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- PDB-7uvg: First cohesin of Sca5 from Ruminococcus bromii -

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Basic information

Entry
Database: PDB / ID: 7uvg
TitleFirst cohesin of Sca5 from Ruminococcus bromii
ComponentsCoh5
KeywordsPROTEIN BINDING / amylosome cohesin dockerin Ruminococcus bromii
Function / homologyIODIDE ION
Function and homology information
Biological speciesRuminococcus bromii L2-63 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.77 Å
AuthorsCerqueira, F. / Koropatkin, N.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Structures of Sca5 cohesin modules from Ruminococcus bromii
Authors: Cerqueira, F. / Koropatkin, N.
History
DepositionMay 1, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 3, 2023Provider: repository / Type: Initial release
Revision 1.1May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Coh5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,62610
Polymers20,5491
Non-polymers1,0779
Water1,29772
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)31.040, 137.790, 85.550
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-512-

HOH

21A-549-

HOH

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Components

#1: Protein Coh5


Mass: 20548.709 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 'BL21-Gold(DE3)pLysS AG' (bacteria)
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: I
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 72 / 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: 2.23 Å3/Da / Density % sol: 44.74 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.2M ZnCl2, 18% PEG 8000, 100mM Na cacodylate

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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: RAYONIX MX300-HS / Detector: CCD / Date: Feb 6, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.77→22.04 Å / Num. obs: 17738 / % possible obs: 96.4 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.051 / Net I/σ(I): 11.47
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsDiffraction-ID% possible all
1.77-1.8240.9971749196.5
7.92-223.20.03215989193.7

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Processing

Software
NameVersionClassification
xia2data scaling
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
xia2data reduction
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 1.77→22 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.919 / SU B: 12.069 / SU ML: 0.156 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.266 / ESU R Free: 0.155 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2772 2150 12 %RANDOM
Rwork0.2133 ---
obs0.2211 15582 96.09 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 130.55 Å2 / Biso mean: 38.235 Å2 / Biso min: 27.38 Å2
Baniso -1Baniso -2Baniso -3
1--1.47 Å2-0 Å20 Å2
2--2.89 Å2-0 Å2
3----1.42 Å2
Refinement stepCycle: final / Resolution: 1.77→22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1301 0 12 72 1385
Biso mean--47.79 52.02 -
Num. residues----166
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.0131328
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161245
X-RAY DIFFRACTIONr_angle_refined_deg1.1821.651806
X-RAY DIFFRACTIONr_angle_other_deg1.0661.5862878
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6115164
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.62925.96862
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.78615224
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.443152
X-RAY DIFFRACTIONr_chiral_restr0.0350.2183
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.021493
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02279
X-RAY DIFFRACTIONr_rigid_bond_restr1.17632569
LS refinement shellResolution: 1.77→1.816 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.303 147 -
Rwork0.275 1162 -
all-1309 -
obs--96.25 %

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