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- PDB-2wiu: Mercury-modified bacterial persistence regulator hipBA -

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Basic information

Entry
Database: PDB / ID: 2wiu
TitleMercury-modified bacterial persistence regulator hipBA
Components
  • HTH-TYPE TRANSCRIPTIONAL REGULATOR HIPB
  • PROTEIN HIPA
KeywordsTRANSFERASE/TRANSCRIPTION / TRANSFERASE TRANSCRIPTION COMPLEX / SERINE KINASE / DNA-BINDING / MERCURY DERIVATIVE / REPRESSOR / TRANSCRIPTION REGULATION / SAD / TRANSFERASE-TRANSCRIPTION complex
Function / homology
Function and homology information


dormancy process / toxin-antitoxin complex / single-species biofilm formation / regulation of growth / DNA-binding transcription repressor activity / core promoter sequence-specific DNA binding / protein-DNA complex / sequence-specific DNA binding / non-specific serine/threonine protein kinase / transcription cis-regulatory region binding ...dormancy process / toxin-antitoxin complex / single-species biofilm formation / regulation of growth / DNA-binding transcription repressor activity / core promoter sequence-specific DNA binding / protein-DNA complex / sequence-specific DNA binding / non-specific serine/threonine protein kinase / transcription cis-regulatory region binding / phosphorylation / response to antibiotic / protein serine kinase activity / protein serine/threonine kinase activity / negative regulation of DNA-templated transcription / DNA-templated transcription / regulation of DNA-templated transcription / magnesium ion binding / protein homodimerization activity / ATP binding / cytosol
Similarity search - Function
HipA, N-terminal subdomain 1 / HipA N-terminal domain / HipA-like, C-terminal / HipA-like C-terminal domain / Helix-turn-helix / Helix-turn-helix XRE-family like proteins / Cro/C1-type HTH domain profile. / lambda repressor-like DNA-binding domains / Cro/C1-type helix-turn-helix domain / 434 Repressor (Amino-terminal Domain) ...HipA, N-terminal subdomain 1 / HipA N-terminal domain / HipA-like, C-terminal / HipA-like C-terminal domain / Helix-turn-helix / Helix-turn-helix XRE-family like proteins / Cro/C1-type HTH domain profile. / lambda repressor-like DNA-binding domains / Cro/C1-type helix-turn-helix domain / 434 Repressor (Amino-terminal Domain) / Lambda repressor-like, DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
: / Antitoxin HipB / Serine/threonine-protein kinase toxin HipA
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.35 Å
AuthorsEvdokimov, A. / Voznesensky, I. / Fennell, K. / Anderson, M. / Smith, J.F. / Fisher, D.A.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2009
Title: New Kinase Regulation Mechanism Found in Hipba: A Bacterial Persistence Switch.
Authors: Evdokimov, A. / Voznesensky, I. / Fennell, K. / Anderson, M. / Smith, J.F. / Fisher, D.A.
History
DepositionMay 17, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 28, 2009Provider: repository / Type: Initial release
Revision 1.1Apr 4, 2012Group: Database references / Derived calculations ...Database references / Derived calculations / Non-polymer description / Other / Refinement description / Structure summary / Version format compliance
Revision 1.2May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROTEIN HIPA
B: HTH-TYPE TRANSCRIPTIONAL REGULATOR HIPB
C: PROTEIN HIPA
D: HTH-TYPE TRANSCRIPTIONAL REGULATOR HIPB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,14021
Polymers120,3824
Non-polymers1,75917
Water5,008278
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9460 Å2
ΔGint-297.5 kcal/mol
Surface area41060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)166.933, 166.933, 124.577
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number93
Space group name H-MP4222

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Components

#1: Protein PROTEIN HIPA / PROTEIN KINASE COMPONENT OF PERSISTENCE REGULATOR HIPA


Mass: 50166.531 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: DH5ALPHA / Description: INVITROGEN DH5ALPHA CELLS / Plasmid: PET28A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P23874, non-specific serine/threonine protein kinase
#2: Protein HTH-TYPE TRANSCRIPTIONAL REGULATOR HIPB / DNA-INDING COMPONENT OF PERSISTENCE REGULATOR HIPBA


Mass: 10024.329 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: DH5ALPHA / Description: INVITROGEN DH5ALPHA / Plasmid: PET28A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P23873
#3: Chemical
ChemComp-HG / MERCURY (II) ION


Mass: 200.590 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Hg
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 278 / 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: 3.86 Å3/Da / Density % sol: 67.89 %
Description: HG-SAD AT 1.01A USING SHARP, DENSITY MODIFIED IN SOLOMON AND RESOLVE
Crystal growpH: 7.5
Details: 2M AMMONIUM SULFATE, HEPES PH 7.6, 6% ETHYLENE GLYCOL 10 MG/ML PROTEIN

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.01
DetectorType: ADSC CCD / Detector: CCD / Date: Aug 6, 2008 / Details: MIRRORS
RadiationMonochromator: SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.01 Å / Relative weight: 1
ReflectionResolution: 2.35→100 Å / Num. obs: 73235 / % possible obs: 99.5 % / Observed criterion σ(I): 0 / Redundancy: 8.8 % / Biso Wilson estimate: 48 Å2 / Rmerge(I) obs: 0.03 / Net I/σ(I): 23.26
Reflection shellResolution: 2.35→2.45 Å / Redundancy: 7.8 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 3.9 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data reduction
SCALEPACKdata scaling
SHARPphasing
SOLOMONphasing
REFMAC5.2.0005refinement
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 2.35→166.67 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.925 / SU B: 6.764 / SU ML: 0.161 / Cross valid method: THROUGHOUT / ESU R: 0.241 / ESU R Free: 0.215 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. DISORDERED REGIONS WERE MOSTLY OMITTED. REGIONS IN THE VICINITY OF BOUND MERCURY IONS ARE POORLY RESOLVED DUE TO DISORDER AND PARTIAL OCCUPANCY
RfactorNum. reflection% reflectionSelection details
Rfree0.26389 3691 5.1 %RANDOM
Rwork0.21599 ---
obs0.21843 69360 99.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 49.022 Å2
Baniso -1Baniso -2Baniso -3
1-1.26 Å20 Å20 Å2
2--1.26 Å20 Å2
3----2.52 Å2
Refinement stepCycle: LAST / Resolution: 2.35→166.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7718 0 17 278 8013
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0227910
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.0771.96810701
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg11.7555970
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.62723.775355
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.677151394
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.4541560
X-RAY DIFFRACTIONr_chiral_restr0.1780.21217
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.025904
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2780.23447
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3280.25270
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2090.2389
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2010.237
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1540.28
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.3311.54977
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it6.06127877
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it8.37233264
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it11.1264.52820
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.35→2.411 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.408 291 -
Rwork0.299 5047 -
obs--99.61 %

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