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- PDB-7uwv: CBM74 from Ruminococcus bromii Sas6 with maltodecaose -

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Basic information

Entry
Database: PDB / ID: 7uwv
TitleCBM74 from Ruminococcus bromii Sas6 with maltodecaose
ComponentsCBM74
KeywordsSUGAR BINDING PROTEIN / CBM74 / Sas6 / Ruminococcus bromii / starch binding protein / maltodecaose
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
Dockerin type I repeat
Similarity search - Component
Biological speciesRuminococcus bromii L2-63 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 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 / _citation_author.identifier_ORCID / _citation_author.name
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: CBM74
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,1117
Polymers57,5261
Non-polymers3,5846
Water12,142674
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)69.690, 160.071, 67.858
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-983-

HOH

21A-1149-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein CBM74


Mass: 57526.461 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ruminococcus bromii L2-63 (bacteria) / Gene: RBL236_00020 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A2N0UYM2

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Sugars , 2 types, 2 molecules

#2: Polysaccharide alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D- ...alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose


Type: oligosaccharide / Mass: 1963.705 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-4DGlcpa1-4DGlcpa1-4DGlcpa1-4DGlcpa1-4DGlcpa1-4DGlcpa1-4DGlcpa1-4DGlcpa1-4DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,12,11/[a2122h-1a_1-5]/1-1-1-1-1-1-1-1-1-1-1-1/a4-b1_b4-c1_c4-d1_d4-e1_e4-f1_f4-g1_g4-h1_h4-i1_i4-j1_j4-k1_k4-l1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}}}}}}}}}}}LINUCSPDB-CARE
#3: Polysaccharide alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D- ...alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose


Type: oligosaccharide / Mass: 1477.282 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-4DGlcpa1-4DGlcpa1-4DGlcpa1-4DGlcpa1-4DGlcpa1-4DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,9,8/[a2122h-1a_1-5]/1-1-1-1-1-1-1-1-1/a4-b1_b4-c1_c4-d1_d4-e1_e4-f1_f4-g1_g4-h1_h4-i1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}}}}}}}}LINUCSPDB-CARE

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Non-polymers , 3 types, 678 molecules

#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 674 / 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: 3.29 Å3/Da / Density % sol: 62.61 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 30% Tacsimate, 0.1M HEPES

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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: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 5, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.7→80.04 Å / Num. obs: 84139 / % possible obs: 99.9 % / Redundancy: 6.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.053 / Rpim(I) all: 0.023 / Rrim(I) all: 0.057 / Net I/σ(I): 17.2 / Num. measured all: 512902 / 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
1.7-1.796.20.67774784121210.860.2960.742.5100
5.38-80.045.50.0241588428730.9990.0110.02646.699.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
Aimless0.7.7data scaling
PDB_EXTRACT3.27data extraction
autoPROCdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7UWU

7uwu


Resolution: 1.7→80.04 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.961 / SU B: 3.882 / SU ML: 0.07 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.086 / ESU R Free: 0.085 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1982 4057 4.8 %RANDOM
Rwork0.1727 ---
obs0.1739 80016 99.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 73 Å2 / Biso mean: 30.171 Å2 / Biso min: 17.82 Å2
Baniso -1Baniso -2Baniso -3
1--2.1 Å20 Å2-0 Å2
2---0.73 Å20 Å2
3---2.83 Å2
Refinement stepCycle: final / Resolution: 1.7→80.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4038 0 237 674 4949
Biso mean--31.46 41.79 -
Num. residues----531
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0134388
X-RAY DIFFRACTIONr_bond_other_d0.0010.0163816
X-RAY DIFFRACTIONr_angle_refined_deg1.2921.725957
X-RAY DIFFRACTIONr_angle_other_deg1.2481.6498862
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5095637
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.91525.303198
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.60715.314669
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.851157
X-RAY DIFFRACTIONr_chiral_restr0.0490.2650
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024860
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02930
LS refinement shellResolution: 1.701→1.745 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.259 319 -
Rwork0.259 5822 -
all-6141 -
obs--99.95 %
Refinement TLS params.Method: refined / Origin x: 38.9175 Å / Origin y: 41.2688 Å / Origin z: 43.5364 Å
111213212223313233
T0.0222 Å20.0082 Å20.006 Å2-0.0144 Å20.0002 Å2--0.0049 Å2
L0.067 °20.0667 °20.0483 °2-0.132 °20.019 °2--0.0559 °2
S-0.014 Å °0.0035 Å °-0.0048 Å °0.0089 Å °0.0103 Å °-0.0091 Å °-0.013 Å °-0.0035 Å °0.0037 Å °

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