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- PDB-7urp: Second cohesin module from Sca5 of Ruminococcus bromii -

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Basic information

Entry
Database: PDB / ID: 7urp
TitleSecond cohesin module from Sca5 of Ruminococcus bromii
ComponentsRibonucleases G and E
KeywordsPROTEIN BINDING / Cohesin / amylosome
Function / homologycellulose catabolic process / Immunoglobulin-like fold / metal ion binding / membrane / Ribonucleases G and E
Function and homology information
Biological speciesRuminococcus bromii L2-63 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / molecular replacement / Resolution: 1.03 Å
AuthorsCerqueira, F. / Koropatkin, N.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Structures of cohesin modules from Sca5 of Ruminococcus bromii
Authors: Cerqueira, F. / Koropatkin, N.
History
DepositionApr 22, 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: Ribonucleases G and E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,1714
Polymers17,0461
Non-polymers1253
Water4,342241
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)120.570, 30.050, 49.940
Angle α, β, γ (deg.)90.000, 94.530, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Ribonucleases G and E


Mass: 17045.668 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ruminococcus bromii L2-63 (bacteria) / Gene: RBL236_00045
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A0A2N0UYJ0
#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-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 241 / Source method: isolated from a natural source / Formula: H2O
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: 2.65 Å3/Da / Density % sol: 53.51 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.06M CaCl2, 0.06M MgCl2, 0.1M imidazole, 0.1M MES pH = 6.5, 30% PEG 20K, 30% PEGMME 500

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.729 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Sep 10, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.729 Å / Relative weight: 1
ReflectionResolution: 1.03→30.1 Å / Num. obs: 87298 / % possible obs: 98.6 % / Redundancy: 13.4 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 12
Reflection shell
Resolution (Å)Redundancy (%)Num. unique obsCC1/2Diffraction-ID% possible allRmerge(I) obs
1.03-1.068.763770.42198.3
4.61-30.0512.71028195.40.056

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
xia2data scaling
PHASERphasing
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
RefinementMethod to determine structure: SAD / Resolution: 1.03→30.07 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.975 / SU B: 0.979 / SU ML: 0.021 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.022 / ESU R Free: 0.023 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1647 4476 5.1 %RANDOM
Rwork0.1425 ---
obs0.1436 82774 98.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 100.89 Å2 / Biso mean: 18.107 Å2 / Biso min: 10.15 Å2
Baniso -1Baniso -2Baniso -3
1--0.15 Å2-0 Å20.4 Å2
2---0.46 Å20 Å2
3---0.54 Å2
Refinement stepCycle: final / Resolution: 1.03→30.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1186 0 6 241 1433
Biso mean--29.24 35.22 -
Num. residues----159
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0131227
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161140
X-RAY DIFFRACTIONr_angle_refined_deg1.5111.6281679
X-RAY DIFFRACTIONr_angle_other_deg1.5181.5882628
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.95166
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.46327.85756
X-RAY DIFFRACTIONr_dihedral_angle_3_deg9.22615197
X-RAY DIFFRACTIONr_chiral_restr0.0750.2169
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021457
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02251
X-RAY DIFFRACTIONr_rigid_bond_restr6.93532367
LS refinement shellResolution: 1.03→1.057 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.317 331 -
Rwork0.319 6046 -
all-6377 -
obs--98.12 %

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