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- PDB-7uwu: Starch adherence system protein 6 (Sas6) -

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Basic information

Entry
Database: PDB / ID: 7uwu
TitleStarch adherence system protein 6 (Sas6)
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 / metal ion binding
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 / SAD / Resolution: 2.19 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 1.1Jan 17, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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 1.2Feb 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)138,56117
Polymers137,8222
Non-polymers73915
Water17,366964
1
A: Starch Adherence System protein 6 (Sas6)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,37010
Polymers68,9111
Non-polymers4599
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)69,1927
Polymers68,9111
Non-polymers2806
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)69.170, 82.370, 213.320
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#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 / Plasmid: pETite Nhis / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3) pLysS / References: UniProt: A0A2N0UYM2
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


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


Mass: 58.082 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: CNS
#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 964 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.2 Å3/Da / Density % sol: 44.21 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: PEG 3350, potassium thiocyanate, Anderson Evans polyoxotungstate (TEW)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / 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: 2.19→44.77 Å / Num. obs: 63244 / % possible obs: 99.3 % / Redundancy: 16.6 % / CC1/2: 0.99 / CC star: 0.99 / Rmerge(I) obs: 0.09 / Net I/σ(I): 22.7
Reflection shellResolution: 2.19→2.27 Å / Rmerge(I) obs: 0.19 / Mean I/σ(I) obs: 14.3 / Num. unique obs: 309 / CC1/2: 0.99 / CC star: 0.99

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PDB_EXTRACT3.27data extraction
xia2data reduction
xia2data scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 2.19→44.77 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 25.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2551 3200 5.06 %
Rwork0.1858 --
obs0.1893 63244 99.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.19→44.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9527 0 32 964 10523
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007
X-RAY DIFFRACTIONf_angle_d0.851
X-RAY DIFFRACTIONf_dihedral_angle_d5.9531330
X-RAY DIFFRACTIONf_chiral_restr0.0521431
X-RAY DIFFRACTIONf_plane_restr0.0051734
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.19-2.220.35011360.26682602X-RAY DIFFRACTION100
2.22-2.260.331270.25782555X-RAY DIFFRACTION100
2.26-2.290.33481640.25092598X-RAY DIFFRACTION100
2.29-2.330.32541540.24052569X-RAY DIFFRACTION100
2.33-2.380.35741530.242583X-RAY DIFFRACTION100
2.38-2.420.3051290.23442593X-RAY DIFFRACTION100
2.42-2.470.28511220.22542617X-RAY DIFFRACTION100
2.47-2.530.29231390.21572569X-RAY DIFFRACTION100
2.53-2.580.32281280.22462612X-RAY DIFFRACTION100
2.58-2.650.30731230.21742638X-RAY DIFFRACTION100
2.65-2.720.29861230.21712585X-RAY DIFFRACTION100
2.72-2.80.29631410.20442606X-RAY DIFFRACTION100
2.8-2.890.2871410.20952633X-RAY DIFFRACTION100
2.89-2.990.2821620.20582578X-RAY DIFFRACTION100
2.99-3.110.28041240.19922597X-RAY DIFFRACTION100
3.11-3.260.25051480.19112630X-RAY DIFFRACTION99
3.26-3.430.26091230.17812620X-RAY DIFFRACTION99
3.43-3.640.241290.16462615X-RAY DIFFRACTION99
3.64-3.920.22891420.14932608X-RAY DIFFRACTION99
3.92-4.320.18121480.13652625X-RAY DIFFRACTION99
4.32-4.940.17081460.12622623X-RAY DIFFRACTION99
4.94-6.220.22091650.15042654X-RAY DIFFRACTION99
6.22-44.770.18981330.16152734X-RAY DIFFRACTION96

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