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- PDB-7f9h: complex structure of EnrR-DNA -

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Basic information

Entry
Database: PDB / ID: 7f9h
Titlecomplex structure of EnrR-DNA
Components
  • EnrR repressor
  • target DNA
KeywordsDNA BINDING PROTEIN / EnrR / Repressor / DNA complex
Function / homologyDNA / DNA (> 10)
Function and homology information
Biological speciesEdwardsiella piscicida (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.78 Å
AuthorsGan, J.H. / Wang, Q.Y.
CitationJournal: Nucleic Acids Res. / Year: 2022
Title: Xenogeneic nucleoid-associated EnrR thwarts H-NS silencing of bacterial virulence with unique DNA binding.
Authors: Ma, R. / Liu, Y. / Gan, J. / Qiao, H. / Ma, J. / Zhang, Y. / Bu, Y. / Shao, S. / Zhang, Y. / Wang, Q.
History
DepositionJul 4, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 11, 2022Provider: repository / Type: Initial release
Revision 1.1May 18, 2022Group: Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: EnrR repressor
B: EnrR repressor
C: target DNA
D: target DNA


Theoretical massNumber of molelcules
Total (without water)34,3994
Polymers34,3994
Non-polymers00
Water4,107228
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7120 Å2
ΔGint-27 kcal/mol
Surface area13950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.228, 58.490, 67.569
Angle α, β, γ (deg.)90.000, 98.370, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein EnrR repressor


Mass: 10371.302 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Edwardsiella piscicida (bacteria) / Production host: Escherichia coli (E. coli)
#2: DNA chain target DNA


Mass: 6828.298 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 228 / 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: 2.99 Å3/Da / Density % sol: 58.81 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: PEG3350 and potassium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97928 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Aug 25, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97928 Å / Relative weight: 1
ReflectionResolution: 1.75→30 Å / Num. obs: 38808 / % possible obs: 66.8 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.054 / Rpim(I) all: 0.022 / Rrim(I) all: 0.058 / Χ2: 0.867 / Net I/σ(I): 9 / Num. measured all: 259037
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.75-1.8460.38338810.9460.1660.4180.95767
1.84-1.956.70.29858080.9760.1230.3230.934100
1.95-2.16.50.18857970.9850.0790.2050.89799.9
2.1-2.326.90.11357930.9920.0460.1220.809100
2.32-2.656.70.06958120.9940.0280.0740.69999.8
2.65-3.346.80.04258100.9990.0170.0450.60199.5
3.34-306.90.03659070.9910.0150.0391.19799.3

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Processing

Software
NameVersionClassification
HKL-2000data scaling
REFMAC5.8.0135refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 1.78→29.63 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.92 / SU B: 1.886 / SU ML: 0.061 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.107 / ESU R Free: 0.102 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.222 1903 5 %RANDOM
Rwork0.2006 ---
obs0.2017 36096 98.12 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 67.79 Å2 / Biso mean: 17.588 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å2-0 Å20 Å2
2--0.01 Å2-0 Å2
3---0 Å2
Refinement stepCycle: final / Resolution: 1.78→29.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1155 898 0 228 2281
Biso mean---22.36 -
Num. residues----188
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0152194
X-RAY DIFFRACTIONr_bond_other_d0.0050.021667
X-RAY DIFFRACTIONr_angle_refined_deg1.3091.6033151
X-RAY DIFFRACTIONr_angle_other_deg1.3933837
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.6795144
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.88720.16461
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.84515196
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.0781522
X-RAY DIFFRACTIONr_chiral_restr0.0740.2298
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021859
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02505
LS refinement shellResolution: 1.78→1.826 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.229 111 -
Rwork0.221 2319 -
all-2430 -
obs--84.82 %

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