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- PDB-7rft: Domain 1 of Starch adherence system protein 20 (Sas20) from Rumin... -

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Basic information

Entry
Database: PDB / ID: 7rft
TitleDomain 1 of Starch adherence system protein 20 (Sas20) from Ruminococcus bromii with maltotriose
ComponentsDockerin domain-containing protein
KeywordsSUGAR BINDING PROTEIN / Starch-binding protein domain in the Ruminococcus bromii amylosome protein Sas20
Function / homology
Function and homology information


cellulose catabolic process / hydrolase activity, hydrolyzing O-glycosyl compounds / metal ion binding
Similarity search - Function
Dockerin domain / Dockerin domain profile. / Dockerin type I domain / Dockerin type I repeat / Dockerin domain superfamily / Prokaryotic membrane lipoprotein lipid attachment site profile. / Immunoglobulin-like fold
Similarity search - Domain/homology
alpha-maltotriose / Dockerin domain-containing protein
Similarity search - Component
Biological speciesRuminococcus bromii L2-63 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.53 Å
AuthorsKoropatkin, N. / Cerqueira, F.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)F31 GM137488 United States
CitationJournal: J.Biol.Chem. / Year: 2022
Title: Sas20 is a highly flexible starch-binding protein in the Ruminococcus bromii cell-surface amylosome.
Authors: Cerqueira, F.M. / Photenhauer, A.L. / Doden, H.L. / Brown, A.N. / Abdel-Hamid, A.M. / Morais, S. / Bayer, E.A. / Wawrzak, Z. / Cann, I. / Ridlon, J.M. / Hopkins, J.B. / Koropatkin, N.M.
History
DepositionJul 14, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 13, 2022Provider: repository / Type: Initial release
Revision 1.1May 25, 2022Group: Database references / Category: citation / citation_author / Item: _citation.journal_volume / _citation_author.name
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Dockerin domain-containing protein
B: Dockerin domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,26012
Polymers51,8012
Non-polymers1,45910
Water10,106561
1
A: Dockerin domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,6927
Polymers25,9011
Non-polymers7926
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Dockerin domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,5685
Polymers25,9011
Non-polymers6674
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)121.837, 64.668, 64.734
Angle α, β, γ (deg.)90.000, 102.760, 90.000
Int Tables number5
Space group name H-MC121

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Components

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Protein / Sugars , 2 types, 4 molecules AB

#1: Protein Dockerin domain-containing protein


Mass: 25900.578 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ruminococcus bromii L2-63 (bacteria) / Gene: RBL236_01231 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A2N0URA4
#2: Polysaccharide alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 504.438 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-maltotriose
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,3,2/[a2122h-1a_1-5]/1-1-1/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}}LINUCSPDB-CARE

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Non-polymers , 4 types, 569 molecules

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


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 561 / 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: 2.4 Å3/Da / Density % sol: 48.77 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / Details: 27% PEG 4000, 0.2M MgCl, 0.1M Tris

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.979 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Aug 1, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.53→30 Å / Num. obs: 74182 / % possible obs: 100 % / Redundancy: 4.6 % / Rmerge(I) obs: 0.047 / Rpim(I) all: 0.025 / Rrim(I) all: 0.053 / Χ2: 1.254 / Net I/σ(I): 10.7 / Num. measured all: 339801
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.53-1.5641.44436990.3640.8281.6711.05799.9
1.56-1.584.41.16936870.4740.631.3321.021100
1.58-1.624.61.03237020.5690.5441.171.056100
1.62-1.654.60.82236770.6490.4350.9331.062100
1.65-1.684.60.63537040.7630.3350.721.085100
1.68-1.724.60.51937180.8010.2740.5891.109100
1.72-1.774.60.40236840.8890.2120.4561.151100
1.77-1.814.60.31336830.9310.1650.3551.174100
1.81-1.874.60.24237060.9550.1270.2741.197100
1.87-1.934.60.19136760.9710.1010.2171.291100
1.93-24.60.13836870.9830.0720.1561.267100
2-2.084.60.10637200.9920.0560.121.3799.9
2.08-2.174.70.08237160.9940.0430.0931.409100
2.17-2.294.60.06536910.9960.0340.0741.41100
2.29-2.434.70.05537100.9970.0280.0621.422100
2.43-2.624.70.04837090.9980.0250.0551.525100
2.62-2.884.70.04137360.9980.0210.0461.586100
2.88-3.294.70.03137400.9990.0160.0351.463100
3.29-4.154.60.02337300.9990.0120.0261.14699.8
4.15-304.50.02338070.9990.0120.0261.19399.6

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Processing

Software
NameVersionClassification
HKL-2000data scaling
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7RAW

7raw


Resolution: 1.53→29.52 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.964 / SU B: 3.128 / SU ML: 0.06 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.077 / ESU R Free: 0.076 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1971 3699 5 %RANDOM
Rwork0.175 ---
obs0.1761 70481 99.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 87.77 Å2 / Biso mean: 24.288 Å2 / Biso min: 14.33 Å2
Baniso -1Baniso -2Baniso -3
1-0.23 Å20 Å20.03 Å2
2---0.24 Å20 Å2
3----0 Å2
Refinement stepCycle: final / Resolution: 1.53→29.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3565 0 88 561 4214
Biso mean--23.93 36.06 -
Num. residues----468
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0133827
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173405
X-RAY DIFFRACTIONr_angle_refined_deg1.2031.6835253
X-RAY DIFFRACTIONr_angle_other_deg1.2311.6047934
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3945494
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.29325.09167
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.41815571
X-RAY DIFFRACTIONr_dihedral_angle_4_deg4.618156
X-RAY DIFFRACTIONr_chiral_restr0.0490.2553
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.024345
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02795
LS refinement shellResolution: 1.53→1.567 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.338 251 -
Rwork0.319 5079 -
obs--97.67 %
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)
10.1436-0.0674-0.00450.33920.01210.5432-0.01720.00690.00950.01550.0183-0.0323-0.01120.0103-0.00120.0033-0.00520.00020.03960.0010.025738.043830.848939.2443
20.6434-0.24580.26040.4164-0.05010.1369-0.0456-0.07790.03980.07470.0518-0.0317-0.0229-0.0541-0.00630.02170.02470.00480.05170.0040.026521.977851.920848.3933
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A34 - 532
2X-RAY DIFFRACTION2B34 - 301

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