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- PDB-6m5f: Crystal structure of HinK, a LysR family transcriptional regulato... -

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Basic information

Entry
Database: PDB / ID: 6m5f
TitleCrystal structure of HinK, a LysR family transcriptional regulator from Pseudomonas aeruginosa
ComponentsProbable transcriptional regulator
KeywordsDNA BINDING PROTEIN / LysR family / Transcriptional regulator / transcription
Function / homology
Function and homology information


protein-DNA complex / DNA-binding transcription factor activity / regulation of DNA-templated transcription / DNA binding
Similarity search - Function
LysR, substrate-binding / LysR substrate binding domain / LysR-type HTH domain profile. / Transcription regulator HTH, LysR / Bacterial regulatory helix-turn-helix protein, lysR family / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
Probable transcriptional regulator
Similarity search - Component
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
AuthorsWang, Y. / Lan, L. / Cao, Q. / Gan, J. / Wang, F.
Funding support China, 3items
OrganizationGrant numberCountry
National Science Foundation (NSF, China)31670136 China
National Science Foundation (NSF, China)31870127 China
National Science Foundation (NSF, China)81861138047 China
CitationJournal: To Be Published
Title: Crystal structure of HinK, a LysR family transcriptional regulator from Pseudomonas aeruginosa
Authors: Wang, Y. / Lan, L. / Cao, Q. / Gan, J. / Wang, F.
History
DepositionMar 10, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 17, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Probable transcriptional regulator
B: Probable transcriptional regulator
C: Probable transcriptional regulator
D: Probable transcriptional regulator


Theoretical massNumber of molelcules
Total (without water)144,7974
Polymers144,7974
Non-polymers00
Water37821
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15390 Å2
ΔGint-78 kcal/mol
Surface area46760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.534, 152.493, 72.646
Angle α, β, γ (deg.)90.000, 91.800, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and ((resid 4 and (name N or name...
21(chain B and ((resid 4 and (name N or name...

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
11TYRTYRTYRTYR(chain A and ((resid 4 and (name N or name...AA422
12TYRTYRLYSLYS(chain A and ((resid 4 and (name N or name...AA4 - 30022 - 318
13TYRTYRLYSLYS(chain A and ((resid 4 and (name N or name...AA4 - 30022 - 318
14TYRTYRLYSLYS(chain A and ((resid 4 and (name N or name...AA4 - 30022 - 318
15TYRTYRLYSLYS(chain A and ((resid 4 and (name N or name...AA4 - 30022 - 318
16TYRTYRLYSLYS(chain A and ((resid 4 and (name N or name...AA4 - 30022 - 318
17TYRTYRLYSLYS(chain A and ((resid 4 and (name N or name...AA4 - 30022 - 318
18TYRTYRLYSLYS(chain A and ((resid 4 and (name N or name...AA4 - 30022 - 318
21TYRTYRTYRTYR(chain B and ((resid 4 and (name N or name...BB422
22SERSERALAALA(chain B and ((resid 4 and (name N or name...BB3 - 30221 - 320
23SERSERALAALA(chain B and ((resid 4 and (name N or name...BB3 - 30221 - 320
24SERSERALAALA(chain B and ((resid 4 and (name N or name...BB3 - 30221 - 320
25SERSERALAALA(chain B and ((resid 4 and (name N or name...BB3 - 30221 - 320
26SERSERALAALA(chain B and ((resid 4 and (name N or name...BB3 - 30221 - 320
27SERSERALAALA(chain B and ((resid 4 and (name N or name...BB3 - 30221 - 320
28SERSERALAALA(chain B and ((resid 4 and (name N or name...BB3 - 30221 - 320

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Components

#1: Protein
Probable transcriptional regulator


Mass: 36199.316 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Gene: PA0218 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9I6S0
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 21 / 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: 2.05 Å3/Da / Density meas: 39.91 Mg/m3 / Density % sol: 39.91 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.2M Ammonium citrate dibasic, 20% w/v Polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97935 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 28, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97935 Å / Relative weight: 1
ReflectionResolution: 2.75→50 Å / Num. obs: 29609 / % possible obs: 98.2 % / Redundancy: 4 % / Biso Wilson estimate: 59.72 Å2 / Rmerge(I) obs: 0.09 / Rpim(I) all: 0.05 / Rrim(I) all: 0.104 / Χ2: 1.059 / Net I/σ(I): 9.8 / Num. measured all: 116999
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.75-2.83.90.60915170.7050.3470.7051.00198.9
2.8-2.853.80.55614540.7610.320.6451.00897.7
2.85-2.93.90.46414540.7890.2680.5391.06297.6
2.9-2.963.70.39314770.8350.230.4581.07997
2.96-3.033.50.3414110.8420.2070.4021.08295.8
3.03-3.13.40.26914300.9010.1630.3171.10195.2
3.1-3.174.10.25715120.9310.1420.2951.14399
3.17-3.264.20.21814910.9370.1180.2491.15899.4
3.26-3.364.20.17614870.9680.0970.2021.16699.5
3.36-3.464.30.1514710.9690.0820.1721.1299.5
3.46-3.594.10.12715200.9810.070.1461.0899.3
3.59-3.734.20.10814860.9820.0590.1241.04299.4
3.73-3.94.10.10114940.9880.0550.1161.04799.3
3.9-4.114.10.08615140.9880.0480.0990.99299.1
4.11-4.3640.07614720.9910.0430.0881.04398.9
4.36-4.73.90.06814820.9920.0390.0780.98998.9
4.7-5.173.90.06214910.9940.0350.0720.90598.1
5.17-5.923.60.0614210.9930.0340.0690.97993.2
5.92-7.464.10.05714980.9960.030.0651.07998.6
7.46-503.90.04715270.9960.0260.0541.07298.9

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3FZV

3fzv


Resolution: 2.75→43.738 Å / SU ML: 0.38 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 28.94
RfactorNum. reflection% reflection
Rfree0.2569 1509 5.1 %
Rwork0.1958 --
obs0.199 29571 97.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 146.54 Å2 / Biso mean: 65.9258 Å2 / Biso min: 29.86 Å2
Refinement stepCycle: final / Resolution: 2.75→43.738 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8719 0 0 21 8740
Biso mean---44.83 -
Num. residues----1156
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0058904
X-RAY DIFFRACTIONf_angle_d0.89412103
X-RAY DIFFRACTIONf_chiral_restr0.0481396
X-RAY DIFFRACTIONf_plane_restr0.0061571
X-RAY DIFFRACTIONf_dihedral_angle_d20.1235329
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2346X-RAY DIFFRACTION14.301TORSIONAL
12B2346X-RAY DIFFRACTION14.301TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.7503-2.8390.33221250.253247094
2.839-2.94050.36371370.272251998
2.9405-3.05820.38111400.2553250396
3.0582-3.19730.31991470.2323252598
3.1973-3.36590.26011240.2093260599
3.3659-3.57660.28111480.201258199
3.5766-3.85270.25811170.1936262499
3.8527-4.24010.26091340.1868257899
4.2401-4.85290.24171440.1654257199
4.8529-6.11150.24021470.1894246695
6.1115-43.7380.19171460.1768262099
Refinement TLS params.Method: refined / Origin x: 21.4544 Å / Origin y: 2.6938 Å / Origin z: 18.9272 Å
111213212223313233
T0.289 Å2-0.0119 Å2-0.0115 Å2-0.4292 Å2-0.0409 Å2--0.4096 Å2
L0.2228 °2-0.0426 °20.0234 °2-0.2258 °20.077 °2--0.6485 °2
S-0.0086 Å °0.0333 Å °-0.0145 Å °-0.0239 Å °0.0094 Å °0.0139 Å °0.0671 Å °-0.0381 Å °0.0015 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA4 - 300
2X-RAY DIFFRACTION1allB3 - 302
3X-RAY DIFFRACTION1allC3 - 301
4X-RAY DIFFRACTION1allD3 - 302
5X-RAY DIFFRACTION1allS1 - 40

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