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- PDB-1wb6: S954A mutant of the feruloyl esterase module from clostridium the... -

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Basic information

Entry
Database: PDB / ID: 1wb6
TitleS954A mutant of the feruloyl esterase module from clostridium thermocellum complexed with vanillate
ComponentsENDO-1,4-BETA-XYLANASE Y
KeywordsHYDROLASE / ESTERASE FAMILY 1 / FERULIC ACID / GLYCOSIDASE / XYLAN DEGRADATION
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-like domain superfamily / Alpha/Beta hydrolase fold, catalytic domain / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / Alpha/Beta hydrolase fold / Glycoside hydrolase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / : / METHYL VANILLATE / Endo-1,4-beta-xylanase Y
Similarity search - Component
Biological speciesCLOSTRIDIUM THERMOCELLUM (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsTarbouriech, N. / Prates, J.A. / Fontes, C. / Davies, G.J.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2005
Title: Molecular Determinants of Substrate Specificity in the Feruloyl Esterase Module of Xylanase 10B from Clostridium Thermocellum
Authors: Tarbouriech, N. / Prates, J.A. / Fontes, C. / Davies, G.J.
History
DepositionOct 30, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 24, 2006Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 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_asym_id / _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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_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_conn.ptnr2_symmetry / _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)70,87233
Polymers67,4972
Non-polymers3,37531
Water12,358686
1
A: ENDO-1,4-BETA-XYLANASE Y
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,39016
Polymers33,7491
Non-polymers1,64215
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)35,48217
Polymers33,7491
Non-polymers1,73416
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)64.994, 108.462, 113.026
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein ENDO-1,4-BETA-XYLANASE Y / XYLANASE Y / XYLY / 1 / 4-BETA-D-XYLAN XYLANOHYDROLASE Y / XYLANASE XYN10B


Mass: 33748.539 Da / Num. of mol.: 2 / Fragment: FERULOYL ESTERASE DOMAIN, RESIDUES 792-1077 / 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(DE3) / References: UniProt: P51584, endo-1,4-beta-xylanase

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Non-polymers , 5 types, 717 molecules

#2: Chemical ChemComp-VXX / METHYL VANILLATE


Mass: 182.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H10O4
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: Cd
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 686 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsENGINEERED MUTATION IN CHAIN A, SER 954 TO ALA ENGINEERED MUTATION IN CHAIN B, SER 954 TO ALA ...ENGINEERED MUTATION IN CHAIN A, SER 954 TO ALA ENGINEERED MUTATION IN CHAIN B, SER 954 TO ALA CATALYTIC ACTIVITY: ENDOHYDROLYSIS OF 1,4-BETA-D-XYLOSIDIC LINKAGES IN XYLANS.
Sequence detailsONLY THE FERULOYL ESTERASE DOMAIN WAS SUBCLONED. S954A MUTANT

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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: 2.95 Å3/Da / Density % sol: 58 %
Crystal growpH: 7.5
Details: 1M NA ACETATE 100MM HEPES PH 7.5, 50MM CD ACETATE, 5% GLYCEROL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.934
DetectorType: ADSC CCD / Detector: CCD / Date: Oct 12, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 1.4→80 Å / Num. obs: 157680 / % possible obs: 99.3 % / Observed criterion σ(I): 2 / Redundancy: 4.4 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 26.3
Reflection shellResolution: 1.4→1.42 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 3.1 / % possible all: 94.7

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1GKL

1gkl


Resolution: 1.4→20 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.974 / SU B: 0.53 / SU ML: 0.021 / Cross valid method: THROUGHOUT / ESU R: 0.04 / ESU R Free: 0.039 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.14 7757 5 %RANDOM
Rwork0.117 ---
obs0.118 147390 98.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 12.18 Å2
Baniso -1Baniso -2Baniso -3
1-0.13 Å20 Å20 Å2
2---0.3 Å20 Å2
3---0.17 Å2
Refinement stepCycle: LAST / Resolution: 1.4→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4570 0 96 686 5352
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0214968
X-RAY DIFFRACTIONr_bond_other_d0.0920.024097
X-RAY DIFFRACTIONr_angle_refined_deg1.6831.9256753
X-RAY DIFFRACTIONr_angle_other_deg2.62239602
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9845586
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1250.2657
X-RAY DIFFRACTIONr_gen_planes_refined0.040.025645
X-RAY DIFFRACTIONr_gen_planes_other0.0710.021111
X-RAY DIFFRACTIONr_nbd_refined0.2350.2994
X-RAY DIFFRACTIONr_nbd_other0.2580.24995
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0930.22519
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1460.2411
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2380.214
X-RAY DIFFRACTIONr_symmetry_vdw_other0.30.229
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1560.218
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.6561.52885
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.34924663
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.10232081
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.3624.52087
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: 1.4→1.44 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.213 516
Rwork0.169 9913

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