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- PDB-2vz4: The N-terminal domain of MerR-like protein TipAL bound to promoter DNA -

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Basic information

Entry
Database: PDB / ID: 2vz4
TitleThe N-terminal domain of MerR-like protein TipAL bound to promoter DNA
Components
  • 5'-D(*CP*TP*CP*CP*TP*CP*AP*CP*GP*TP *CP*AP*CP*GP*TP*GP*AP*GP*GP*TP*G)-3'
  • HTH-TYPE TRANSCRIPTIONAL ACTIVATOR TIPA
KeywordsTRANSCRIPTION / RESISTANCE / ANTIBIOTIC / DNA-BINDING / STREPTOMYCES / TRANSCRIPTION FACTOR / ALTERNATIVE INITIATION / TRANSCRIPTION REGULATION / DNA / MERR / DRUG / TIPAL / TIPAN / TIPAS / ACTIVATOR
Function / homology
Function and homology information


DNA-binding transcription factor activity / DNA binding
Similarity search - Function
TipA-like multidrug resistance regulator, antibiotic-recognition domain / TipAS antibiotic-recognition domain / TipAS antibiotic-recognition domain / Multidrug-efflux Transporter Regulator; Chain: A; Domain 2 - #10 / Multidrug-efflux Transporter Regulator; Chain: A; Domain 2 / MerR-type HTH domain signature. / : / MerR HTH family regulatory protein / MerR-type HTH domain profile. / helix_turn_helix, mercury resistance ...TipA-like multidrug resistance regulator, antibiotic-recognition domain / TipAS antibiotic-recognition domain / TipAS antibiotic-recognition domain / Multidrug-efflux Transporter Regulator; Chain: A; Domain 2 - #10 / Multidrug-efflux Transporter Regulator; Chain: A; Domain 2 / MerR-type HTH domain signature. / : / MerR HTH family regulatory protein / MerR-type HTH domain profile. / helix_turn_helix, mercury resistance / MerR-type HTH domain / Putative DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
: / DNA / DNA (> 10) / HTH-type transcriptional activator TipA
Similarity search - Component
Biological speciesSTREPTOMYCES LIVIDANS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsAllan, M.G. / Stetefeld, J. / Schirmer, T.
CitationJournal: To be Published
Title: Structure of the Transcriptionally Inactive Merr Domain Tipan in Complex with DNA
Authors: Allan, M.G. / Newberry, K.J. / Schuman, J. / Brennan, R.G. / Stetefeld, J. / Grzesiek, S. / Schirmer, T.
History
DepositionJul 30, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 17, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2May 8, 2019Group: Advisory / Data collection ...Advisory / Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc ...exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / pdbx_seq_map_depositor_info / pdbx_unobs_or_zero_occ_atoms
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval / _pdbx_seq_map_depositor_info.one_letter_code_mod
Revision 1.3Dec 13, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HTH-TYPE TRANSCRIPTIONAL ACTIVATOR TIPA
B: 5'-D(*CP*TP*CP*CP*TP*CP*AP*CP*GP*TP *CP*AP*CP*GP*TP*GP*AP*GP*GP*TP*G)-3'


Theoretical massNumber of molelcules
Total (without water)20,0252
Polymers20,0252
Non-polymers00
Water00
1
A: HTH-TYPE TRANSCRIPTIONAL ACTIVATOR TIPA
B: 5'-D(*CP*TP*CP*CP*TP*CP*AP*CP*GP*TP *CP*AP*CP*GP*TP*GP*AP*GP*GP*TP*G)-3'

A: HTH-TYPE TRANSCRIPTIONAL ACTIVATOR TIPA
B: 5'-D(*CP*TP*CP*CP*TP*CP*AP*CP*GP*TP *CP*AP*CP*GP*TP*GP*AP*GP*GP*TP*G)-3'


Theoretical massNumber of molelcules
Total (without water)40,0494
Polymers40,0494
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
Buried area6320 Å2
ΔGint-57.41 kcal/mol
Surface area17870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.850, 67.467, 73.129
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein HTH-TYPE TRANSCRIPTIONAL ACTIVATOR TIPA / TIPAL


Mass: 12053.574 Da / Num. of mol.: 1 / Fragment: DNA-BINDING DOMAIN TIPAN, RESIDUES 2-109
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) STREPTOMYCES LIVIDANS (bacteria) / Plasmid: MODIFIED PET22B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P0A4T9
#2: DNA chain 5'-D(*CP*TP*CP*CP*TP*CP*AP*CP*GP*TP *CP*AP*CP*GP*TP*GP*AP*GP*GP*TP*G)-3' / TIPA PROMOTER


Mass: 7971.114 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) STREPTOMYCES LIVIDANS (bacteria) / References: GenBank: 408222
Sequence detailsTIPAN IS THE N-TERMINAL DOMAIN OF TIPAL. RESIDUE M1 WAS CLEAVED DURING EXPRESSION. THE SEQUENCE IS ...TIPAN IS THE N-TERMINAL DOMAIN OF TIPAL. RESIDUE M1 WAS CLEAVED DURING EXPRESSION. THE SEQUENCE IS DESCRIBED IN HOLMES ET AL. (1993) EMBO J, VOL. 12, P. 3183. THE CRYSTAL CONTAINED DOUBLE-STRANDED DNA WITH SEQUENCES TTGCACCTCACGTCACGTGAGGAGGC (PLUS STRAND) AND AGCCTCCTCACGTGACGTGAGGTGCA (MINUS STRAND). BOTH STRANDS WERE MODELED AS CHAIN B WITH SEQUENCE CTCCTCACGTCACGTGAGGTG.

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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: 2.83 Å3/Da / Density % sol: 60 % / Description: NONE
Crystal growMethod: vapor diffusion, sitting drop / pH: 8.5
Details: SITTING DROP CONTAINING 4 MICROLITERS PROTEIN-DNA SOLUTION PLUS 6 MICROLITERS RESERVOIR SOLUTION. PROTEIN-DNA SOLUTION: 500 MICROMOLAR (6 MILLIGRAMS/MILLILITER) PROTEIN, 275 MICROMOLAR ...Details: SITTING DROP CONTAINING 4 MICROLITERS PROTEIN-DNA SOLUTION PLUS 6 MICROLITERS RESERVOIR SOLUTION. PROTEIN-DNA SOLUTION: 500 MICROMOLAR (6 MILLIGRAMS/MILLILITER) PROTEIN, 275 MICROMOLAR DOUBLE-STRANDED DNA, 123 MILLIMOLAR SODIUM CHLORIDE, 16 MILLIMOLAR TRIS (TRIS(HYDROXYMETHYL)AMINOMETHANE), 8 MILLIMOLAR SODIUM CACODYLATE, 4 MILLIMOLAR MAGNESIUM CHLORIDE, 0.8 MILLIMOLAR EDTA (ETHYLENEDIAMINETETRAACETIC ACID), PH 8. RESERVOIR SOLUTION: 15% (WEIGHT/VOLUME) PEG-8K (POLY(ETHYLENE GLYCOL) WITH MOLECULAR MASS 8000 GRAMS/MOLE), 200 MILLIMOLAR MAGNESIUM CHLORIDE, 100 MILLIMOLAR TRIS (TRIS(HYDROXYMETHYL)AMINOMETHANE), PH 8.5.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9001
DetectorType: MARRESEARCH / Detector: CCD / Date: Jun 20, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9001 Å / Relative weight: 1
ReflectionResolution: 2.9→72.74 Å / Num. obs: 5321 / % possible obs: 99.5 % / Observed criterion σ(I): 0 / Redundancy: 6.3 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 20.2
Reflection shellResolution: 2.9→3.06 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 5.5 / % possible all: 99.5

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1R8D

1r8d


Resolution: 2.9→30 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.872 / SU B: 56.04 / SU ML: 0.423 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 1.777 / ESU R Free: 0.401 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.274 230 4.5 %RANDOM
Rwork0.239 ---
obs0.24 4922 95.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 47.66 Å2
Baniso -1Baniso -2Baniso -3
1-1.5 Å20 Å20 Å2
2---4.37 Å20 Å2
3---2.87 Å2
Refinement stepCycle: LAST / Resolution: 2.9→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms794 428 0 0 1222
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0211245
X-RAY DIFFRACTIONr_bond_other_d0.0010.02712
X-RAY DIFFRACTIONr_angle_refined_deg1.3372.3911771
X-RAY DIFFRACTIONr_angle_other_deg0.91231730
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.115598
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.98822.35334
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.31315122
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.876157
X-RAY DIFFRACTIONr_chiral_restr0.0510.2203
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.021084
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02207
X-RAY DIFFRACTIONr_nbd_refined0.2010.2244
X-RAY DIFFRACTIONr_nbd_other0.1760.2739
X-RAY DIFFRACTIONr_nbtor_refined0.1990.2545
X-RAY DIFFRACTIONr_nbtor_other0.0840.2511
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1220.218
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1520.212
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3740.238
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0750.26
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.5191.5530
X-RAY DIFFRACTIONr_mcbond_other0.3421.5203
X-RAY DIFFRACTIONr_mcangle_it2.3852771
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.3593980
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.0194.51000
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: 2.9→2.98 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.415 13
Rwork0.358 356
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)
14.5435-0.2022.317310.6024-2.80748.17520.2364-0.0725-0.17550.3104-0.08240.2870.509-0.5064-0.1541-0.1605-0.09670.0309-0.2264-0.05530.0883-2.361416.1282-22.1389
29.49783.1998-0.45859.20330.2661.22580.528-0.61040.18760.1041-0.60460.48230.0742-0.13950.0766-0.12710.0135-0.02560.0360.02660.0274-4.663534.385-40.2169
35.26781.44913.212414.57350.34315.8529-0.0416-0.7602-0.14381.4002-0.0204-0.3927-0.11130.5620.0620.5467-0.1269-0.2977-0.07030.21340.16817.28618.6586-7.7848
41.52322.04511.6343.61881.02013.3314-0.1944-0.88470.67531.8058-0.30931.1840.3043-0.68060.50370.5439-0.05730.38160.1859-0.19640.3402-7.865848.302-8.0472
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 71
2X-RAY DIFFRACTION2A77 - 106
3X-RAY DIFFRACTION3B-11 - -2
4X-RAY DIFFRACTION4B1 - 11

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