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- PDB-3fnk: Crystal structure of the second type II cohesin module from the c... -

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Basic information

Entry
Database: PDB / ID: 3fnk
TitleCrystal structure of the second type II cohesin module from the cellulosomal adaptor ScaA scaffoldin of Acetivibrio cellulolyticus
ComponentsCellulosomal scaffoldin adaptor protein B
KeywordsSTRUCTURAL PROTEIN / CohB / Dockerin-binding module / beta barrel / alpha helix / beta flaps
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 ...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
ACETATE ION / 1,4-BUTANEDIOL / 1,3-PROPANDIOL / Cellulosomal scaffoldin adaptor protein B
Similarity search - Component
Biological speciesAcetivibrio cellulolyticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.99 Å
AuthorsNoach, I. / Frolow, F. / Bayer, E.A.
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.W. / Bayer, E.A.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2008
Title: Crystallization and preliminary X-ray analysis of Acetivibrio cellulolyticus cellulosomal type II cohesin module: two versions having different linker lengths
Authors: Noach, I. / Alber, O. / Bayer, E.A. / Lamed, R. / Levy-Assaraf, M. / Shimon, L.J.W. / Frolow, F.
History
DepositionDec 25, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 23, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Nov 1, 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

Downloads & links

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Assembly

Deposited unit
A: Cellulosomal scaffoldin adaptor protein B
B: Cellulosomal scaffoldin adaptor protein B
C: Cellulosomal scaffoldin adaptor protein B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,53319
Polymers61,4823
Non-polymers1,05116
Water9,746541
1
A: Cellulosomal scaffoldin adaptor protein B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,6914
Polymers20,4941
Non-polymers1973
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Cellulosomal scaffoldin adaptor protein B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,0309
Polymers20,4941
Non-polymers5368
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Cellulosomal scaffoldin adaptor protein B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,8126
Polymers20,4941
Non-polymers3185
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)90.359, 68.645, 111.294
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 3 molecules ABC

#1: Protein Cellulosomal scaffoldin adaptor protein B


Mass: 20494.070 Da / Num. of mol.: 3 / Fragment: Cohesin module, UNP residues 190-368
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(DE3)pLysS / References: UniProt: Q7WYN3

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Non-polymers , 5 types, 557 molecules

#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical
ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-PDO / 1,3-PROPANDIOL / 1,3-Propanediol


Mass: 76.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O2
#5: Chemical ChemComp-BU1 / 1,4-BUTANEDIOL / 1,4-Butanediol


Mass: 90.121 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 541 / 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: 2.81 Å3/Da / Density % sol: 56.18 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 0.2M ammonium sulfate, 0.1M Sodium acetate trihydrate, 25% PEG 4000, 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: ID14-3 / Wavelength: 0.9393 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 19, 2006
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9393 Å / Relative weight: 1
ReflectionResolution: 1.99→30 Å / Num. all: 47999 / Num. obs: 47999 / % possible obs: 95.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.45 % / Biso Wilson estimate: 24 Å2 / Rmerge(I) obs: 0.096 / Rsym value: 0.096 / Net I/σ(I): 19.6
Reflection shellResolution: 1.99→2.07 Å / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 2.1 / Num. unique all: 3559 / Rsym value: 0.48 / % possible all: 74.9

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Processing

Software
NameVersionClassification
ProDCdata collection
MOLREPphasing
REFMAC5.5.0044refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1QZN

1qzn


Resolution: 1.99→29.07 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.932 / SU B: 3.784 / SU ML: 0.105 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.163 / ESU R Free: 0.155 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22884 2305 5 %RANDOM
Rwork0.18239 ---
all0.18472 47999 --
obs0.18472 43461 95.14 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.01 Å2
Baniso -1Baniso -2Baniso -3
1-2.23 Å2-0 Å2-0 Å2
2---0.24 Å20 Å2
3----2 Å2
Refine analyzeLuzzati coordinate error obs: 0.215 Å
Refinement stepCycle: LAST / Resolution: 1.99→29.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4069 0 54 556 4679
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0224216
X-RAY DIFFRACTIONr_angle_refined_deg1.5691.9735731
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.285547
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.89125.893168
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.98915705
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.531159
X-RAY DIFFRACTIONr_chiral_restr0.1180.2663
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213162
X-RAY DIFFRACTIONr_mcbond_it0.931.52661
X-RAY DIFFRACTIONr_mcangle_it1.63224345
X-RAY DIFFRACTIONr_scbond_it2.43931555
X-RAY DIFFRACTIONr_scangle_it3.9584.51379
LS refinement shellResolution: 1.991→2.043 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.277 122 -
Rwork0.236 2259 -
obs--68.34 %

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