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- PDB-1h6y: The role of conserved amino acids in the cleft of the C-terminal ... -

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Basic information

Entry
Database: PDB / ID: 1h6y
TitleThe role of conserved amino acids in the cleft of the C-terminal family 22 carbohydrate binding module of Clostridium thermocellum Xyn10B in ligand binding
ComponentsENDO-1,4-BETA-XYLANASE Y
KeywordsHYDROLASE / XYLAN DEGRADATION / GLYCOSIDASE
Function / homology
Function and homology information


cellulosome / endo-1,4-beta-xylanase activity / endo-1,4-beta-xylanase / xylan catabolic process
Similarity search - Function
Carbohydrate-binding, CenC-like / Carbohydrate binding domain / Esterase-like / Putative esterase / Clostridium cellulosome enzymes repeated domain signature. / Glycosyl hydrolases family 10, active site / Glycosyl hydrolases family 10 (GH10) active site. / Dockerin domain / Dockerin domain profile. / Dockerin type I domain ...Carbohydrate-binding, CenC-like / Carbohydrate binding domain / Esterase-like / Putative esterase / Clostridium cellulosome enzymes repeated domain signature. / Glycosyl hydrolases family 10, active site / Glycosyl hydrolases family 10 (GH10) active site. / Dockerin domain / Dockerin domain profile. / Dockerin type I domain / Dockerin type I repeat / Dockerin domain superfamily / Glycosyl hydrolases family 10 (GH10) domain profile. / Glycoside hydrolase family 10 / Glycoside hydrolase family 10 domain / Glycosyl hydrolase family 10 / Glycosyl hydrolase family 10 / Galactose-binding domain-like / Galactose-binding-like domain superfamily / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / Alpha/Beta hydrolase fold / Glycoside hydrolase superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Endo-1,4-beta-xylanase Y
Similarity search - Component
Biological speciesCLOSTRIDIUM THERMOCELLUM (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsXie, H. / Bolam, D.N. / Charnock, S.J. / Davies, G.J. / Williamson, M.P. / Simpson, P.J. / Fontes, C.M.G.A. / Ferreira, L.M.A. / Gilbert, H.J.
Citation
Journal: Biochemistry / Year: 2001
Title: Clostridium Thermocellum Xyn10B Carbohydrate-Binding Module 22-2: The Role of Conserved Amino Acids in Ligand Binding
Authors: Xie, H. / Gilbert, H.J. / Charnock, S.J. / Davies, G.J. / Williamson, M.P. / Simpson, P.J. / Raghothama, S. / Fontes, C.M.G.A. / Dias, F.M. / Ferreira, L.M.A. / Bolam, D.N.
#1: Journal: Biochemistry / Year: 2000
Title: The X6 "Thermostabilizing" Domains of Xylanases are Carbohydrate-Binding Modules:Structure and Biochemistry of the Clostridium Thermocellum X6B Domain
Authors: Charnock, S.J. / Bolam, D.N. / Turkenburg, J.P. / Gilbert, H.J. / Ferreira, L.M.A. / Davies, G.J. / Fontes, C.M.G.A.
History
DepositionJun 29, 2001Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 27, 2002Provider: repository / Type: Initial release
Revision 1.1Nov 16, 2011Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Non-polymer description / Other / Structure summary
Revision 1.2Dec 13, 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 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ENDO-1,4-BETA-XYLANASE Y
B: ENDO-1,4-BETA-XYLANASE Y
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,9604
Polymers37,8802
Non-polymers802
Water5,332296
1
A: ENDO-1,4-BETA-XYLANASE Y
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,9802
Polymers18,9401
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: ENDO-1,4-BETA-XYLANASE Y
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,9802
Polymers18,9401
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)89.869, 89.869, 209.003
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein ENDO-1,4-BETA-XYLANASE Y / CBM22-2 / XYLANASE Y / XYLY / 1 / 4-BETA-D-XYLAN XYLANOHYDROLASE Y


Mass: 18939.848 Da / Num. of mol.: 2 / Fragment: XYLAN BINDING DOMAIN RESIDUE 560-720 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CLOSTRIDIUM THERMOCELLUM (bacteria) / Strain: YS / Plasmid: PET21A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: P51584
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 296 / Source method: isolated from a natural source / Formula: H2O
Compound detailsCHAIN A ENGINEERED MUTATION GLU696ALA CHAIN B ENGINEERED MUTATION GLU696ALA

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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: 3.22 Å3/Da / Density % sol: 61.75 %
Crystal growpH: 4.6
Details: 0.1 M NAAC(PH 4.6),10 MM DTT, 25% GLYCEROL,12% PEG8000
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop / pH: 4.6
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
150 mg/mlprotein1drop
20.1 mg/ml1dropNaAcpH4.6
310 mMdithiothreitol1drop
425 %(v/v)glycerol1drop
512 %(w/v)PEG80001drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934
DetectorType: MARRESEARCH / Detector: CCD / Date: Jul 15, 2000 / Details: FOCUSING AND MULTILAYER
RadiationMonochromator: GE(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2.2→25 Å / Num. obs: 26510 / % possible obs: 99.9 % / Observed criterion σ(I): 3 / Redundancy: 28.3 % / Rmerge(I) obs: 0.068 / Net I/σ(I): 24
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 25.5 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 5.8 / % possible all: 100
Reflection
*PLUS
Lowest resolution: 25 Å
Reflection shell
*PLUS
% possible obs: 100 %

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Processing

Software
NameClassification
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1DYO

1dyo


Resolution: 2.2→25 Å / Cross valid method: THROUGHOUT / σ(F): 3
RfactorNum. reflection% reflectionSelection details
Rfree0.228 -5 %RANDOM
Rwork0.194 ---
obs-26510 99.9 %-
Refinement stepCycle: LAST / Resolution: 2.2→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2438 0 2 296 2736
Refinement
*PLUS
Lowest resolution: 25 Å / Rfactor Rwork: 0.192
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.011
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg1.377

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