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- PDB-7y8z: CcpS -

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Basic information

Entry
Database: PDB / ID: 7y8z
TitleCcpS
ComponentsUPF0297 protein A7J08_00425
KeywordsGENE REGULATION / CcpS / wild type
Function / homologyIreB regulatory phosphoprotein / IreB regulatory phosphoprotein / UPF0297 protein A7J08_00425
Function and homology information
Biological speciesStreptococcus suis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsTang, J.S. / Ran, T.T. / Wang, W.W. / Fan, H.J.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31770074 China
CitationJournal: Nat Commun / Year: 2023
Title: A link between STK signalling and capsular polysaccharide synthesis in Streptococcus suis.
Authors: Tang, J. / Guo, M. / Chen, M. / Xu, B. / Ran, T. / Wang, W. / Ma, Z. / Lin, H. / Fan, H.
History
DepositionJun 24, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 10, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 29, 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: UPF0297 protein A7J08_00425
B: UPF0297 protein A7J08_00425


Theoretical massNumber of molelcules
Total (without water)20,7732
Polymers20,7732
Non-polymers00
Water1,47782
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2710 Å2
ΔGint-24 kcal/mol
Surface area8320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.341, 48.607, 84.505
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein UPF0297 protein A7J08_00425


Mass: 10386.598 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus suis (bacteria)
Gene: A7J08_00425, APQ97_00335, BKM67_00415, DAT299_00590, DAT300_00590, DF184_00385, DP112_00390, E8L09_09180, E8M06_00415, EI993_07725, ERS132356_01127, ERS132370_01942, ERS132372_02013, ERS132374_ ...Gene: A7J08_00425, APQ97_00335, BKM67_00415, DAT299_00590, DAT300_00590, DF184_00385, DP112_00390, E8L09_09180, E8M06_00415, EI993_07725, ERS132356_01127, ERS132370_01942, ERS132372_02013, ERS132374_01629, ERS132389_01056, ERS132393_01831, ERS132399_01807, ERS132406_01864, ERS132410_02099, ERS132417_01758, ERS132421_02063, ERS132427_01991, ERS132440_00037, ERS132441_01121, ERS132442_01629, ERS132444_01898, ERS132452_01291, ERS132453_01607, ERS132457_01187, ERS132462_01903, ERS132522_01747, ERS132536_02055, ERS132551_01632, ERS156295_01913, FAJ36_09955, FAJ40_03240, FH688_09640, FH691_09925, FH692_09625, FH693_09180, HU146_07120, I5V48_00400, JZY07_00375, XK26_09590
Production host: Escherichia coli (E. coli) / References: UniProt: A0A0K2E3A3
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 82 / Source method: isolated from a natural source / Formula: H2O

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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: 2.04 Å3/Da / Density % sol: 39.81 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: PEG

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jan 14, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.6→84.51 Å / Num. obs: 23141 / % possible obs: 100 % / Redundancy: 12.2 % / CC1/2: 0.999 / Rpim(I) all: 0.04 / Net I/σ(I): 11.7
Reflection shellResolution: 1.6→1.64 Å / Num. unique obs: 2270 / CC1/2: 0.507

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Processing

Software
NameVersionClassification
PHENIX1.16refinement
autoPROCdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7y86

7y86


Resolution: 1.6→42.13 Å / Cross valid method: FREE R-VALUE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2314 --
Rwork0.2132 --
obs-23117 99.87 %
Displacement parametersBiso mean: 33.93 Å2
Refinement stepCycle: LAST / Resolution: 1.6→42.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1223 0 0 82 1305
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00711255
X-RAY DIFFRACTIONf_angle_d0.93811692
X-RAY DIFFRACTIONf_chiral_restr0.0616180
X-RAY DIFFRACTIONf_plane_restr0.0044222
X-RAY DIFFRACTIONf_dihedral_angle_d21.6368771

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