID C3 / PROPANEDIOLIC ACID / METHANEDICARBOXYLIC ACID / Malonic acid


Mass: 104.061 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H4O4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 647 / 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: 2.33 Å3/Da / Density % sol: 47.2 % / Description: NONE
Crystal growDetails: 0.2 M POTASSIUM SULFATE 20 % (W/V) POLYETHYLENE GLYCOL 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.826
DetectorType: ADSC QUANTUM 315r / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.826 Å / Relative weight: 1
ReflectionResolution: 1.4→42.93 Å / Num. obs: 76088 / % possible obs: 97.2 % / Observed criterion σ(I): 3.5 / Redundancy: 4.6 % / Rmerge(I) obs: 0.2 / Net I/σ(I): 3.5
Reflection shellResolution: 1.4→1.48 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.86 / Mean I/σ(I) obs: 1.3 / % possible all: 95.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0071refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3GTN

3gtn


Resolution: 1.4→51.39 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.963 / SU B: 2.581 / SU ML: 0.05 / Cross valid method: THROUGHOUT / ESU R: 0.056 / ESU R Free: 0.058 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1715 3804 5 %RANDOM
Rwork0.14841 ---
obs0.14958 72006 96.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.54 Å2-0.19 Å20.26 Å2
2---0.16 Å20 Å2
3----0.28 Å2
Refinement stepCycle: LAST / Resolution: 1.4→51.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3168 0 7 647 3822
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0193365
X-RAY DIFFRACTIONr_bond_other_d0.0010.023095
X-RAY DIFFRACTIONr_angle_refined_deg1.8371.9244600
X-RAY DIFFRACTIONr_angle_other_deg0.94337123
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6525425
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.75224.138174
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.11815553
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.361522
X-RAY DIFFRACTIONr_chiral_restr0.1180.2485
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0213922
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02844
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_it1.180.8871608
X-RAY DIFFRACTIONr_mcbond_other1.1050.8831607
X-RAY DIFFRACTIONr_mcangle_it1.9541.3212014
X-RAY DIFFRACTIONr_mcangle_other1.9591.3252015
X-RAY DIFFRACTIONr_scbond_it1.7521.0891757
X-RAY DIFFRACTIONr_scbond_other1.7491.0891755
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.6971.5652569
X-RAY DIFFRACTIONr_long_range_B_refined6.2989.9284412
X-RAY DIFFRACTIONr_long_range_B_other6.3019.9364412
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.4→1.436 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.277 273 -
Rwork0.277 5194 -
obs--94.57 %
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)
11.33520.1733-0.12320.6641-0.87981.61990.01870.02030.09470.0274-0.07710.0171-0.07690.11460.05850.0183-0.0044-0.00050.01050.0020.020739.216547.8963-12.6335
20.10930.01030.03430.0637-0.08010.1904-0.0044-0.0061-0.003-0.00620.00620.00430.00810-0.00190.012-0.00560.00120.00550.00110.005720.788236.30789.3187
30.2327-0.0994-0.08580.2076-0.10130.14840.01880.02840.0088-0.0408-0.0251-0.01210.01580.00210.00630.0250.0005-0.00460.00570.00360.003629.463549.5064-15.7827
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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