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- PDB-1gmm: Carbohydrate binding module CBM6 from xylanase U Clostridium ther... -

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Basic information

Entry
Database: PDB / ID: 1gmm
TitleCarbohydrate binding module CBM6 from xylanase U Clostridium thermocellum
ComponentsCBM6
KeywordsXYLANASE / CARBOHYDRATE BINDING MODULE / CBM FAMILY 6 / XYLAN BINDING
Function / homology
Function and homology information


hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds / endo-1,4-beta-xylanase activity / endo-1,4-beta-xylanase / xylan catabolic process / carbohydrate binding / metal ion binding
Similarity search - Function
NodB homology domain profile. / Cellulose binding, type IV / Cellulose Binding Domain Type IV / NodB homology domain / Polysaccharide deacetylase / Carbohydrate binding module (family 6) / Clostridium cellulosome enzymes repeated domain signature. / CBM6 (carbohydrate binding type-6) domain profile. / Carbohydrate binding module family 6 / Glycoside hydrolase family 11, active site 2 ...NodB homology domain profile. / Cellulose binding, type IV / Cellulose Binding Domain Type IV / NodB homology domain / Polysaccharide deacetylase / Carbohydrate binding module (family 6) / Clostridium cellulosome enzymes repeated domain signature. / CBM6 (carbohydrate binding type-6) domain profile. / Carbohydrate binding module family 6 / Glycoside hydrolase family 11, active site 2 / Glycosyl hydrolases family 11 (GH11) active site signature 2. / Glycoside hydrolase family 11, active site 1 / Glycosyl hydrolases family 11 (GH11) active site signature 1. / Glycoside hydrolase family 11 / Glycosyl hydrolases family 11 (GH11) domain / Glycosyl hydrolases family 11 / Glycosyl hydrolases family 11 (GH11) domain profile. / Dockerin domain / Dockerin domain profile. / Glycoside hydrolase/deacetylase, beta/alpha-barrel / Dockerin type I domain / Dockerin type I repeat / Dockerin domain superfamily / Glycoside hydrolase family 11/12 / Galactose-binding domain-like / Galactose-binding-like domain superfamily / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
endo-1,4-beta-xylanase
Similarity search - Component
Biological speciesCLOSTRIDIUM THERMOCELLUM (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å
AuthorsCzjzek, M. / Mosbah, A. / Bolam, D. / Allouch, J. / Zamboni, V. / Henrissat, B. / Gilbert, H.J.
Citation
Journal: J.Biol.Chem. / Year: 2001
Title: The Location of the Ligand-Binding Site of Carbohydrate-Binding Modules that Have Evolved from a Common Sequence is not Conserved.
Authors: Czjzek, M. / Bolam, D. / Mosbah, A. / Allouch, J. / Fontes, C.M. / Ferreira, L.M. / Bornet, O. / Zamboni, V. / Darbon, H. / Smith, N.L. / Black, G.W. / Henrissat, B. / Gilbert, H.J.
#1: Journal: Biochem.J. / Year: 1999
Title: Homologous Xylanases from Clostridium Thermocellum: Evidence for Bi-Functional Activity, Synergism between Xylanase Catalytic Modules and the Presence of Xylan-Binding Domains in Enzyme Complexes
Authors: Fernandes, A. / Fontes, C.M.G.A. / Gilbert, H.J. / Hazelwood, G.P. / Fernandes, T.H. / Ferreira, L.M.A. / Gilbert, H.J.
History
DepositionSep 19, 2001Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 28, 2001Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CBM6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,2744
Polymers14,1151
Non-polymers1593
Water3,243180
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)59.650, 59.650, 157.450
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein CBM6


Mass: 14115.347 Da / Num. of mol.: 1 / Fragment: XYLAN BINDING MODULE (DOMAIN), RESIDUE 248-380
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CLOSTRIDIUM THERMOCELLUM (bacteria) / Strain: F1 / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: O52780, endo-1,4-beta-xylanase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 180 / 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: 2.73 Å3/Da / Density % sol: 55 %
Crystal growpH: 5.5
Details: 30% PEG 4000, 100MM NA-CITRATE PH 5.5, 100MM (NH4)2SO4
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
112 mg/mlprotein1drop
220 mMsodium acetate1droppH5.0
330 %PEG40001reservoir
4100 mMsodium citrate1reservoirpH5.5
5100 mMammonium sulfate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9793, 0.9795, 0.9465, 0.933
DetectorDetector: CCD / Date: Dec 15, 2000 / Details: MIRRORS
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97931
20.97951
30.94651
40.9331
ReflectionResolution: 2→39.22 Å / Num. obs: 11981 / % possible obs: 99.3 % / Observed criterion σ(I): 0.01 / Redundancy: 6.6 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 9.3
Reflection shellResolution: 2→2.11 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.204 / Mean I/σ(I) obs: 1.2 / % possible all: 98.2
Reflection
*PLUS
Rmerge(I) obs: 0.055
Reflection shell
*PLUS
% possible obs: 98.2 %

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Processing

Software
NameClassification
REFMACrefinement
DENZOdata reduction
SCALAdata scaling
SHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 2→39 Å / SU B: 3.345 / SU ML: 0.095 / Cross valid method: THROUGHOUT / σ(F): 0.01 / ESU R Free: 0.142
Details: TLS REFINEMENT WAS PERFORMED ON 6 GROUPS. FOUR RESIDUES, THR A 65, THR A 67, SER A 99 AND THR A 103 HAVE BEEN MODELED WITH MULTIPLE ALTERNATE CONFORMATIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.2159 571 4.8 %RANDOM
Rwork0.2077 ---
obs0.20809 11375 99.3 %-
Refinement stepCycle: LAST / Resolution: 2→39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms942 0 7 180 1129
Refinement
*PLUS
Highest resolution: 2.1 Å / Lowest resolution: 32 Å / Rfactor obs: 0.2 / Rfactor Rfree: 0.216 / Rfactor Rwork: 0.2
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.009
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg1.55

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