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- PDB-7uww: Sas6 with alpha-cyclodextrin -

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Basic information

Entry
Database: PDB / ID: 7uww
TitleSas6 with alpha-cyclodextrin
ComponentsStarch Adherence System protein 6 (Sas6)
KeywordsSUGAR BINDING PROTEIN / CBM74 / CBM26 / carbohydrate-binding module / starch-binding protein
Function / homology
Function and homology information


cellulose catabolic process / hydrolase activity, hydrolyzing O-glycosyl compounds
Similarity search - Function
Starch-binding module 26 / Starch-binding module 26 / Dockerin domain / Dockerin domain profile. / Dockerin type I domain / Dockerin type I repeat / Dockerin domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
THIOCYANATE ION / Dockerin type I repeat
Similarity search - Component
Biological speciesRuminococcus bromii L2-63 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.61 Å
AuthorsPhotenhauer, A.L. / Koropatkin, N.M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Center for Complementary and Integrative Health (NIH/NCCIH)1F32AT011278 United States
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2024
Title: The Ruminococcus bromii amylosome protein Sas6 binds single and double helical alpha-glucan structures in starch.
Authors: Photenhauer, A.L. / Villafuerte-Vega, R.C. / Cerqueira, F.M. / Armbruster, K.M. / Marecek, F. / Chen, T. / Wawrzak, Z. / Hopkins, J.B. / Vander Kooi, C.W. / Janecek, S. / Ruotolo, B.T. / Koropatkin, N.M.
History
DepositionMay 4, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 14, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Jan 17, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Feb 28, 2024Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Starch Adherence System protein 6 (Sas6)
B: Starch Adherence System protein 6 (Sas6)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)142,09745
Polymers137,8222
Non-polymers4,27543
Water26,1401451
1
A: Starch Adherence System protein 6 (Sas6)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,94921
Polymers68,9111
Non-polymers2,03820
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Starch Adherence System protein 6 (Sas6)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,14824
Polymers68,9111
Non-polymers2,23723
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)69.450, 82.530, 213.470
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein / Sugars , 2 types, 4 molecules AB

#1: Protein Starch Adherence System protein 6 (Sas6)


Mass: 68911.086 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ruminococcus bromii L2-63 (bacteria) / Gene: Sas6 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3) pLysS / References: UniProt: A0A2N0UYM2
#2: Polysaccharide Cyclohexakis-(1-4)-(alpha-D-glucopyranose)


Type: oligosaccharide / Mass: 990.860 Da / Num. of mol.: 2 / Source method: obtained synthetically
DescriptorTypeProgram
WURCS=2.0/1,6,6/[a2122h-1a_1-5]/1-1-1-1-1-1/a1-f4_a4-b1_b4-c1_c4-d1_d4-e1_e4-f1WURCSPDB2Glycan 1.1.0

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Non-polymers , 4 types, 1492 molecules

#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-SCN / THIOCYANATE ION / Thiocyanate


Mass: 58.082 Da / Num. of mol.: 19 / Source method: obtained synthetically / Formula: CNS
#5: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: Ca
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1451 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.24 Å3/Da / Density % sol: 44.98 %
Crystal growTemperature: 293 K / Method: batch mode / pH: 7 / Details: PEG 3350, Potassium thiocyanate, TEW

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Aug 13, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.61→35 Å / Num. obs: 122358 / % possible obs: 77 % / Redundancy: 13.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.092 / Rpim(I) all: 0.025 / Rrim(I) all: 0.095 / Net I/σ(I): 16 / Num. measured all: 1690626 / Scaling rejects: 1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.61-1.6510.71.7992930927270.5490.5631.8891.123.5
7.2-3513.20.062581019560.9980.0170.06336.398.6

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
Aimless0.7.4data scaling
PDB_EXTRACT3.27data extraction
xia2data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7UWU

7uwu


Resolution: 1.61→34.995 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 23.67 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2116 6093 4.98 %
Rwork0.1675 116222 -
obs0.1697 122315 76.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 84.22 Å2 / Biso mean: 23.7454 Å2 / Biso min: 5.74 Å2
Refinement stepCycle: final / Resolution: 1.61→34.995 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9637 0 457 1451 11545
Biso mean--37.47 29.99 -
Num. residues----1259
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.61-1.62830.2764580.2384107422
1.6283-1.64750.3061570.233123225
1.6475-1.66760.2684860.2419138828
1.6676-1.68870.2411850.2257156531
1.6887-1.71090.2722990.2248175835
1.7109-1.73430.25211100.2252197240
1.7343-1.75910.26361500.2207223245
1.7591-1.78540.23211220.2119254651
1.7854-1.81320.26731630.2037282657
1.8132-1.8430.23451590.2065327465
1.843-1.87480.23721750.1998384076
1.8748-1.90880.24212540.1914448190
1.9088-1.94560.22712370.1832473794
1.9456-1.98530.25572590.1831481896
1.9853-2.02840.22952540.1806481396
2.0284-2.07560.22462810.1807483396
2.0756-2.12750.21122530.1741482797
2.1275-2.1850.22572430.1667488397
2.185-2.24930.22122590.1622487897
2.2493-2.32190.21952660.1607485697
2.3219-2.40490.22972610.1614488397
2.4049-2.50110.19122550.1656484096
2.5011-2.61490.19212410.175441788
2.6149-2.75270.23132430.1797501598
2.7527-2.92510.23612350.173499798
2.9251-3.15080.20812510.1734503998
3.1508-3.46770.21442500.1626502898
3.4677-3.96880.18172510.1443503098
3.9688-4.9980.17792470.1278479892
4.998-34.9950.18422890.1666534299

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