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- PDB-3dnt: structures of MDT proteins -

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Basic information

Entry
Database: PDB / ID: 3dnt
Titlestructures of MDT proteins
ComponentsProtein hipA
KeywordsTRANSFERASE / MDT / persistence / multidrug resistance / tolerance
Function / homology
Function and homology information


dormancy process / toxin-antitoxin complex / single-species biofilm formation / regulation of growth / DNA-binding transcription repressor activity / protein-DNA complex / sequence-specific DNA binding / transcription cis-regulatory region binding / non-specific serine/threonine protein kinase / phosphorylation ...dormancy process / toxin-antitoxin complex / single-species biofilm formation / regulation of growth / DNA-binding transcription repressor activity / protein-DNA complex / sequence-specific DNA binding / transcription cis-regulatory region binding / non-specific serine/threonine protein kinase / phosphorylation / response to antibiotic / protein serine kinase activity / protein serine/threonine kinase activity / regulation of DNA-templated transcription / magnesium ion binding / ATP binding / cytosol
Similarity search - Function
HipA, N-terminal subdomain 1 / HipA N-terminal domain / HipA-like, C-terminal / HipA-like C-terminal domain
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / Serine/threonine-protein kinase toxin HipA
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.66 Å
AuthorsSchumacher, M.A.
CitationJournal: Science / Year: 2009
Title: Molecular mechanisms of HipA-mediated multidrug tolerance and its neutralization by HipB.
Authors: Schumacher, M.A. / Piro, K.M. / Xu, W. / Hansen, S. / Lewis, K. / Brennan, R.G.
History
DepositionJul 2, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 27, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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.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.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _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_asym_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_ref_seq_dif.details / _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: Protein hipA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,03710
Polymers99,7332
Non-polymers1,3048
Water14,898827
1
A: Protein hipA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,5185
Polymers49,8671
Non-polymers6524
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Protein hipA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,5185
Polymers49,8671
Non-polymers6524
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)68.540, 84.090, 69.250
Angle α, β, γ (deg.)90.00, 91.56, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Protein hipA


Mass: 49866.551 Da / Num. of mol.: 2 / Mutation: D309Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: hipA, b1507, JW1500 / Plasmid: pBAD22 / Production host: Escherichia coli (E. coli) / Strain (production host): bl21(DE3) / References: UniProt: P23874
#2: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 827 / 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 Å3/Da / Density % sol: 38.51 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 9.5
Details: PEG 600, pH 9.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 0.989 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Dec 23, 2007 / Details: mirrors
RadiationMonochromator: graphite / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.989 Å / Relative weight: 1
ReflectionResolution: 1.66→42.6 Å / Num. all: 89509 / Num. obs: 89050 / % possible obs: 96 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4 % / Biso Wilson estimate: 20.1 Å2 / Rmerge(I) obs: 0.055 / Rsym value: 0.054 / Net I/σ(I): 10.5
Reflection shellResolution: 1.66→1.76 Å / Redundancy: 425 % / Rmerge(I) obs: 0.29 / Mean I/σ(I) obs: 3.2 / Num. unique all: 2688 / Rsym value: 0.295 / % possible all: 0.98

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Processing

Software
NameVersionClassification
CNS1.1refinement
ADSCQuantumdata collection
MOSFLMdata reduction
SCALAdata scaling
CNSphasing
RefinementMethod to determine structure: MAD / Resolution: 1.66→42.58 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 1346396.86 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.217 16843 9.7 %RANDOM
Rwork0.184 ---
obs0.184 89050 94.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 49.6849 Å2 / ksol: 0.355196 e/Å3
Displacement parametersBiso mean: 24.4 Å2
Baniso -1Baniso -2Baniso -3
1-5.45 Å20 Å2-0.71 Å2
2---2.61 Å20 Å2
3----2.84 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.21 Å0.18 Å
Luzzati d res low-5 Å
Luzzati sigma a0.15 Å0.14 Å
Refinement stepCycle: LAST / Resolution: 1.66→42.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6596 0 76 827 7499
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d23
X-RAY DIFFRACTIONc_improper_angle_d1
LS refinement shellResolution: 1.66→1.76 Å / Rfactor Rfree error: 0.006 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.285 2688 9.5 %
Rwork0.261 25546 -
obs-26889 92.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2atp.paramatp-top.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top

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