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- PDB-9kkd: the structure of StnY -

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Basic information

Entry
Database: PDB / ID: 9kkd
Titlethe structure of StnY
ComponentsRibbon-helix-helix protein, CopG family
KeywordsDNA BINDING PROTEIN / Inhibitor
Function / homologyRibbon-helix-helix protein, CopG / Ribbon-helix-helix protein, copG family / Arc-type ribbon-helix-helix / Ribbon-helix-helix / regulation of DNA-templated transcription / Ribbon-helix-helix protein, CopG family
Function and homology information
Biological speciesStreptomyces albus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsYang, S.Q. / Guo, W.L. / Yang, X. / Liang, R.B. / Huang, T.T. / Fan, C.P. / Zheng, J.T. / Lin, S.J.
Funding support China, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2023YFA0914200 China
CitationJournal: To Be Published
Title: RHH family transcription factor serves as molecular switch of antibiotics resistance operon coupling of drug efflux pump and drug binding protein
Authors: Yang, S.Q. / Guo, W.L. / Yang, X. / Liang, R.B. / Huang, T.T. / Fan, C.P. / Zheng, J.T. / Lin, S.J.
History
DepositionNov 13, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Nov 19, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ribbon-helix-helix protein, CopG family
B: Ribbon-helix-helix protein, CopG family
C: Ribbon-helix-helix protein, CopG family
D: Ribbon-helix-helix protein, CopG family


Theoretical massNumber of molelcules
Total (without water)29,0654
Polymers29,0654
Non-polymers00
Water73941
1
A: Ribbon-helix-helix protein, CopG family
B: Ribbon-helix-helix protein, CopG family


Theoretical massNumber of molelcules
Total (without water)14,5322
Polymers14,5322
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3490 Å2
ΔGint-31 kcal/mol
Surface area5730 Å2
MethodPISA
2
C: Ribbon-helix-helix protein, CopG family
D: Ribbon-helix-helix protein, CopG family


Theoretical massNumber of molelcules
Total (without water)14,5322
Polymers14,5322
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3410 Å2
ΔGint-31 kcal/mol
Surface area5770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)30.706, 53.626, 103.937
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Ribbon-helix-helix protein, CopG family / StnY


Mass: 7266.186 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces albus (bacteria) / Gene: D8771_34895 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A6C1BW07
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 41 / Source method: isolated from a natural source / Formula: H2O
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: 1.5 Å3/Da / Density % sol: 16.9 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: sodium cacodylate trihydrate, sodium acetate trihydrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 2, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. obs: 15363 / % possible obs: 99.9 % / Redundancy: 12.3 % / CC1/2: 0.996 / CC star: 0.999 / Rpim(I) all: 0.017 / Rrim(I) all: 0.058 / Χ2: 0.539 / Net I/σ(I): 35.24
Reflection shellResolution: 1.85→1.88 Å / Mean I/σ(I) obs: 2.18 / Num. unique obs: 755 / CC1/2: 0.889 / CC star: 0.97 / Rpim(I) all: 0.26 / Rrim(I) all: 0.939 / Χ2: 0.441 / % possible all: 97

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Processing

Software
NameVersionClassification
REFMAC5.8.0430refinement
HKL-2000data collection
PHASERphasing
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.85→29.47 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.931 / SU B: 4.008 / SU ML: 0.121 / Cross valid method: THROUGHOUT / ESU R: 0.164 / ESU R Free: 0.154 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.25484 750 4.9 %RANDOM
Rwork0.20849 ---
obs0.21082 14563 99.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 38.826 Å2
Baniso -1Baniso -2Baniso -3
1-1.28 Å20 Å2-0 Å2
2--0.53 Å20 Å2
3----1.81 Å2
Refinement stepCycle: 1 / Resolution: 1.85→29.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1460 0 0 41 1501
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0121484
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161442
X-RAY DIFFRACTIONr_angle_refined_deg1.8211.8481996
X-RAY DIFFRACTIONr_angle_other_deg0.6251.7823284
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2335172
X-RAY DIFFRACTIONr_dihedral_angle_2_deg6.022518
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.3410270
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0880.2220
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021778
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02382
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.7883.431700
X-RAY DIFFRACTIONr_mcbond_other3.7843.431700
X-RAY DIFFRACTIONr_mcangle_it4.7416.114868
X-RAY DIFFRACTIONr_mcangle_other4.7386.12869
X-RAY DIFFRACTIONr_scbond_it5.8244.27784
X-RAY DIFFRACTIONr_scbond_other5.824.272785
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other8.4487.4911129
X-RAY DIFFRACTIONr_long_range_B_refined10.1942.011665
X-RAY DIFFRACTIONr_long_range_B_other10.19441.721661
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.294 52 -
Rwork0.262 1045 -
obs--99.19 %

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