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- PDB-3f2l: Crystal structure analysis of the K171A mutation of N-terminal ty... -

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Basic information

Entry
Database: PDB / ID: 3f2l
TitleCrystal structure analysis of the K171A mutation of N-terminal type II cohesin 1 from the cellulosomal ScaB subunit of Acetivibrio cellulolyticus
ComponentsCellulosomal scaffoldin adaptor protein B
KeywordsSTRUCTURAL PROTEIN / Point mutation
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
AMMONIUM ION / NITRATE ION / Cellulosomal scaffoldin adaptor protein B
Similarity search - Component
Biological speciesAcetivibrio cellulolyticus (bacteria)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 1.85 Å
AuthorsFrolow, F. / Freeman, A. / Wine, Y. / Eppel, A. / Shanzer, M. / Stempler, S.
CitationJournal: To be Published
Title: Crystal structure analysis of the K171A mutation of N-terminal type II cohesin 1 from the cellulosomal ScaB subunit of Acetivibrio cellulolyticus
Authors: Frolow, F. / Freeman, A. / Wine, Y. / Eppel, A. / Shanzer, M. / Stempler, S.
History
DepositionOct 30, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 2, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 10, 2021Group: Database references / Derived calculations / Category: database_2 / 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
Revision 1.3Nov 1, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)19,59321
Polymers18,7041
Non-polymers88920
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)53.934, 53.934, 112.318
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: 18703.969 Da / Num. of mol.: 1
Fragment: N-terminal type II cohesin 1 from the cellulosomal ScaB subunit, UNP residues 28-199
Mutation: K171A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acetivibrio cellulolyticus (bacteria) / Plasmid: pET28a+ / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q7WYN3
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical
ChemComp-NH4 / AMMONIUM ION


Mass: 18.038 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: H4N
#4: Chemical ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NO3
#5: 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: 2.52 Å3/Da / Density % sol: 51.21 %
Crystal growTemperature: 293 K / Method: microbatch / pH: 8.5
Details: 2.4M di-ammonium hydrogen phosphate, 0.1M Tris pH 8.5, Microbatch, temperature 293K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: May 1, 2006 / Details: Osmic Confocal Mirrors
RadiationMonochromator: Osmic Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. all: 16830 / Num. obs: 16830 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 5.7 % / Biso Wilson estimate: 27.53 Å2 / Rmerge(I) obs: 0.097 / Rsym value: 0.097 / Net I/σ(I): 11.4
Reflection shellResolution: 1.85→1.85 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 1.7 / Num. unique all: 16830 / Rsym value: 0.49 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 1qzn

1qzn


Resolution: 1.85→29.21 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.919 / SU B: 5.631 / SU ML: 0.078 / Isotropic thermal model: Anisotropic / Cross valid method: THROUGHOUT / ESU R: 0.313 / ESU R Free: 0.128 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21218 851 5.1 %RANDOM
Rwork0.13895 ---
all0.14245 15926 --
obs0.14245 15926 99.94 %-
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: 28.048 Å2
Baniso -1Baniso -2Baniso -3
1--0.16 Å2-0.08 Å20 Å2
2---0.16 Å20 Å2
3---0.25 Å2
Refinement stepCycle: LAST / Resolution: 1.85→29.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1341 0 60 240 1641
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0221410
X-RAY DIFFRACTIONr_angle_refined_deg1.1941.9761913
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2275190
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.18826.72755
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.71715231
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.305153
X-RAY DIFFRACTIONr_chiral_restr0.0770.2230
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021047
X-RAY DIFFRACTIONr_nbd_refined0.1990.2648
X-RAY DIFFRACTIONr_nbtor_refined0.3020.2976
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1190.2212
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1950.245
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1360.223
X-RAY DIFFRACTIONr_mcbond_it3.4273928
X-RAY DIFFRACTIONr_mcangle_it4.43251475
X-RAY DIFFRACTIONr_scbond_it5.9767537
X-RAY DIFFRACTIONr_scangle_it7.64410433
X-RAY DIFFRACTIONr_rigid_bond_restr3.50431465
X-RAY DIFFRACTIONr_sphericity_free8.4093248
X-RAY DIFFRACTIONr_sphericity_bonded5.4531394
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.233 81 -
Rwork0.142 1131 -
obs--100 %

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