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- PDB-9fa0: The structure of ScoC, a global regulator protein from Geobacillu... -

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Basic information

Entry
Database: PDB / ID: 9fa0
TitleThe structure of ScoC, a global regulator protein from Geobacillus kaustophilus
ComponentsScoC
KeywordsDNA BINDING PROTEIN / ScoC / Global regulator / Geobacillus stearothermophilus / Tetramer / DNA Bending / Hpr
Biological speciesGeobacillus kaustophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.15 Å
AuthorsHadad, N. / Shulami, S. / Pomyalov, S. / Lansky, S. / Lavid, N. / Shoham, Y. / Shoham, G.
Funding support Israel, 1items
OrganizationGrant numberCountry
Israel Science Foundation500/10 Israel
CitationJournal: To Be Published
Title: The structure of ScoC, a global regulator protein from Geobacillus kaustophilus
Authors: Hadad, N. / Shulami, S. / Pomyalov, S. / Lansky, S. / Lavid, N. / Shoham, Y. / Shoham, G.
History
DepositionMay 9, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 21, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: ScoC


Theoretical massNumber of molelcules
Total (without water)24,5851
Polymers24,5851
Non-polymers00
Water00
1
B: ScoC

B: ScoC

B: ScoC

B: ScoC


Theoretical massNumber of molelcules
Total (without water)98,3414
Polymers98,3414
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_545y+1/2,x-1/2,-z+1/21
crystal symmetry operation10_655-x+1,-y,z1
crystal symmetry operation16_555-y+1/2,-x+1/2,-z+1/21
Buried area16020 Å2
ΔGint-142 kcal/mol
Surface area33190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.182, 95.182, 156.018
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number98
Space group name H-MI4122
Space group name HallI4bw2bw
Symmetry operation#1: x,y,z
#2: -y+1/2,x,z+3/4
#3: y+1/2,-x,z+3/4
#4: x+1/2,-y,-z+3/4
#5: -x+1/2,y,-z+3/4
#6: -x,-y,z
#7: y,x,-z
#8: -y,-x,-z
#9: x+1/2,y+1/2,z+1/2
#10: -y+1,x+1/2,z+5/4
#11: y+1,-x+1/2,z+5/4
#12: x+1,-y+1/2,-z+5/4
#13: -x+1,y+1/2,-z+5/4
#14: -x+1/2,-y+1/2,z+1/2
#15: y+1/2,x+1/2,-z+1/2
#16: -y+1/2,-x+1/2,-z+1/2

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Components

#1: Protein ScoC


Mass: 24585.248 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus kaustophilus (bacteria) / Production host: Escherichia coli (E. coli)
Has protein modificationN

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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: 3.59 Å3/Da / Density % sol: 50 % / Description: Diamonds
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 20% PEG 3350 and 8% Tacsimate pH 4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.96 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 10, 2017
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96 Å / Relative weight: 1
ReflectionResolution: 3.15→47.59 Å / Num. obs: 6497 / % possible obs: 99.7 % / Redundancy: 13.1 % / Biso Wilson estimate: 112.84 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.069 / Rpim(I) all: 0.02 / Rrim(I) all: 0.07 / Net I/σ(I): 24.6
Reflection shellResolution: 3.15→3.26 Å / Rmerge(I) obs: 0.92 / Mean I/σ(I) obs: 2.9 / Num. unique obs: 1143 / CC1/2: 0.84 / Rpim(I) all: 0.25 / Rrim(I) all: 0.96

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.15→47.59 Å / SU ML: 0.3484 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.6918
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.25 329 5.08 %
Rwork0.2341 6153 -
obs0.2349 6481 99.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 97.79 Å2
Refinement stepCycle: LAST / Resolution: 3.15→47.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1477 0 0 0 1477
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01271512
X-RAY DIFFRACTIONf_angle_d1.29082028
X-RAY DIFFRACTIONf_chiral_restr0.0615211
X-RAY DIFFRACTIONf_plane_restr0.0076256
X-RAY DIFFRACTIONf_dihedral_angle_d19.4679188
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.15-3.970.27741570.25883025X-RAY DIFFRACTION99.94
3.97-47.590.2431720.22663128X-RAY DIFFRACTION99.16

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