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- PDB-3zqx: Carbohydrate-binding module CBM3b from the cellulosomal cellobioh... -

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Basic information

Entry
Database: PDB / ID: 3zqx
TitleCarbohydrate-binding module CBM3b from the cellulosomal cellobiohydrolase 9A from Clostridium thermocellum
ComponentsCELLULOSE 1,4-BETA-CELLOBIOSIDASE
KeywordsHYDROLASE / CELLULOSE BINDING PROTEIN
Function / homology
Function and homology information


Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds / cellulose binding / cellulase activity / cellulose catabolic process / metal ion binding
Similarity search - Function
Bacterial Ig domain / Endoglucanase-like / Cellulase N-terminal ig-like domain / Cellulase, Ig-like domain / Glycoside hydrolase family 9, His active site / Glycosyl hydrolases family 9 (GH9) active site signature 2. / Glycosyl hydrolases family 9, Asp/Glu active sites / Glycosyl hydrolases family 9 (GH9) active site signature 3. / Cellulose binding domain / Cellulose binding domain ...Bacterial Ig domain / Endoglucanase-like / Cellulase N-terminal ig-like domain / Cellulase, Ig-like domain / Glycoside hydrolase family 9, His active site / Glycosyl hydrolases family 9 (GH9) active site signature 2. / Glycosyl hydrolases family 9, Asp/Glu active sites / Glycosyl hydrolases family 9 (GH9) active site signature 3. / Cellulose binding domain / Cellulose binding domain / Carbohydrate-binding module 3 / Carbohydrate-binding module 3 superfamily / CBM3 (carbohydrate binding type-3) domain profile. / Glycoside hydrolase family 9 / Glycosyl hydrolase family 9 / Carbohydrate-binding, CenC-like / Carbohydrate binding domain / Clostridium cellulosome enzymes repeated domain signature. / Dockerin domain / Dockerin domain profile. / Dockerin type I domain / Dockerin type I repeat / Dockerin domain superfamily / CBM2/CBM3, carbohydrate-binding domain superfamily / Six-hairpin glycosidase-like superfamily / Six-hairpin glycosidase superfamily / Galactose-binding-like domain superfamily / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / Immunoglobulin E-set / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesCLOSTRIDIUM THERMOCELLUM (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.04 Å
AuthorsYaniv, O. / Petkun, S. / Shimon, L.J.W. / Bayer, E.A. / Lamed, R. / Frolow, F.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2012
Title: A Single Mutation Reforms the Binding Activity of an Adhesion-Deficient Family 3 Carbohydrate-Binding Module
Authors: Yaniv, O. / Petkun, S. / Shimon, L.J.W. / Bayer, E.A. / Lamed, R. / Frolow, F.
History
DepositionJun 12, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 25, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 27, 2012Group: Other
Revision 1.2Jul 11, 2012Group: Other
Revision 1.3May 1, 2024Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CELLULOSE 1,4-BETA-CELLOBIOSIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,7042
Polymers16,6631
Non-polymers401
Water4,306239
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)50.036, 50.036, 122.595
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-2008-

HOH

21A-2209-

HOH

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Components

#1: Protein CELLULOSE 1,4-BETA-CELLOBIOSIDASE


Mass: 16663.482 Da / Num. of mol.: 1
Fragment: FAMILY 3B CARBOHYDRATE BINDING MODULE, RESIDUES 1004-1148
Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CLOSTRIDIUM THERMOCELLUM (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): RIL
References: UniProt: Q59325, cellulose 1,4-beta-cellobiosidase (non-reducing end)
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 239 / 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: 2.05 Å3/Da / Density % sol: 40.17 % / Description: NONE
Crystal growpH: 7.5
Details: 30%(V/V) TERT-BUTANOL 0.1 M TRI-NA CITRATE DEHYDRATE, PH 5.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9395
DetectorType: ADSC CCD / Detector: CCD / Date: Feb 17, 2010 / Details: MIRRORS
RadiationMonochromator: SAGITALLY FOCUSED SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9395 Å / Relative weight: 1
ReflectionResolution: 1.04→50 Å / Num. obs: 75775 / % possible obs: 97.5 % / Observed criterion σ(I): 0 / Redundancy: 10.17 % / Biso Wilson estimate: 8.2 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 52.9
Reflection shellResolution: 1.04→1.06 Å / Mean I/σ(I) obs: 3.4 / % possible all: 95.4

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE: DEV_669)refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: WILD-TYPE MOLECULE OF SAME PROTEIN

Resolution: 1.04→46.33 Å / SU ML: 0.18 / σ(F): 1.34 / Phase error: 14.11 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.171 3733 5.1 %
Rwork0.167 --
obs0.167 73783 97.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 32.99 Å2 / ksol: 0.35 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.6438 Å20 Å20 Å2
2--1.6438 Å20 Å2
3----3.2875 Å2
Refinement stepCycle: LAST / Resolution: 1.04→46.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1179 0 1 239 1419
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061242
X-RAY DIFFRACTIONf_angle_d1.2511690
X-RAY DIFFRACTIONf_dihedral_angle_d14.794454
X-RAY DIFFRACTIONf_chiral_restr0.101174
X-RAY DIFFRACTIONf_plane_restr0.008223
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.04-1.07710.21563430.20916765X-RAY DIFFRACTION96
1.0771-1.12030.16783470.17346806X-RAY DIFFRACTION96
1.1203-1.17120.16333720.16076853X-RAY DIFFRACTION97
1.1712-1.2330.16593840.15716853X-RAY DIFFRACTION97
1.233-1.31030.1763880.15646938X-RAY DIFFRACTION98
1.3103-1.41140.15723830.15916989X-RAY DIFFRACTION98
1.4114-1.55350.16893570.15837079X-RAY DIFFRACTION99
1.5535-1.77830.15484070.15287128X-RAY DIFFRACTION99
1.7783-2.24040.16093750.15737188X-RAY DIFFRACTION99
2.2404-46.37210.18073770.17697451X-RAY DIFFRACTION97
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)
10.60940.0867-0.10712.16660.2660.7747-0.0690.07020.0251-0.13950.04010.1843-0.0201-0.0520.02870.0837-0.0043-0.01770.10280.00770.0976-30.01856.55345.3159
20.96930.50990.10120.7563-0.02640.6016-0.0057-0.0323-0.0266-0.025-0.0176-0.06020.00210.02780.02470.0703-0.0013-0.00110.0744-0.00110.0779-19.212311.118110.7157
30.74210.20520.12971.2934-0.07730.5513-0.03970.053-0.0116-0.10730.04-0.02390.01880.0024-0.00170.076-0.0061-0.00180.0716-0.00420.0617-21.38035.15586.5046
41.0389-0.2646-0.05611.0605-0.33541.4117-0.0177-0.1730.06210.1204-0.00210.0367-0.0628-0.0130.03150.0975-0.0039-0.0030.0631-0.00410.0975-23.339314.913415.4589
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 1:19)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 20:49)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 50:120)
4X-RAY DIFFRACTION4(CHAIN A AND RESID 121:144)

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