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- PDB-3l8q: Structure analysis of the type II cohesin dyad from the adaptor S... -

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Basic information

Entry
Database: PDB / ID: 3l8q
TitleStructure analysis of the type II cohesin dyad from the adaptor ScaA scaffoldin of Acetivibrio cellulolyticus
ComponentsCellulosomal scaffoldin adaptor protein B
KeywordsSTRUCTURAL PROTEIN / PROTEIN BINDING / Dockerin-binding module / protein-protein interactions / linker segment / scaffoldin arrangement / beta sandwich / 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
HEXANE-1,6-DIOL / 1,3-PROPANDIOL / Cellulosomal scaffoldin adaptor protein B
Similarity search - Component
Biological speciesAcetivibrio cellulolyticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.57 Å
AuthorsNoach, I. / Frolow, F. / Bayer, E.A.
Citation
Journal: J.Mol.Biol. / Year: 2010
Title: Modular Arrangement of a Cellulosomal Scaffoldin Subunit Revealed from the Crystal Structure of a Cohesin Dyad
Authors: Noach, I. / Levy-Assaraf, M. / Lamed, R. / Shimon, L.J.W. / Frolow, F. / Bayer, E.A.
#1: 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.
History
DepositionJan 3, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 5, 2010Provider: 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
D: Cellulosomal scaffoldin adaptor protein B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)153,53634
Polymers151,5904
Non-polymers1,94630
Water38,8402156
1
A: Cellulosomal scaffoldin adaptor protein B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,4089
Polymers37,8971
Non-polymers5118
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)38,3267
Polymers37,8971
Non-polymers4296
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)38,47010
Polymers37,8971
Non-polymers5739
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Cellulosomal scaffoldin adaptor protein B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,3328
Polymers37,8971
Non-polymers4347
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)59.225, 73.912, 90.793
Angle α, β, γ (deg.)100.25, 94.26, 112.15
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Cellulosomal scaffoldin adaptor protein B


Mass: 37897.426 Da / Num. of mol.: 4 / Fragment: Cohesin dyad, UNP residues 28-368
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
#2: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 27 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-PDO / 1,3-PROPANDIOL


Mass: 76.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O2
#4: Chemical ChemComp-HEZ / HEXANE-1,6-DIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2156 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE DEPOSITORS SUSPECT THAT THE ORIGINAL SEQUENCING WAS MISTAKEN AT THIS POSITION. THEIR RESULTS ...THE DEPOSITORS SUSPECT THAT THE ORIGINAL SEQUENCING WAS MISTAKEN AT THIS POSITION. THEIR RESULTS CLEARLY SHOW THR IN THIS POSITION AND NOT ILE

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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: 2.43 Å3/Da / Density % sol: 49.51 %
Description: THE STRUCTURE FACTOR FILE CONTAINS FRIEDEL PAIRS.
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 3.5
Details: 0.15M citric acid pH 3.5, 16% w/v PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.93 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 8, 2007
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.93 Å / Relative weight: 1
ReflectionResolution: 1.57→30 Å / Num. obs: 192139 / % possible obs: 97 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Biso Wilson estimate: 17.3 Å2 / Rmerge(I) obs: 0.077 / Rsym value: 0.077 / Net I/σ(I): 23.9 / Num. measured all: 707451
Reflection shellResolution: 1.57→1.6 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.446 / Mean I/σ(I) obs: 2.1 / Num. unique all: 8616 / Rsym value: 0.446 / % possible all: 95.4

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Processing

Software
NameVersionClassification
ProDCdata collection
MOLREPphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1ZV9

1zv9


Resolution: 1.57→29.63 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.935 / SU B: 3.799 / SU ML: 0.062 / Cross valid method: THROUGHOUT / ESU R: 0.129 / ESU R Free: 0.098 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.; THE FRIEDEL PAIRS WERE USED FOR phasing.
RfactorNum. reflection% reflectionSelection details
Rfree0.22554 9366 5 %RANDOM
Rwork0.17813 ---
obs0.1805 176887 97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.626 Å2
Baniso -1Baniso -2Baniso -3
1--1.11 Å2-0.36 Å20.49 Å2
2--0.75 Å20.21 Å2
3---0.25 Å2
Refine analyzeLuzzati coordinate error obs: 0.203 Å
Refinement stepCycle: LAST / Resolution: 1.57→29.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10245 0 126 2156 12527
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.02210658
X-RAY DIFFRACTIONr_bond_other_d0.0010.026992
X-RAY DIFFRACTIONr_angle_refined_deg1.3331.96714464
X-RAY DIFFRACTIONr_angle_other_deg0.845317285
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.251380
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.39626.048420
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.116151786
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.8411525
X-RAY DIFFRACTIONr_chiral_restr0.0810.21719
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02111801
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021924
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.35436788
X-RAY DIFFRACTIONr_mcbond_other0.72832770
X-RAY DIFFRACTIONr_mcangle_it3.585511085
X-RAY DIFFRACTIONr_scbond_it5.72673870
X-RAY DIFFRACTIONr_scangle_it7.76103372
X-RAY DIFFRACTIONr_rigid_bond_restr1.917317650
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.572→1.603 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.281 646 -
Rwork0.189 12151 -
obs--95.4 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.32970.0186-0.02660.0913-0.06930.17080.0517-0.0370.0330.0105-0.03910.01680.04320.0528-0.01260.04710.0036-0.00720.0411-0.00350.02410.6330.1180.032
20.31480.02190.06710.0628-0.08290.29330.01590.00690.00930.0037-0.02260.01070.02330.05880.00660.04020.0069-0.01670.033-0.00480.020413.12624.28643.473
30.28390.0541-0.21290.013-0.03140.46820.00260.0418-00.00550.0036-0.0047-0.0028-0.0811-0.00610.03820.00670.00770.02820.00550.03244.36516.8688.567
40.16140.0504-0.02150.0208-0.01430.13160.00330.0138-0.0263-0.001-0.0056-0.0044-0.0187-0.01520.00220.04010.0060.00270.0279-0.0060.038831.791-7.51246.022
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 338
2X-RAY DIFFRACTION2B1 - 341
3X-RAY DIFFRACTION3C3 - 337
4X-RAY DIFFRACTION4D4 - 340

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