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- PDB-1qzn: Crystal Structure Analysis of a type II cohesin domain from the c... -

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Basic information

Entry
Database: PDB / ID: 1qzn
TitleCrystal Structure Analysis of a type II cohesin domain from the cellulosome of Acetivibrio cellulolyticus
Componentscellulosomal scaffoldin adaptor protein B
KeywordsSTRUCTURAL PROTEIN / Keywords: cohesins TYPE 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 ...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
Cellulosomal scaffoldin adaptor protein B
Similarity search - Component
Biological speciesAcetivibrio cellulolyticus (bacteria)
MethodX-RAY DIFFRACTION / SIRAS / Resolution: 1.9 Å
AuthorsFrolow, F. / Noach, I. / Rosenheck, S. / Lamed, R. / Qi, X. / Shimon, L.J.W. / Bayer, E.A.
CitationJournal: J.Mol.Biol. / Year: 2005
Title: Crystal structure of a type-II cohesin module from the Bacteroides cellulosolvens cellulosome reveals novel and distinctive secondary structural elements.
Authors: Noach, I. / Frolow, F. / Jakoby, H. / Rosenheck, S. / Shimon, L.W. / Lamed, R. / Bayer, E.A.
History
DepositionSep 17, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 21, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model / refine / Item: _refine.pdbx_starting_model

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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


Theoretical massNumber of molelcules
Total (without water)18,4601
Polymers18,4601
Non-polymers00
Water1,72996
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.088, 55.088, 112.553
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein cellulosomal scaffoldin adaptor protein B


Mass: 18459.680 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 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q7WYN3
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 96 / 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: 2.67 Å3/Da / Density % sol: 53.94 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: ammonium sulfate, sodium acetate trihydrate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU ULTRAX 18 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Feb 10, 2002 / Details: OSMIC confocal multi-layer mirrors
RadiationMonochromator: OSMIC CONFOCAL MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→47.68 Å / Num. all: 16118 / Num. obs: 16118 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 8 % / Biso Wilson estimate: 20 Å2 / Rmerge(I) obs: 0.072 / Rsym value: 0.072 / Net I/σ(I): 20.8
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 6 % / Rmerge(I) obs: 0.662 / Mean I/σ(I) obs: 2.016 / Num. unique all: 759 / Rsym value: 0.662 / % possible all: 99.1

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
MLPHAREphasing
RefinementMethod to determine structure: SIRAS / Resolution: 1.9→47.67 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.962 / SU B: 3.077 / SU ML: 0.088 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.117 / ESU R Free: 0.116 / Stereochemistry target values: Engh & Huber / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19868 810 5 %RANDOM
Rwork0.15933 ---
all0.16133 15308 --
obs0.16133 15308 99.71 %-
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: 26.327 Å2
Baniso -1Baniso -2Baniso -3
1--0.53 Å2-0.27 Å20 Å2
2---0.53 Å20 Å2
3---0.8 Å2
Refinement stepCycle: LAST / Resolution: 1.9→47.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1286 0 0 96 1382
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0270.0221304
X-RAY DIFFRACTIONr_bond_other_d0.0020.021180
X-RAY DIFFRACTIONr_angle_refined_deg2.0211.9541775
X-RAY DIFFRACTIONr_angle_other_deg0.9132763
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.285170
X-RAY DIFFRACTIONr_chiral_restr0.1230.2218
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021447
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02231
X-RAY DIFFRACTIONr_nbd_refined0.250.2189
X-RAY DIFFRACTIONr_nbd_other0.2530.21339
X-RAY DIFFRACTIONr_nbtor_other0.090.2857
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2050.273
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2650.26
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3620.218
X-RAY DIFFRACTIONr_mcbond_it1.4891.5851
X-RAY DIFFRACTIONr_mcangle_it2.84821387
X-RAY DIFFRACTIONr_scbond_it4.0283453
X-RAY DIFFRACTIONr_scangle_it6.4074.5388
LS refinement shellResolution: 1.901→1.95 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.27 58 -
Rwork0.255 1082 -
obs-1253 99.1 %

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