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- PDB-2zf9: Crystal structure of a type III cohesin module from the celluloso... -

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Basic information

Entry
Database: PDB / ID: 2zf9
TitleCrystal structure of a type III cohesin module from the cellulosomal ScaE cell-surface anchoring scaffoldin of Ruminococcus flavefaciens
ComponentsScaE cell-surface anchored scaffoldin protein
KeywordsSTRUCTURAL PROTEIN / Dockerin-binding module / anchoring module / alpha helix / beta flaps
Function / homology: / Immunoglobulin-like - #680 / cell periphery / Immunoglobulin-like / Sandwich / Mainly Beta / membrane / ScaE cell-surface anchored scaffoldin protein
Function and homology information
Biological speciesRuminococcus flavefaciens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.95 Å
AuthorsFrolow, F. / Bayer, E. / Alber, O.
Citation
Journal: Proteins / Year: 2009
Title: Cohesin diversity revealed by the crystal structure of the anchoring cohesin from Ruminococcus flavefaciens.
Authors: Alber, O. / Noach, I. / Rincon, M.T. / Flint, H.J. / Shimon, L.J.W. / Lamed, R. / Frolow, F. / Bayer, E.A.
#1: Journal: To be Published
Title: Preliminary X-ray characterization of a novel type of anchoring cohesin from the cellulosome of Ruminococcus flavefaciens
Authors: Alber, O. / Noach, I. / Lamed, R. / Shimon, J.W.L. / Bayer, E.A. / Frolow, F.
History
DepositionDec 26, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 30, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Oct 11, 2017Group: Refinement description / Category: software
Revision 1.3Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / 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_conn.pdbx_leaving_atom_flag / _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: ScaE cell-surface anchored scaffoldin protein
B: ScaE cell-surface anchored scaffoldin protein
C: ScaE cell-surface anchored scaffoldin protein
D: ScaE cell-surface anchored scaffoldin protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,2986
Polymers84,1714
Non-polymers1282
Water15,853880
1
A: ScaE cell-surface anchored scaffoldin protein


Theoretical massNumber of molelcules
Total (without water)21,0431
Polymers21,0431
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: ScaE cell-surface anchored scaffoldin protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,1703
Polymers21,0431
Non-polymers1282
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: ScaE cell-surface anchored scaffoldin protein


Theoretical massNumber of molelcules
Total (without water)21,0431
Polymers21,0431
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: ScaE cell-surface anchored scaffoldin protein


Theoretical massNumber of molelcules
Total (without water)21,0431
Polymers21,0431
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)155.56, 69.25, 93.03
Angle α, β, γ (deg.)90.00, 123.37, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-399-

HOH

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Components

#1: Protein
ScaE cell-surface anchored scaffoldin protein


Mass: 21042.678 Da / Num. of mol.: 4 / Fragment: UNP residues 30-211
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ruminococcus flavefaciens (bacteria) / Strain: 17 / Gene: scaE / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: Q4A3Y2
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 880 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.49 Å3/Da / Density % sol: 50.52 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.1M Bis-Tris, 23% PEG 3350, 0.1M calcium chloride, pH 5.5, 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: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 24, 2007
RadiationMonochromator: Double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.95→23.8 Å / Num. all: 60499 / Num. obs: 60499 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.73 % / Biso Wilson estimate: 25.8 Å2 / Rmerge(I) obs: 0.078 / Rsym value: 0.078 / Net I/σ(I): 29.9
Reflection shellResolution: 1.95→1.98 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.372 / Mean I/σ(I) obs: 2.26 / Num. unique all: 2738 / Rsym value: 0.372 / % possible all: 89.8

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MxCuBEdata collection
DENZOdata reduction
SCALEPACKdata scaling
SHELXCDphasing
SHELXEmodel building
RefinementMethod to determine structure: SAD / Resolution: 1.95→23.69 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.945 / SU B: 3.276 / SU ML: 0.094 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.145 / ESU R Free: 0.14 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21122 3032 5.1 %RANDOM
Rwork0.16163 ---
all0.16413 60499 --
obs0.16413 56820 98.84 %-
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: 30.461 Å2
Baniso -1Baniso -2Baniso -3
1-0.85 Å20 Å20.66 Å2
2---1.4 Å20 Å2
3---1.28 Å2
Refine analyzeLuzzati coordinate error obs: 0.187 Å
Refinement stepCycle: LAST / Resolution: 1.95→23.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5428 0 7 880 6315
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0225560
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4211.9667564
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4095732
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.03126.624237
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.44915918
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.7771512
X-RAY DIFFRACTIONr_chiral_restr0.0980.2874
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024208
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2030.22484
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3030.23799
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1620.2624
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2090.263
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2020.243
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.30133699
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.18355787
X-RAY DIFFRACTIONr_scbond_it5.17872090
X-RAY DIFFRACTIONr_scangle_it7.458101771
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.948→1.999 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.279 197 -
Rwork0.217 3794 -
obs--89.85 %

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