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Basic information

Entry
Database: PDB / ID: 4aem
TitleStructural and biochemical characterization of a novel Carbohydrate Binding Module of endoglucanase Cel5A from Eubacterium cellulosolvens
ComponentsENDOGLUCANASE CEL5A
KeywordsHYDROLASE / FAMILY 5 GLYCOSIDE HYDROLASE / CELLULOSOME
Function / homology
Function and homology information


organic substance metabolic process / hydrolase activity, hydrolyzing O-glycosyl compounds
Similarity search - Function
Jelly Rolls - #1070 / Carbohydrate binding module 65 domain 1 / Carbohydrate binding module 65 domain 1 / Glycoside hydrolase, family 5 / Cellulase (glycosyl hydrolase family 5) / Glycoside hydrolase superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesEUBACTERIUM CELLULOSOLVENS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsLuis, A.S. / Venditto, I. / Prates, J.A.M. / Ferreira, L.M.A. / Gilbert, H.J. / Fontes, C.M.G.A. / Najmudin, S.
Citation
Journal: J.Biol.Chem. / Year: 2013
Title: Understanding How Non-Catalytic Carbohydrate Binding Modules Can Display Specificity for Xyloglucan
Authors: Luis, A.S. / Venditto, I. / Prates, J.A.M. / Ferreira, L.M.A. / Temple, M.J. / Rogowski, A. / Basle, A. / Xue, J. / Knox, J.P. / Najmudin, S. / Fontes, C.M.G.A. / Gilbert, H.J.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2011
Title: Overproduction, Purification, Crystallization and Preliminary X-Ray Characterization of a Novel Carbohydrate-Binding Module of Endoglucanase Cel5A from Eubacterium Cellulosolvens.
Authors: Luis, A.S. / Alves, V.D. / Romao, M.J. / Prates, J.A.M. / Fontes, C.M.G.A. / Najmudin, S.
History
DepositionJan 11, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 23, 2013Provider: repository / Type: Initial release
Revision 1.1Jan 30, 2013Group: Database references
Revision 1.2Feb 27, 2013Group: Database references
Revision 1.3May 8, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval
Revision 1.4Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ENDOGLUCANASE CEL5A


Theoretical massNumber of molelcules
Total (without water)14,7991
Polymers14,7991
Non-polymers00
Water1,65792
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)79.320, 79.320, 44.440
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein ENDOGLUCANASE CEL5A


Mass: 14799.314 Da / Num. of mol.: 1 / Fragment: CARBOHYDRATE BINDING MODULE, RESIDUES 37-170
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) EUBACTERIUM CELLULOSOLVENS (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q3LHN3
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 92 / 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: 2.32 Å3/Da / Density % sol: 47 % / Description: NONE
Crystal growTemperature: 292 K / pH: 4.76
Details: 100 MG/ML PROTEIN WAS USED AT 292 K WITH 0.2 M AMMONIUM SULFATE, 0.1 M SODIUM ACETATE TRIHYDRATE PH 4.6, 30% W/V PEG 2K MME. 30% GLYCEROL WAS USED AS CRYOPROTECTANT

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9793
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 24, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.1→68.69 Å / Num. obs: 8165 / % possible obs: 83.6 % / Redundancy: 11.2 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 15.3
Reflection shellResolution: 2.1→2.21 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.8 / Mean I/σ(I) obs: 2.4 / % possible all: 53.4

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4AEK

4aek


Resolution: 2.1→68.69 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.931 / SU B: 10.403 / SU ML: 0.132 / Cross valid method: THROUGHOUT / ESU R: 0.223 / ESU R Free: 0.194 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT. PHENIX-1.7.2-869 WAS ALSO USED FOR REFINEMENT, TO GENERATE TLS GROUPS AND UPDATE WATERS. ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT. PHENIX-1.7.2-869 WAS ALSO USED FOR REFINEMENT, TO GENERATE TLS GROUPS AND UPDATE WATERS. RESIDUES A37-38 AND A165-170 ARE DISORDERERED. GLU 65, ILE 111, AND GLU 126 WERE GIVEN DUAL CONFORMATIONS. DISORDERED SIDE CHAINS WERE MODELED STEREOCHEMICALLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.22704 417 5.1 %RANDOM
Rwork0.17053 ---
obs0.17353 7748 84.37 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.376 Å2
Baniso -1Baniso -2Baniso -3
1--0.65 Å2-0.33 Å20 Å2
2---0.65 Å20 Å2
3---0.98 Å2
Refinement stepCycle: LAST / Resolution: 2.1→68.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms998 0 0 92 1090
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.021050
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.2131.941439
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7415131
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.03625.20848
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.5815160
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.226151
X-RAY DIFFRACTIONr_chiral_restr0.1450.2154
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.021818
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
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: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.281 22 -
Rwork0.28 318 -
obs--49.49 %
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)
14.5927-1.6352-3.55136.20971.7222.8454-0.19920.1123-0.08130.40910.2453-0.49880.3153-0.0775-0.04610.31290.0173-0.16910.16580.01320.134258.068714.5234.904
25.27651.8104-2.83352.4212-2.09312.4043-0.0029-0.1619-0.03710.23010.01420.0701-0.08250.0524-0.01130.12560.004100.1169-0.01780.015756.728526.17429.6716
31.36090.2428-0.27492.8605-0.26780.906-0.03610.1115-0.1176-0.1806-0.0216-0.08090.06310.05120.05770.0878-0.0091-0.00810.1367-0.02230.019153.933722.9325-2.0047
42.6021-0.0417-0.13142.47810.31791.8245-0.0832-0.02930.2566-0.06910.0953-0.0467-0.13380.0039-0.01210.0867-0.0147-0.00870.13690.0030.043547.598626.1345-1.2311
51.3795-0.06470.41551.390.37620.6141-0.04370.13370.0154-0.17580.0021-0.08460.08090.06710.04160.1104-0.00260.02560.1540.00070.017252.593623.86870.2826
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A39 - 52
2X-RAY DIFFRACTION2A53 - 71
3X-RAY DIFFRACTION3A72 - 99
4X-RAY DIFFRACTION4A100 - 127
5X-RAY DIFFRACTION5A128 - 164

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