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Basic information

Entry
Database: PDB / ID: 2w9x
TitleThe active site of a carbohydrate esterase displays divergent catalytic and non-catalytic binding functions
ComponentsPUTATIVE ACETYL XYLAN ESTERASE
KeywordsHYDROLASE / CARBOHYDRATE ESTERASE FAMILY 2 / ACETYL XYLAN ESTERASE
Function / homology
Function and homology information


glucomannan catabolic process / acetylxylan esterase / acetylxylan esterase activity / Hydrolases; Acting on ester bonds; Carboxylic-ester hydrolases / hydrolase activity, acting on glycosyl bonds / xylan catabolic process / extracellular region
Similarity search - Function
Carbohydrate esterase 2, N-terminal / Carbohydrate esterase 2 N-terminal / CtCE2-like domain / : / SGNH hydrolase / SGNH hydrolase-type esterase domain / GDSL-like Lipase/Acylhydrolase family / SGNH hydrolase superfamily / Galactose-binding domain-like / Jelly Rolls ...Carbohydrate esterase 2, N-terminal / Carbohydrate esterase 2 N-terminal / CtCE2-like domain / : / SGNH hydrolase / SGNH hydrolase-type esterase domain / GDSL-like Lipase/Acylhydrolase family / SGNH hydrolase superfamily / Galactose-binding domain-like / Jelly Rolls / Sandwich / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Acetylxylan esterase / glucomannan deacetylase
Similarity search - Component
Biological speciesCELLVIBRIO JAPONICUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsMontanier, C. / Money, V.A. / Pires, V. / Flint, J.E. / Benedita, P.A. / Goyal, A. / Prates, J.A. / Izumi, A. / Stalbrand, H. / Morland, C. ...Montanier, C. / Money, V.A. / Pires, V. / Flint, J.E. / Benedita, P.A. / Goyal, A. / Prates, J.A. / Izumi, A. / Stalbrand, H. / Morland, C. / Cartmell, A. / Kolenova, K. / Topakas, E. / Dobson, E. / Bolam, D.N. / Davies, G.J. / Fontes, C.M. / Gilbert, H.J.
CitationJournal: Plos Biol. / Year: 2009
Title: The Active Site of a Carbohydrate Esterase Displays Divergent Catalytic and Noncatalytic Binding Functions.
Authors: Montanier, C. / Money, V.A. / Pires, V. / Flint, J.E. / Benedita, P.A. / Goyal, A. / Prates, J.A. / Izumi, A. / Stalbrand, H. / Morland, C. / Cartmell, A. / Kolenova, K. / Topakas, E. / ...Authors: Montanier, C. / Money, V.A. / Pires, V. / Flint, J.E. / Benedita, P.A. / Goyal, A. / Prates, J.A. / Izumi, A. / Stalbrand, H. / Morland, C. / Cartmell, A. / Kolenova, K. / Topakas, E. / Dodson, E.J. / Bolam, D.N. / Davies, G.J. / Fontes, C.M. / Gilbert, H.J.
History
DepositionJan 29, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 24, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 9, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / 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 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

Downloads & links

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Assembly

Deposited unit
A: PUTATIVE ACETYL XYLAN ESTERASE
B: PUTATIVE ACETYL XYLAN ESTERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,4579
Polymers81,8122
Non-polymers6457
Water7,530418
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1250 Å2
ΔGint-24.8 kcal/mol
Surface area33630 Å2
MethodPQS
Unit cell
Length a, b, c (Å)75.274, 75.274, 141.620
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.8324, 0.5539, -0.01636), (0.5538, -0.8326, -0.006154), (-0.01703, -0.003938, -0.9998))

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Components

#1: Protein PUTATIVE ACETYL XYLAN ESTERASE / AXE2A / CJCE2B


Mass: 40906.086 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CELLVIBRIO JAPONICUS (bacteria) / Plasmid: PET22B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: B3PDE5
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 418 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.57 Å3/Da / Density % sol: 51.68 % / Description: NONE
Crystal growpH: 8 / Details: 0.1 M IMIDAZOLE PH 8.0, 10% PEG 8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: ADSC CCD / Detector: CCD / Date: Apr 19, 2008 / Details: MIRRORS
RadiationMonochromator: DIAMOND (111), GE(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2→53.22 Å / Num. obs: 53120 / % possible obs: 100 % / Observed criterion σ(I): 0.03 / Redundancy: 5.7 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 15.6
Reflection shellResolution: 2→2.11 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.63 / Mean I/σ(I) obs: 3 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 2→50 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.936 / SU B: 7.62 / SU ML: 0.122 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.172 / ESU R Free: 0.156 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.231 2699 5.1 %RANDOM
Rwork0.191 ---
obs0.193 50355 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 40.34 Å2
Baniso -1Baniso -2Baniso -3
1--0.09 Å20 Å20 Å2
2---0.09 Å20 Å2
3---0.18 Å2
Refinement stepCycle: LAST / Resolution: 2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5097 0 42 418 5557
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0225239
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2751.9477108
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0215643
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.64824.502251
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.35415836
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.9441525
X-RAY DIFFRACTIONr_chiral_restr0.0870.2768
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.024019
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1970.22363
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3010.23506
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1450.2473
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2140.240
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.140.220
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5281.53294
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.8425152
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.41732228
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.1714.51952
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: 2→2.05 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.321 220 -
Rwork0.254 3704 -
obs--99.95 %
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)
11.80530.1639-0.66091.8389-0.59143.293-0.15690.00590.4521-0.2575-0.02940.6741-0.5229-0.6170.18630.15890.3954-0.25920.1739-0.19720.24037.92564.06-14.514
21.04360.32550.79893.57860.12992.05510.11490.0113-0.34130.1032-0.19760.30780.8827-0.25530.08270.3403-0.14260.1442-0.1059-0.12940.035627.371-0.76313.903
31.41140.05040.3331.689-0.04891.5355-0.0999-0.12390.2755-0.1755-0.15350.378-0.5869-0.45380.25330.06090.2777-0.15590.0302-0.1515-0.059820.11256.674-11.495
41.66760.1327-0.06331.8784-0.59591.9577-0.03880.1502-0.3768-0.0461-0.15170.10270.7001-0.06320.19050.0895-0.03670.1291-0.1544-0.0955-0.108932.5510.9111.013
51.3631-0.0730.31141.12020.17272.8382-0.1418-0.14920.0870.0155-0.12370.0771-0.4714-0.21370.2656-0.08580.1062-0.0734-0.1408-0.0606-0.199834.27346.949-5.462
60.83330.2365-0.36821.5418-0.42343.452-0.05960.1271-0.0642-0.0986-0.2163-0.0450.31360.14720.2759-0.15930.04540.059-0.129-0.0092-0.224640.08728.3064.687
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A6 - 95
2X-RAY DIFFRACTION2B6 - 95
3X-RAY DIFFRACTION3A96 - 240
4X-RAY DIFFRACTION4B96 - 240
5X-RAY DIFFRACTION5A241 - 340
6X-RAY DIFFRACTION6B241 - 340

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