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- PDB-2c71: The structure of a family 4 acetyl xylan esterase from Clostridiu... -

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Basic information

Entry
Database: PDB / ID: 2c71
TitleThe structure of a family 4 acetyl xylan esterase from Clostridium thermocellum in complex with a magnesium ion.
ComponentsGLYCOSIDE HYDROLASE, FAMILY 11\:CLOSTRIDIUM CELLULOSOME ENZYME, DOCKERIN TYPE I\:POLYSACCHARIDE
KeywordsHYDROLASE / ACETYL-XYLAN / ESTERASES / METAL-ION
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
Glycoside hydrolase/deacetylase / NodB homology domain profile. / NodB homology domain / Polysaccharide deacetylase / 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 ...Glycoside hydrolase/deacetylase / NodB homology domain profile. / NodB homology domain / Polysaccharide deacetylase / 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 / 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-like domain superfamily / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / Concanavalin A-like lectin/glucanase domain superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
endo-1,4-beta-xylanase / :
Similarity search - Component
Biological speciesCLOSTRIDIUM THERMOCELLUM (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.05 Å
AuthorsTaylor, E.J. / Turkenburg, P.J. / Vincent, F. / Brzozowski, A.M. / Gloster, T.M. / Dupont, C. / Shareck, F. / Centeno, M.S.J. / Prates, J.A.M. / Ferreira, L.M.A. ...Taylor, E.J. / Turkenburg, P.J. / Vincent, F. / Brzozowski, A.M. / Gloster, T.M. / Dupont, C. / Shareck, F. / Centeno, M.S.J. / Prates, J.A.M. / Ferreira, L.M.A. / Fontes, C.M.G.A. / Biely, P. / Davies, G.J.
CitationJournal: J.Biol.Chem. / Year: 2006
Title: Structure and Activity of Two Metal-Ion Dependent Acetyl Xylan Esterases Involved in Plant Cell-Wall Degradation Reveals a Close Similarity to Peptidoglycan Deacetylases.
Authors: Taylor, E.J. / Gloster, T.M. / Turkenburg, P.J. / Vincent, F. / Brzozowski, A.M. / Dupont, C. / Shareck, F. / Centeno, M.S.J. / Prates, J.A.M. / Ferreira, L.M.A. / Fontes, C.M.G.A. / Biely, P. / Davies, G.J.
History
DepositionNov 17, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 23, 2006Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 28, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4May 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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_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
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GLYCOSIDE HYDROLASE, FAMILY 11\:CLOSTRIDIUM CELLULOSOME ENZYME, DOCKERIN TYPE I\:POLYSACCHARIDE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,9552
Polymers23,9301
Non-polymers241
Water6,774376
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)106.064, 106.064, 35.466
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-2005-

HOH

21A-2064-

HOH

31A-2123-

HOH

41A-2268-

HOH

51A-2274-

HOH

61A-2291-

HOH

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Components

#1: Protein GLYCOSIDE HYDROLASE, FAMILY 11\:CLOSTRIDIUM CELLULOSOME ENZYME, DOCKERIN TYPE I\:POLYSACCHARIDE / ACETYL XYLAN ESTERASE


Mass: 23930.213 Da / Num. of mol.: 1 / Fragment: RESIDUES 480-683
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CLOSTRIDIUM THERMOCELLUM (bacteria) / Strain: F1 / YS / Plasmid: PET 21A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21
References: UniProt: Q4CFF1, UniProt: O87119*PLUS, acetylxylan esterase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 376 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE N-TERMINAL RESIDUES PAN AND C-TERMINAL RESIDUES LEHHHHHH ARE DERIVED FROM THE CLONING VECTOR PET 21A

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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: 1.52 Å3/Da / Density % sol: 18.91 %
Crystal growDetails: 0.2M MGCL 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9756
DetectorType: ADSC CCD / Detector: CCD / Date: Oct 30, 2004 / Details: TOROIDAL MIRROR
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9756 Å / Relative weight: 1
ReflectionResolution: 1.05→30 Å / Num. obs: 89153 / % possible obs: 20.8 % / Observed criterion σ(I): 2 / Redundancy: 3.8 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 20.8
Reflection shellResolution: 1.05→1.07 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 3.5 / % possible all: 91.3

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
SHELXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.05→28.41 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.976 / SU B: 0.615 / SU ML: 0.015 / Cross valid method: THROUGHOUT / ESU R: 0.024 / ESU R Free: 0.025 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.142 4437 5 %RANDOM
Rwork0.124 ---
obs0.125 84596 94.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 7.43 Å2
Baniso -1Baniso -2Baniso -3
1-0.08 Å20 Å20 Å2
2--0.08 Å20 Å2
3----0.16 Å2
Refinement stepCycle: LAST / Resolution: 1.05→28.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1587 0 1 376 1964
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0221815
X-RAY DIFFRACTIONr_bond_other_d0.0020.021235
X-RAY DIFFRACTIONr_angle_refined_deg1.9891.9652499
X-RAY DIFFRACTIONr_angle_other_deg2.37333034
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4485242
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.63923.62580
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.27115306
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.8071516
X-RAY DIFFRACTIONr_chiral_restr0.290.2289
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022072
X-RAY DIFFRACTIONr_gen_planes_other0.0060.02362
X-RAY DIFFRACTIONr_nbd_refined0.2820.2350
X-RAY DIFFRACTIONr_nbd_other0.2420.21304
X-RAY DIFFRACTIONr_nbtor_refined0.1770.2894
X-RAY DIFFRACTIONr_nbtor_other0.0920.2924
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2410.2224
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1090.28
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3130.232
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1520.254
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.5271.51464
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it4.51621890
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.4563759
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.334.5603
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: 1.05→1.08 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.187 328
Rwork0.166 5776

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