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- PDB-2c4x: Structural basis for the promiscuous specificity of the carbohydr... -

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Basic information

Entry
Database: PDB / ID: 2c4x
TitleStructural basis for the promiscuous specificity of the carbohydrate- binding modules from the beta-sandwich super family
ComponentsENDOGLUCANASE
KeywordsHYDROLASE / CELLULASE CTCEL9D-CEL44A / PKD DOMAIN / CBM44 / CARBOHYDRATE BINDING MODULE / BETA-SANDWICH PROTEINS / CELLULOSOME / SEMET DERIVATIVE
Function / homology
Function and homology information


cellulase activity / cellulose catabolic process / metal ion binding
Similarity search - Function
: / Carbohydrate binding domain 30 / Glycoside hydrolase, family 44 / Glycoside hydrolase family 44 / Cellulase N-terminal ig-like domain / Cellulase, Ig-like domain / PKD domain / Glycoside hydrolase family 9 / Glycosyl hydrolase family 9 / Polycystic kidney disease (PKD) domain profile. ...: / Carbohydrate binding domain 30 / Glycoside hydrolase, family 44 / Glycoside hydrolase family 44 / Cellulase N-terminal ig-like domain / Cellulase, Ig-like domain / PKD domain / Glycoside hydrolase family 9 / Glycosyl hydrolase family 9 / Polycystic kidney disease (PKD) domain profile. / PKD domain / PKD domain superfamily / PKD/Chitinase domain / Repeats in polycystic kidney disease 1 (PKD1) and other proteins / Dockerin domain / Dockerin domain profile. / Dockerin type I domain / Dockerin type I repeat / Dockerin domain superfamily / Six-hairpin glycosidase-like superfamily / Six-hairpin glycosidase superfamily / Galactose-binding domain-like / Glycosyl hydrolase, all-beta / Galactose-binding-like domain superfamily / Immunoglobulin E-set / Glycoside hydrolase superfamily / Jelly Rolls / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesCLOSTRIDIUM THERMOCELLUM (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 2 Å
AuthorsNajmudin, S. / Guerreiro, C.I.P.D. / Carvalho, A.L. / Bolam, D.N. / Prates, J.A.M. / Correia, M.A.S. / Alves, V.D. / Ferreira, L.M.A. / Romao, M.J. / Gilbert, H.J. / Fontes, C.M.G.A.
Citation
Journal: J.Biol.Chem. / Year: 2006
Title: Xyloglucan is Recognized by Carbohydrate-Binding Modules that Interact with Beta-Glucan Chains.
Authors: Najmudin, S. / Guerreiro, C.I.P.D. / Carvalho, A.L. / Prates, J.A.M. / Correia, M.A.S. / Alves, V.D. / Ferreira, L.M.A. / Romao, M.J. / Gilbert, H.J. / Bolam, D.N. / Fontes, C.M.G.A.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2005
Title: Overexpression, Purification and Crystallization of the Two C-Terminal Domains of the Bifunctional Cellulase Ctcel9D-Cel44A from Clostridium Thermocellum.
Authors: Najmudin, S. / Guerreiro, C.I.P.D. / Ferreira, L.M.A. / Romao, M.J. / Fontes, C.M.G.A. / Prates, J.A.M.
History
DepositionOct 25, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 27, 2005Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
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: ENDOGLUCANASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,1396
Polymers28,8731
Non-polymers2665
Water6,864381
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)86.899, 86.899, 108.242
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein ENDOGLUCANASE / CTCEL9D-CEL44A


Mass: 28872.941 Da / Num. of mol.: 1
Fragment: C-TERMINAL PKD AND CBM44 DOMAINS, RESIDUES 1353-1601
Mutation: YES
Source method: isolated from a genetically manipulated source
Details: CONTAINS 2 CALCIUM IONS / Source: (gene. exp.) CLOSTRIDIUM THERMOCELLUM (bacteria) / Strain: YS / Plasmid: PET21A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): B834 (DE3) / References: UniProt: P71140
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 381 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, ALA 1394 TO VAL
Sequence detailsSEQUENCE START IN FULL PROTEIN CORRESPONDS TO RESIDUE NUMBER 1353 AT VAL.

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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: 3.6 Å3/Da / Density % sol: 66 %
Crystal growpH: 4.5 / Details: 0.1M NA ACETATE,PH 4.5, 0.2M CACL2, 22.5% ETHANOL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.94645
DetectorType: ADSC CCD / Detector: CCD / Date: May 1, 2005
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.94645 Å / Relative weight: 1
ReflectionResolution: 2→67.7 Å / Num. obs: 28686 / % possible obs: 99.9 % / Observed criterion σ(I): 1.9 / Redundancy: 7.5 % / Biso Wilson estimate: 39.1 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 21.8
Reflection shellResolution: 2→2.11 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.93 / Mean I/σ(I) obs: 1.9 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
SCALAdata scaling
SHELXDphasing
RefinementMethod to determine structure: SIRAS / Resolution: 2→67.73 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.955 / SU B: 6.688 / SU ML: 0.097 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.131 / ESU R Free: 0.128 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE FIRST 4 RESIDUES MASV AND THE C- TERMINAL HIS TAG (X6) ARE DISORDERED AND NOT INCLUDED.
RfactorNum. reflection% reflectionSelection details
Rfree0.215 1427 5 %RANDOM
Rwork0.179 ---
obs0.181 27200 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 43.53 Å2
Baniso -1Baniso -2Baniso -3
1-0.63 Å20 Å20 Å2
2--0.63 Å20 Å2
3----1.26 Å2
Refinement stepCycle: LAST / Resolution: 2→67.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1936 0 14 381 2331
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0221998
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2091.9332732
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.485249
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.62426.04786
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.19515299
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.259152
X-RAY DIFFRACTIONr_chiral_restr0.0810.2308
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021523
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1930.2874
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3040.21344
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1490.2263
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1790.246
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1550.233
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6061.51272
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.87122030
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.323858
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.0124.5702
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
Rfree0.328 97
Rwork0.273 1979
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)
13.283-1.50842.10322.0485-1.38934.0153-0.00380.0526-0.01160.10480.13010.0732-0.1670.0969-0.1263-0.1011-0.02850.0554-0.04810.0001-0.10596.829343.78359.9529
22.2607-0.85350.4093.17120.84742.5876-0.1416-0.39240.2894-0.11150.0181-0.0187-0.2831-0.14520.1235-0.10960.0319-0.0289-0.0517-0.0858-0.093439.765720.40119.809
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 93
2X-RAY DIFFRACTION2A94 - 251

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