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- PDB-3bwz: Crystal structure of the type II cohesin module from the cellulos... -

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Basic information

Entry
Database: PDB / ID: 3bwz
TitleCrystal structure of the type II cohesin module from the cellulosome of Acetivibrio cellulolyticus with an extended linker conformation
ComponentsCellulosomal scaffoldin adaptor protein B
KeywordsSTRUCTURAL PROTEIN / COHESINS II / CELLULOSOME
Function / homology
Function and homology information


polysaccharide catabolic process / hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate binding / extracellular region / metal ion binding
Similarity search - Function
: / Immunoglobulin-like - #680 / Cellulosome anchoring protein, cohesin domain / Cohesin domain / Dockerin domain / Dockerin domain profile. / Dockerin type I domain / Dockerin type I repeat / Dockerin domain superfamily / CBM2/CBM3, carbohydrate-binding domain superfamily ...: / Immunoglobulin-like - #680 / Cellulosome anchoring protein, cohesin domain / Cohesin domain / Dockerin domain / Dockerin domain profile. / Dockerin type I domain / Dockerin type I repeat / Dockerin domain superfamily / CBM2/CBM3, carbohydrate-binding domain superfamily / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
NITRATE ION / Cellulosomal scaffoldin adaptor protein B
Similarity search - Component
Biological speciesAcetivibrio cellulolyticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å
AuthorsNoach, I. / Lamed, R. / Shimon, L.J.W. / Bayer, E. / Frolow, F.
Citation
Journal: J.Mol.Biol. / Year: 2009
Title: Intermodular linker flexibility revealed from crystal structures of adjacent cellulosomal cohesins of Acetivibrio cellulolyticus.
Authors: Noach, I. / Frolow, F. / Alber, O. / Lamed, R. / Shimon, L.J. / Bayer, E.A.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2003
Title: Preliminary x-ray characterisation and phasing of a type II cohesin domain from the cellulosome of Acetivibrio cellulolyticus
Authors: Noach, I. / Lamed, R. / Xu, Q. / Rosenheck, S. / Shimon, L.J.W. / Bayer, E. / Frolow, F.
History
DepositionJan 10, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 13, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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

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Assembly

Deposited unit
A: Cellulosomal scaffoldin adaptor protein B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,8216
Polymers19,5911
Non-polymers2305
Water6,503361
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)37.455, 55.780, 87.912
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Cellulosomal scaffoldin adaptor protein B


Mass: 19590.951 Da / Num. of mol.: 1 / Fragment: COHESIN II DOMAIN FROM CELLULOSOME ASSEMBLY
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acetivibrio cellulolyticus (bacteria) / Gene: scaB / Plasmid: PET28A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q7WYN3
#2: Chemical ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NO3
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 361 / 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: 2.34 Å3/Da / Density % sol: 47.52 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 2.0 M ammonium sulfate and 0.1 M sodium acetate trihydrate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Dec 14, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 1.2→47.09 Å / Num. all: 53407 / Num. obs: 53407 / % possible obs: 95.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4 % / Biso Wilson estimate: 10.1 Å2 / Rmerge(I) obs: 0.046 / Rsym value: 0.046 / Net I/σ(I): 13
Reflection shellResolution: 1.2→1.22 Å / Redundancy: 4 % / Rmerge(I) obs: 0.17 / Mean I/σ(I) obs: 4 / Num. unique all: 2848 / Rsym value: 0.17 / % possible all: 99.1

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC5.2refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ZV9

1zv9


Resolution: 1.2→47.09 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.968 / SU B: 0.859 / SU ML: 0.018 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.033 / ESU R Free: 0.034 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.15209 2802 5 %RANDOM
Rwork0.12201 ---
all0.12352 0 --
obs0.12352 53047 95.61 %-
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: 9.558 Å2
Baniso -1Baniso -2Baniso -3
1--0.74 Å20 Å20 Å2
2--0.16 Å20 Å2
3---0.58 Å2
Refinement stepCycle: LAST / Resolution: 1.2→47.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1367 0 11 361 1739
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0221405
X-RAY DIFFRACTIONr_bond_other_d0.0030.02915
X-RAY DIFFRACTIONr_angle_refined_deg1.591.9661921
X-RAY DIFFRACTIONr_angle_other_deg2.75932304
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9165194
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.53126.72755
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.82215259
X-RAY DIFFRACTIONr_dihedral_angle_4_deg4.216153
X-RAY DIFFRACTIONr_chiral_restr0.0990.2234
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021564
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02246
X-RAY DIFFRACTIONr_nbd_refined0.2180.2229
X-RAY DIFFRACTIONr_nbd_other0.1880.21000
X-RAY DIFFRACTIONr_nbtor_refined0.170.2714
X-RAY DIFFRACTIONr_nbtor_other0.0920.2781
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1770.2279
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2930.219
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2490.261
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2330.245
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.48231167
X-RAY DIFFRACTIONr_mcbond_other1.3233363
X-RAY DIFFRACTIONr_mcangle_it2.94351484
X-RAY DIFFRACTIONr_scbond_it3.6697571
X-RAY DIFFRACTIONr_scangle_it4.94910426
X-RAY DIFFRACTIONr_rigid_bond_restr1.85632782
X-RAY DIFFRACTIONr_sphericity_free6.4313364
X-RAY DIFFRACTIONr_sphericity_bonded3.64932290
LS refinement shellResolution: 1.2→1.231 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.158 201 -
Rwork0.129 3842 -
obs--95.78 %

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