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- PDB-3bj6: Crystal structure of MarR family transcription regulator SP03579 -

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Basic information

Entry
Database: PDB / ID: 3bj6
TitleCrystal structure of MarR family transcription regulator SP03579
ComponentsTranscriptional regulator, MarR family
KeywordsTRANSCRIPTION REGULATOR / MarR family / helix-turn-helix / trasnscription regulator / Structural Genomics / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


response to stress / DNA-binding transcription factor activity
Similarity search - Function
MarR family / : / MarR-type HTH domain profile. / helix_turn_helix multiple antibiotic resistance protein / MarR-type HTH domain / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
ETHANOL / Transcriptional regulator, MarR family
Similarity search - Component
Biological speciesSilicibacter pomeroyi DSS-3 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.01 Å
AuthorsKim, Y. / Volkart, L. / Keigher, L. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal Structure of MarR family Transcription Regulator SP03579.
Authors: Kim, Y. / Volkart, L. / Keigher, L. / Joachimiak, A.
History
DepositionDec 3, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 18, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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 / _struct_conn.pdbx_leaving_atom_flag / _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: Transcriptional regulator, MarR family
B: Transcriptional regulator, MarR family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,4189
Polymers34,0962
Non-polymers3227
Water7,188399
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.701, 55.778, 125.765
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Transcriptional regulator, MarR family


Mass: 17047.998 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Silicibacter pomeroyi DSS-3 (bacteria) / Species: Silicibacter pomeroyi / Strain: DSS-3, DSM 15171 / Gene: SPO3579 / Plasmid: pMCSG7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q5LMI4
#2: Chemical
ChemComp-EOH / ETHANOL


Mass: 46.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 399 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.86 Å3/Da / Density % sol: 57.07 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 15 % Ethanol, 0.1 M Imidazole pH 8.0, 0.2M MgCl2 pH 7.8, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9793, 0.9795
DetectorType: SBC-3 / Detector: CCD / Date: Nov 21, 2007 / Details: Mirrors
RadiationMonochromator: double crystal, Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97931
20.97951
ReflectionResolution: 2→33.4 Å / Num. all: 26944 / Num. obs: 26944 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.7 % / Biso Wilson estimate: 21.28 Å2 / Rsym value: 0.07 / Net I/σ(I): 7.4
Reflection shellResolution: 2→2.07 Å / Redundancy: 6.2 % / Mean I/σ(I) obs: 5.5 / Num. unique all: 2644 / Rsym value: 0.233 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
SBC-Collectdata collection
HKL-3000data collection
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
SHELXSphasing
MLPHAREphasing
RESOLVEphasing
ARP/wARPmodel building
RefinementMethod to determine structure: MAD / Resolution: 2.01→33.4 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.935 / SU B: 5.622 / SU ML: 0.086 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.154 / ESU R Free: 0.138
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: Program PHENIX has also been used in refinement
RfactorNum. reflection% reflectionSelection details
Rfree0.198 1353 5 %RANDOM
Rwork0.1612 ---
all0.163 25520 --
obs0.163 25520 99.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.037 Å2
Baniso -1Baniso -2Baniso -3
1-0.1 Å20 Å20 Å2
2--0.3 Å20 Å2
3----0.4 Å2
Refinement stepCycle: LAST / Resolution: 2.01→33.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2370 0 21 399 2790
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0212632
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3811.963570
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.5485340
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.55321.562128
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.92815471
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.2591541
X-RAY DIFFRACTIONr_chiral_restr0.0890.2399
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022041
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2170.21354
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2970.21879
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1470.2299
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2730.286
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1670.224
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.3161.51692
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.48222632
X-RAY DIFFRACTIONr_scbond_it2.85531054
X-RAY DIFFRACTIONr_scangle_it4.3034.5938
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.01→2.06 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.221 76 -
Rwork0.163 1805 -
obs-1886 99.84 %
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)
10.0799-0.00270.00961.3425-0.15810.2624-0.0132-0.01210.00350.03510.02370.03440.01370.0047-0.0105-0.05080.00060.0069-0.0211-0.0124-0.042313.496711.619316.7112
21.0375-0.02370.08120.0176-0.03040.26760.01170.0187-0.0282-0.0094-0.00790.0041-0.0023-0.0244-0.0038-0.0264-0.00320.0117-0.0449-0.0086-0.0383-2.482327.494514.7592
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA-2 - 1491 - 152
2X-RAY DIFFRACTION2BB-1 - 1492 - 152

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