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- PDB-3ghp: Structure of the second type II cohesin module from the adaptor S... -

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Basic information

Entry
Database: PDB / ID: 3ghp
TitleStructure of the second type II cohesin module from the adaptor ScaA scaffoldin of Acetivibrio cellulolyticus (including long C-terminal linker)
ComponentsCellulosomal scaffoldin adaptor protein B
KeywordsSTRUCTURAL PROTEIN / Linker segments / 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 - #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 / SYNCHROTRON / Resolution: 2.487 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
DepositionMar 4, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 23, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 12, 2014Group: Database references
Revision 1.3Nov 1, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software / Item: _software.name
Revision 1.4Nov 1, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / 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
B: Cellulosomal scaffoldin adaptor protein B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,83816
Polymers48,9692
Non-polymers86914
Water1,31573
1
A: Cellulosomal scaffoldin adaptor protein B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,8577
Polymers24,4851
Non-polymers3726
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)24,9819
Polymers24,4851
Non-polymers4978
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)68.759, 159.221, 44.213
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Cellulosomal scaffoldin adaptor protein B


Mass: 24484.543 Da / Num. of mol.: 2 / Fragment: Cohesin module residues 190-408
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acetivibrio cellulolyticus (bacteria) / Gene: scaB / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)pLysS / References: UniProt: Q7WYN3
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 73 / 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: 2.47 Å3/Da / Density % sol: 50.23 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M 4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid, 10%(v/v) 2-propanol, 17%(w/v) PEG 4000, pH 7.5, 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: 2.487→50 Å / Num. all: 12802 / Num. obs: 12802 / % possible obs: 71.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4 % / Biso Wilson estimate: 64.4 Å2 / Rmerge(I) obs: 0.073 / Rsym value: 0.073 / Net I/σ(I): 20.7
Reflection shellResolution: 2.487→2.54 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.377 / Mean I/σ(I) obs: 2.1 / Num. unique all: 211 / Rsym value: 0.377 / % possible all: 24.4

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Processing

Software
NameVersionClassification
ProDCdata collection
MOLREPphasing
PHENIX(phenix.refine)refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementStarting model: PDB entry 3FNK

3fnk


Resolution: 2.487→42.601 Å / Occupancy max: 1 / Occupancy min: 0 / SU ML: 2.08 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 1.9 / Phase error: 37.21 / Stereochemistry target values: ML
Details: Refinement made using Refmac 5.5.0066. For the last refinement cycles Phenix was used.
RfactorNum. reflection% reflectionSelection details
Rfree0.317 648 5.07 %RANDOM
Rwork0.212 ---
obs0.217 12779 65.71 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 70.251 Å2 / ksol: 0.301 e/Å3
Displacement parametersBiso max: 206.01 Å2 / Biso mean: 71.096 Å2 / Biso min: 23.09 Å2
Baniso -1Baniso -2Baniso -3
1--19.179 Å2-0 Å20 Å2
2---0.191 Å2-0 Å2
3---19.37 Å2
Refine analyzeLuzzati coordinate error obs: 0.41 Å
Refinement stepCycle: LAST / Resolution: 2.487→42.601 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2831 0 56 73 2960
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012945
X-RAY DIFFRACTIONf_angle_d1.4813986
X-RAY DIFFRACTIONf_chiral_restr0.098471
X-RAY DIFFRACTIONf_plane_restr0.007503
X-RAY DIFFRACTIONf_dihedral_angle_d20.371049
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.487-2.60.398430.26589693923
2.6-2.7370.398900.2871567165740
2.737-2.9090.3831410.2792414255562
2.909-3.1330.3221740.2613130330480
3.133-3.4480.4161650.2543176334181
3.448-3.9470.3171710.1963030320178
3.947-4.9720.2441570.1633066322378
4.972-42.6070.2951570.1913286344384
Refinement TLS params.Method: refined / Details: all / Origin x: 4.0121 Å / Origin y: -31.0123 Å / Origin z: 13.896 Å
111213212223313233
T-0.0189 Å2-0.0244 Å20.0393 Å2--0.0794 Å20.1189 Å2---0.0539 Å2
L1.031 °20.0055 °20.2313 °2-0.8737 °2-0.1059 °2--0.6736 °2
S-0.058 Å °-0.0682 Å °-0.1211 Å °0.0043 Å °-0.018 Å °-0.0181 Å °-0.0594 Å °-0.0312 Å °-0.1612 Å °
Refinement TLS groupSelection details: all

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