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- PDB-2cc0: Family 4 carbohydrate esterase from Streptomyces lividans in comp... -

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Basic information

Entry
Database: PDB / ID: 2cc0
TitleFamily 4 carbohydrate esterase from Streptomyces lividans in complex with acetate
ComponentsACETYL-XYLAN ESTERASE
KeywordsHYDROLASE / CARBOHYDRATE ESTERASE
Function / homology
Function and homology information


hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds / polysaccharide binding / polysaccharide catabolic process / hydrolase activity, hydrolyzing O-glycosyl compounds / metal ion binding / membrane
Similarity search - Function
: / Glycoside hydrolase/deacetylase / NodB homology domain profile. / NodB homology domain / Polysaccharide deacetylase / Carbohydrate-binding type-2 domain / CBM2 (Carbohydrate-binding type-2) domain profile. / CBD_II / CBM2, carbohydrate-binding domain superfamily / Glycoside hydrolase/deacetylase, beta/alpha-barrel ...: / Glycoside hydrolase/deacetylase / NodB homology domain profile. / NodB homology domain / Polysaccharide deacetylase / Carbohydrate-binding type-2 domain / CBM2 (Carbohydrate-binding type-2) domain profile. / CBD_II / CBM2, carbohydrate-binding domain superfamily / Glycoside hydrolase/deacetylase, beta/alpha-barrel / CBM2/CBM3, carbohydrate-binding domain superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / Acetyl-xylan esterase
Similarity search - Component
Biological speciesSTREPTOMYCES LIVIDANS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsTaylor, E.J. / Gloster, T.M. / Turkenburg, J.P. / Vincent, F. / Brzozowski, A.M. / Dupont, C. / Shareck, F. / Centeno, M.S.J. / Prates, J.A.M. / Puchart, V. ...Taylor, E.J. / Gloster, T.M. / Turkenburg, J.P. / Vincent, F. / Brzozowski, A.M. / Dupont, C. / Shareck, F. / Centeno, M.S.J. / Prates, J.A.M. / Puchart, V. / 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, J.P. / Vincent, F. / Brzozowski, A.M. / Dupont, C. / Shareck, F. / Centeno, M.S.J. / Prates, J.A.M. / Puchart, V. / Ferreira, L.M.A. / Fontes, C.M. ...Authors: Taylor, E.J. / Gloster, T.M. / Turkenburg, J.P. / Vincent, F. / Brzozowski, A.M. / Dupont, C. / Shareck, F. / Centeno, M.S.J. / Prates, J.A.M. / Puchart, V. / Ferreira, L.M.A. / Fontes, C.M.G.A. / Biely, P. / Davies, G.J.
History
DepositionJan 10, 2006Deposition 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 1.3Dec 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_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
Revision 1.4Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
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: ACETYL-XYLAN ESTERASE
B: ACETYL-XYLAN ESTERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,4796
Polymers41,2302
Non-polymers2494
Water10,160564
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)95.538, 47.905, 89.842
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.99967, -0.00044, -0.02584), (0.00048, -1, -0.00142), (-0.02584, -0.00143, 0.99967)
Vector: 11.74161, -0.02038, 0.08038)

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Components

#1: Protein ACETYL-XYLAN ESTERASE / CARBOHYDRATE ESTERASE


Mass: 20614.910 Da / Num. of mol.: 2 / Fragment: RESIDUES 42-236
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) STREPTOMYCES LIVIDANS (bacteria) / Production host: STREPTOMYCES LIVIDANS (bacteria) / References: UniProt: Q54413, acetylxylan esterase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 564 / 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: 2.05 Å3/Da / Density % sol: 39.39 %
Crystal growpH: 4.5
Details: 7-13% PEG 4K, 0.2 M KBR, 0.1 M NAAC, PH 4.5. PROTEIN 20 MG/ML.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.979
DetectorType: ADSC CCD / Detector: CCD / Details: TOROIDAL MIRROR
RadiationMonochromator: SI (311) MONOCHROMATOR AND SI(111) MONOCHROMATOR
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.6→40 Å / Num. obs: 51014 / % possible obs: 98 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 17
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.26 / Mean I/σ(I) obs: 4 / % possible all: 91

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2C71

2c71


Resolution: 1.6→65.65 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.955 / SU B: 2.893 / SU ML: 0.047 / Cross valid method: THROUGHOUT / ESU R: 0.108 / ESU R Free: 0.082 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.188 2734 5.1 %RANDOM
Rwork0.15 ---
obs0.152 51014 98.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.32 Å2
Baniso -1Baniso -2Baniso -3
1--0.46 Å20 Å20 Å2
2--0.11 Å20 Å2
3---0.35 Å2
Refinement stepCycle: LAST / Resolution: 1.6→65.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2857 0 10 564 3431
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0213116
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4471.9394289
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg11.2555449
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.42224.429140
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.41415504
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.8091523
X-RAY DIFFRACTIONr_chiral_restr0.0990.2477
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022457
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1990.21586
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3030.22153
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1440.2376
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0120.21
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1840.237
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1540.242
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2031.52047
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.78523234
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.58131208
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.6824.51021
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr1.47133255
X-RAY DIFFRACTIONr_sphericity_free5.2193566
X-RAY DIFFRACTIONr_sphericity_bonded4.22333024
LS refinement shellResolution: 1.6→1.65 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.267 200 -
Rwork0.186 3460 -
obs--92.03 %

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