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- PDB-7rpy: X25-2 domain of Sca5 from Ruminococcus bromii -

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Basic information

Entry
Database: PDB / ID: 7rpy
TitleX25-2 domain of Sca5 from Ruminococcus bromii
ComponentsCohesin-containing protein
KeywordsSUGAR BINDING PROTEIN / Starch-binding protein domain in the Ruminococcus bromii amylosome protein Sca5
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / alpha-maltotriose / ACETATE ION
Function and homology information
Biological speciesRuminococcus bromii L2-63 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.67 Å
AuthorsCerqueira, F. / Koropatkin, N.
Funding support1items
OrganizationGrant numberCountry
Not funded
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
DepositionAug 4, 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 1.2Nov 6, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cohesin-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,09811
Polymers27,9961
Non-polymers1,10210
Water5,477304
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2670 Å2
ΔGint9 kcal/mol
Surface area11790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.820, 100.820, 87.930
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Cohesin-containing protein


Mass: 27995.752 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ruminococcus bromii L2-63 (bacteria) / Production host: Escherichia coli (E. coli)
#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.: 1
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
#3: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 304 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 4.61 Å3/Da / Density % sol: 73.3 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6 / Details: 2M Ammonium sulfate, 0.1M NaAcetate pH=4.6

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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: RAYONIX MX300-HS / Detector: CCD / Date: Dec 5, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.67→50.46 Å / Num. obs: 60154 / % possible obs: 99.98 % / Redundancy: 9.2 % / CC1/2: 1 / Net I/σ(I): 17.1
Reflection shellResolution: 1.67→1.73 Å / Redundancy: 9 % / Num. unique obs: 5957 / CC1/2: 0.48 / CC star: 0.805 / % possible all: 100

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Processing

Software
NameVersionClassification
xia2data scaling
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 1.67→50.46 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.95 / SU B: 3.234 / SU ML: 0.054 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.067 / ESU R Free: 0.066 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1963 3049 5.1 %RANDOM
Rwork0.1816 ---
obs0.1823 57107 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 66.06 Å2 / Biso mean: 22.311 Å2 / Biso min: 10.03 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20.01 Å20 Å2
2--0.02 Å20 Å2
3----0.06 Å2
Refinement stepCycle: final / Resolution: 1.67→50.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1827 0 74 304 2205
Biso mean--34.59 36.9 -
Num. residues----241
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0131991
X-RAY DIFFRACTIONr_bond_other_d0.0020.0181758
X-RAY DIFFRACTIONr_angle_refined_deg1.351.6742739
X-RAY DIFFRACTIONr_angle_other_deg1.3071.6044081
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.025262
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.42327.05395
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.65815278
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.682151
X-RAY DIFFRACTIONr_chiral_restr0.0540.2289
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022315
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02415
LS refinement shellResolution: 1.67→1.714 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.319 248 -
Rwork0.302 4157 -
all-4405 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: 17.5966 Å / Origin y: 54.7123 Å / Origin z: 33.8725 Å
111213212223313233
T0.0647 Å20.0212 Å20.0032 Å2-0.0138 Å20.0052 Å2--0.0166 Å2
L3.2733 °2-1.8537 °2-0.4607 °2-1.5153 °20.6034 °2--0.8569 °2
S0.087 Å °-0.0122 Å °0.0423 Å °-0.1157 Å °-0.0189 Å °-0.0938 Å °-0.0021 Å °0.0335 Å °-0.0681 Å °

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