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- PDB-5byw: Crystal structure of engineered trifunctional CtCEL5E -

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Basic information

Entry
Database: PDB / ID: 5byw
TitleCrystal structure of engineered trifunctional CtCEL5E
ComponentsEndoglucanase H
KeywordsHYDROLASE / Ctcel5E / cellulose
Function / homology
Function and homology information


cellulase / cellulase activity / beta-glucosidase activity / cellulose catabolic process / cell surface / extracellular region
Similarity search - Function
Carbohydrate binding module family 11 / Carbohydrate binding domain (family 11) / Glycosyl hydrolase family 26 / Glycosyl hydrolase family 26 domain / Glycosyl hydrolases family 26 (GH26) domain profile. / : / Clostridium cellulosome enzymes repeated domain signature. / Glycoside hydrolase, family 5, conserved site / Glycosyl hydrolases family 5 signature. / Dockerin domain ...Carbohydrate binding module family 11 / Carbohydrate binding domain (family 11) / Glycosyl hydrolase family 26 / Glycosyl hydrolase family 26 domain / Glycosyl hydrolases family 26 (GH26) domain profile. / : / Clostridium cellulosome enzymes repeated domain signature. / Glycoside hydrolase, family 5, conserved site / Glycosyl hydrolases family 5 signature. / Dockerin domain / Dockerin domain profile. / Dockerin type I domain / Dockerin type I repeat / Dockerin domain superfamily / Glycoside hydrolase, family 5 / Cellulase (glycosyl hydrolase family 5) / Galactose-binding-like domain superfamily / EF-hand calcium-binding domain. / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Biological speciesClostridium thermocellum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
Model detailsbiofunctional cellulase/xylanase
AuthorsLin, W.L. / Liang, P.H. / Ho, M.C.
CitationJournal: to be published
Title: Crystal structure of engineered trifunctional CtCel5E
Authors: Lin, W.L. / Liang, P.H. / Ho, M.C.
History
DepositionJun 11, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 15, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / pdbx_prerelease_seq / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Endoglucanase H
B: Endoglucanase H
C: Endoglucanase H
D: Endoglucanase H
E: Endoglucanase H


Theoretical massNumber of molelcules
Total (without water)236,8635
Polymers236,8635
Non-polymers00
Water3,171176
1
A: Endoglucanase H


Theoretical massNumber of molelcules
Total (without water)47,3731
Polymers47,3731
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Endoglucanase H


Theoretical massNumber of molelcules
Total (without water)47,3731
Polymers47,3731
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Endoglucanase H


Theoretical massNumber of molelcules
Total (without water)47,3731
Polymers47,3731
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Endoglucanase H


Theoretical massNumber of molelcules
Total (without water)47,3731
Polymers47,3731
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Endoglucanase H


Theoretical massNumber of molelcules
Total (without water)47,3731
Polymers47,3731
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)222.325, 222.325, 207.895
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number180
Space group name H-MP6222

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Components

#1: Protein
Endoglucanase H / Cellulase H / Endo-1 / 4-beta-glucanase H / EgH


Mass: 47372.660 Da / Num. of mol.: 5 / Fragment: UNP residues 290-654
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium thermocellum (strain ATCC 27405 / DSM 1237 / NBRC 103400 / NCIMB 10682 / NRRL B-4536 / VPI 7372) (bacteria)
Strain: ATCC 27405 / DSM 1237 / NBRC 103400 / NCIMB 10682 / NRRL B-4536 / VPI 7372
Gene: celH, Cthe_1472 / Plasmid: pHTPP13 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P16218, cellulase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 176 / 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: 3.13 Å3/Da / Density % sol: 60.71 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.6 / Details: 50mM sodium acetate, 8% PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Type: OTHER / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 4, 2014
Diffraction measurementDetails: 0.20 degrees, 6.2 sec, detector distance 350.00 mm / Method: \w scans
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionAv R equivalents: 0.111 / Number: 1371705
ReflectionResolution: 2.6→20 Å / Num. obs: 92695 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 14.8 % / Rmerge(I) obs: 0.111 / Rpim(I) all: 0.029 / Rrim(I) all: 0.115 / Rsym value: 0.111 / Χ2: 1.039 / Net I/av σ(I): 24.531 / Net I/σ(I): 9.8 / Num. measured all: 1371705
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 14.9 % / Rmerge(I) obs: 0.826 / Mean I/σ(I) obs: 3.952 / Rsym value: 0.826 / % possible all: 100
Cell measurementReflection used: 1371705

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Processing

Software
NameVersionClassification
REFMAC5.8.0123refinement
HKL-2000data collection
HKL-2000data scaling
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→20 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.91 / Cross valid method: THROUGHOUT / ESU R: 0.344 / ESU R Free: 0.269 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26048 4551 4.9 %RANDOM
Rwork0.20881 ---
obs0.21133 88143 99.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 49.732 Å2
Baniso -1Baniso -2Baniso -3
1--1.06 Å2-0.53 Å2-0 Å2
2---1.06 Å2-0 Å2
3---3.43 Å2
Refinement stepCycle: LAST / Resolution: 2.6→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13220 0 0 176 13396
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0213598
X-RAY DIFFRACTIONr_bond_other_d00.0212231
X-RAY DIFFRACTIONr_angle_refined_deg1.5191.91318443
X-RAY DIFFRACTIONr_angle_other_deg3.724328057
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.70151591
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.04223.923752
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.363152211
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.7361595
X-RAY DIFFRACTIONr_chiral_restr0.0810.21876
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0215574
X-RAY DIFFRACTIONr_gen_planes_other0.0070.023483
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_it2.9084.8586379
X-RAY DIFFRACTIONr_mcbond_other2.9084.8576378
X-RAY DIFFRACTIONr_mcangle_it4.4197.2777965
X-RAY DIFFRACTIONr_mcangle_other4.4197.2787966
X-RAY DIFFRACTIONr_scbond_it2.8925.087218
X-RAY DIFFRACTIONr_scbond_other2.8915.0817219
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.5587.52310478
X-RAY DIFFRACTIONr_long_range_B_refined6.42639.23216303
X-RAY DIFFRACTIONr_long_range_B_other6.42539.23916289
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.599→2.666 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.384 316 -
Rwork0.345 6438 -
obs--99.7 %

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