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- PDB-7f9i: The apo-form structure of EnrR -

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Basic information

Entry
Database: PDB / ID: 7f9i
TitleThe apo-form structure of EnrR
ComponentsEnrR repressor
KeywordsDNA BINDING PROTEIN / EnrR / Repressor / DNA binding
Biological speciesEdwardsiella piscicida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 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 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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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


Theoretical massNumber of molelcules
Total (without water)20,4612
Polymers20,4612
Non-polymers00
Water362
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.283, 72.379, 34.075
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21(chain B and (resid 16 through 29 or (resid 30...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ALAALALYSLYSchain AAA16 - 8316 - 83
21ALAALAHISHIS(chain B and (resid 16 through 29 or (resid 30...BB16 - 2916 - 29
22LYSLYSLYSLYS(chain B and (resid 16 through 29 or (resid 30...BB3030
23ALAALALYSLYS(chain B and (resid 16 through 29 or (resid 30...BB16 - 8416 - 84
24ALAALALYSLYS(chain B and (resid 16 through 29 or (resid 30...BB16 - 8416 - 84
25ALAALALYSLYS(chain B and (resid 16 through 29 or (resid 30...BB16 - 8416 - 84
26ALAALALYSLYS(chain B and (resid 16 through 29 or (resid 30...BB16 - 8416 - 84
27ALAALALYSLYS(chain B and (resid 16 through 29 or (resid 30...BB16 - 8416 - 84
28ALAALALYSLYS(chain B and (resid 16 through 29 or (resid 30...BB16 - 8416 - 84

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Components

#1: Protein EnrR repressor


Mass: 10230.616 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / 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: 1.7 Å3/Da / Density % sol: 27.48 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: PEG3350 and sodium formate

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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: 2.48→30 Å / Num. obs: 5129 / % possible obs: 97.2 % / Redundancy: 6.1 % / Biso Wilson estimate: 32.8 Å2 / Rmerge(I) obs: 0.143 / Rpim(I) all: 0.054 / Rrim(I) all: 0.153 / Χ2: 0.971 / Net I/σ(I): 7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.5-2.594.20.3824830.8210.1870.4280.94393.2
2.59-2.694.30.344730.9560.160.3780.98894.2
2.69-2.824.30.3024960.9080.1460.3380.88895.2
2.82-2.965.10.2774930.9520.1260.3060.9196.7
2.96-3.155.90.2385170.9720.0980.2580.91998.7
3.15-3.396.30.1855060.9830.0720.1991.00298.8
3.39-3.736.70.1535220.9890.0580.1641.14199.4
3.73-4.276.70.1265220.9940.0470.1341.07397.9
4.27-5.388.40.1135310.9880.040.120.89598.7
5.38-308.20.1165860.9930.040.1230.92998.8

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Processing

Software
NameVersionClassification
PHENIX1.19.1_4122refinement
HKL-2000data scaling
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7F9H

7f9h


Resolution: 2.5→28.14 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.46 / Phase error: 23.01 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2894 215 4.84 %
Rwork0.2424 4224 -
obs0.2449 4439 83.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 76.44 Å2 / Biso mean: 31.4399 Å2 / Biso min: 10.68 Å2
Refinement stepCycle: final / Resolution: 2.5→28.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1061 0 0 2 1063
Biso mean---17.15 -
Num. residues----137
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A414X-RAY DIFFRACTION0.963TORSIONAL
12B414X-RAY DIFFRACTION0.963TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 2

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.48-3.120.3522790.29381714179369
3.12-28.140.27531360.22632510264698
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.031-0.1440.00430.90750.02681.08630.01890.018-0.11880.2815-0.1437-0.3107-0.40030.44810.00960.2046-0.0845-0.04680.2743-0.00860.261411.47483.416218.8855
22.5839-1.626-0.77275.9892.69842.79090.18270.04660.1526-0.45280.4282-0.5067-0.10330.7431-0.02650.39820.0123-0.00360.28250.04730.303221.046781.245714.3897
30.2446-0.04210.1311.89170.31131.860.04610.3351-0.15960.0556-0.0859-0.00390.69740.3415-0.02790.18450.041-0.10140.3107-0.02490.221317.411564.51561.8197
42.2102-0.80830.64324.6851-1.93993.1843-0.4125-0.09890.1606-0.08810.24520.16020.52660.30480.00290.0885-0.0587-0.0530.30910.04990.20077.613667.159-3.0248
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resseq 16:55)A16 - 55
2X-RAY DIFFRACTION2(chain A and resseq 56:83)A56 - 83
3X-RAY DIFFRACTION3(chain B and resseq 16:55)B16 - 55
4X-RAY DIFFRACTION4(chain B and resseq 56:84)B56 - 84

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