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- PDB-2wo4: 3b' carbohydrate-binding module from the Cel9V glycoside hydrolas... -

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Basic information

Entry
Database: PDB / ID: 2wo4
Title3b' carbohydrate-binding module from the Cel9V glycoside hydrolase from Clostridium thermocellum, in-house data
ComponentsGLYCOSIDE HYDROLASE, FAMILY 9
KeywordsHYDROLASE / CELLULOSE DEGRADATION / GLYCOSIDE HYDROLASE
Function / homology
Function and homology information


cellulose binding / polysaccharide catabolic process / hydrolase activity, hydrolyzing O-glycosyl compounds / metal ion binding
Similarity search - Function
Endoglucanase-like / Cellulose binding domain / Carbohydrate-binding module 3 / Cellulose binding domain / CBM3 (carbohydrate binding type-3) domain profile. / Carbohydrate-binding module 3 superfamily / Glycoside hydrolase family 9 / Glycosyl hydrolase family 9 / Clostridium cellulosome enzymes repeated domain signature. / Dockerin domain ...Endoglucanase-like / Cellulose binding domain / Carbohydrate-binding module 3 / Cellulose binding domain / CBM3 (carbohydrate binding type-3) domain profile. / Carbohydrate-binding module 3 superfamily / Glycoside hydrolase family 9 / Glycosyl hydrolase family 9 / 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 / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Glycoside hydrolase family 9
Similarity search - Component
Biological speciesCLOSTRIDIUM THERMOCELLUM (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsPetkun, S. / Jindou, S. / Shimon, L.J.W. / Bayer, E.A. / Lamed, R. / Frolow, F.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2010
Title: Structure of a Family 3B' Carbohydrate-Binding Module from the Cel9V Glycoside Hydrolase from Clostridium Thermocellum: Structural Diversity and Implications for Carbohydrate Binding
Authors: Petkun, S. / Jindou, S. / Shimon, L.J.W. / Bayer, E.A. / Lamed, R. / Frolow, F.
#1: Journal: Fems Microbiol.Lett. / Year: 2006
Title: Novel Architecture of Family-9 Glycoside Hydrolases Identified in Cellulosomal Enzymes of Acetivibrio Cellulolyticus and Clostridium Thermocellum.
Authors: Jindou, S. / Xu, Q. / Kenig, R. / Shulman, M. / Shoham, Y. / Bayer, E.A. / Lamed, R.
History
DepositionJul 21, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 29, 2009Provider: repository / Type: Initial release
Revision 1.1Apr 17, 2013Group: Database references / Derived calculations ...Database references / Derived calculations / Non-polymer description / Other / Refinement description / Source and taxonomy / Version format compliance
Revision 1.2Dec 20, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GLYCOSIDE HYDROLASE, FAMILY 9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,8214
Polymers18,6491
Non-polymers1723
Water3,783210
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)73.897, 73.897, 85.755
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein GLYCOSIDE HYDROLASE, FAMILY 9 / CEL9V GLYCOSIDE HYDROLASE


Mass: 18649.406 Da / Num. of mol.: 1 / Fragment: CARBOHYDRATE-BINDING MODULE3B', RESIDUES 731-888
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CLOSTRIDIUM THERMOCELLUM (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A3DJ30
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 210 / 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: 3.41 Å3/Da / Density % sol: 63.9 % / Description: NONE
Crystal growpH: 5 / Details: 1.8 M AMMONIUM SULFATE, 0.1 M CITRIC ACID PH 5.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS-IV / Detector: IMAGE PLATE / Date: May 5, 2004 / Details: OSMIC CONFOCAL MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.79→30 Å / Num. obs: 23006 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 6.5 % / Biso Wilson estimate: 22.8 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 32.2
Reflection shellResolution: 1.79→1.85 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.76 / Mean I/σ(I) obs: 32.2 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.5.0102refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1NBC

1nbc


Resolution: 1.85→55.98 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.962 / SU B: 2.206 / SU ML: 0.066 / Cross valid method: THROUGHOUT / ESU R: 0.093 / ESU R Free: 0.1 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.U VALUES REFINED INDIVIDUALLY. DISORDERED REGIONS WERE MODELED STEREOCHEMICALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.19138 1063 5.1 %RANDOM
Rwork0.1482 ---
obs0.15037 19775 99.55 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 26.213 Å2
Baniso -1Baniso -2Baniso -3
1-0.61 Å20 Å20 Å2
2--0.61 Å20 Å2
3----1.23 Å2
Refinement stepCycle: LAST / Resolution: 1.85→55.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1210 0 7 210 1427
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0221340
X-RAY DIFFRACTIONr_bond_other_d0.0030.02873
X-RAY DIFFRACTIONr_angle_refined_deg1.9781.9461830
X-RAY DIFFRACTIONr_angle_other_deg1.22432153
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6455179
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.64325.80662
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.92915222
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.502155
X-RAY DIFFRACTIONr_chiral_restr0.130.2201
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021571
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02265
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_it3.1183854
X-RAY DIFFRACTIONr_mcbond_other0.9043350
X-RAY DIFFRACTIONr_mcangle_it5.15651393
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it6.667486
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it10.47810437
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: 1.849→1.897 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.324 69 -
Rwork0.267 1357 -
obs--94.19 %

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