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- PDB-3boq: Crystal structure of MarR family transcriptional regulator from S... -

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Basic information

Entry
Database: PDB / ID: 3boq
TitleCrystal structure of MarR family transcriptional regulator from Silicibacter pomeroyi
ComponentsTranscriptional regulator, MarR family
KeywordsTRANSCRIPTION REGULATOR / Silicibacter pomeroyi / transcriptional regulator / MarR family / Structural Genomics / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG / DNA-binding / Transcription regulation
Function / homology
Function and homology information


DNA-binding transcription factor activity / DNA binding
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
Transcriptional regulator, MarR family
Similarity search - Component
Biological speciesSilicibacter pomeroyi DSS-3 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.39 Å
AuthorsChang, C. / Volkart, L. / Freeman, L. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal structure of MarR family transcriptional regulator.
Authors: Chang, C. / Volkart, L. / Freeman, L. / Joachimiak, A.
History
DepositionDec 17, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 1, 2008Provider: 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
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Transcriptional regulator, MarR family
B: Transcriptional regulator, MarR family


Theoretical massNumber of molelcules
Total (without water)35,0722
Polymers35,0722
Non-polymers00
Water86548
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.567, 110.567, 68.951
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: Protein Transcriptional regulator, MarR family


Mass: 17535.855 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: SPOA0452 / Plasmid: pMCSG / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) derivative / References: UniProt: Q5LLB8
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 48 / 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: 3.47 Å3/Da / Density % sol: 64.54 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 3.5 M Sodium formate pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97935 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 21, 2007
RadiationMonochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97935 Å / Relative weight: 1
ReflectionResolution: 2.39→50 Å / Num. all: 19071 / Num. obs: 18667 / % possible obs: 97.9 % / Observed criterion σ(I): -3 / Redundancy: 8.4 % / Biso Wilson estimate: 59.5 Å2 / Rmerge(I) obs: 0.111 / Net I/σ(I): 17.52
Reflection shellResolution: 2.39→2.49 Å / Redundancy: 8.7 % / Rmerge(I) obs: 0.455 / Mean I/σ(I) obs: 4.98 / Num. unique all: 1884 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
RefinementMethod to determine structure: SAD / Resolution: 2.39→24.96 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.924 / SU B: 13.335 / SU ML: 0.149 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.242 / ESU R Free: 0.199 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23296 958 5.1 %RANDOM
Rwork0.20287 ---
all0.20438 18641 --
obs0.20438 18641 97.66 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 67.031 Å2
Baniso -1Baniso -2Baniso -3
1--3.11 Å2-1.55 Å20 Å2
2---3.11 Å20 Å2
3---4.66 Å2
Refinement stepCycle: LAST / Resolution: 2.39→24.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2061 0 0 48 2109
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0222113
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4561.9752845
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9415278
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.64324.73193
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.86715397
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.3311518
X-RAY DIFFRACTIONr_chiral_restr0.0910.2338
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021551
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2050.2928
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2880.21468
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.140.268
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2180.232
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0910.26
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9971.51431
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.27922164
X-RAY DIFFRACTIONr_scbond_it2.5323771
X-RAY DIFFRACTIONr_scangle_it3.5854.5681
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.39→2.46 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.32 76 -
Rwork0.227 1301 -
obs-1377 97.25 %
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)
115.68288.39689.34256.52794.96387.5962-0.37010.72530.0253-0.43370.4709-0.2657-0.34440.3888-0.1008-0.23190.02290.025-0.2717-0.1317-0.275-19.758979.7965-9.32
28.9255-0.42953.92664.2447-0.88326.62860.2969-0.7379-0.58060.154-0.07190.07880.3412-0.2833-0.225-0.1382-0.0235-0.1348-0.18330.001-0.1029-9.821371.023210.0792
313.6955-8.970310.449512.0296-8.792512.4003-0.5812-0.68881.14840.54830.2954-1.0346-0.4857-0.55370.2858-0.2039-0.0335-0.0636-0.2561-0.2352-0.1177-12.510988.02556.5451
45.79777.88610.564944.7697-1.292.88610.3888-0.37530.32550.7546-0.44890.5771-0.0397-0.33320.0601-0.1978-0.0285-0.0152-0.1406-0.109-0.3626-31.493982.5808-1.918
52.7247-0.4558-0.838917.20817.81496.31580.0967-0.3768-0.13421.0731-0.02390.20680.2024-0.0079-0.0728-0.20310.0053-0.1386-0.1364-0.0151-0.132-22.30674.906-3.0375
68.6601-2.2404-1.30066.86141.31085.83050.25090.09550.8797-0.5472-0.043-0.9946-0.87781.1376-0.20790.1535-0.05140.0854-0.0032-0.18150.2156-9.893770.2933-23.6312
714.3043-4.0119-11.13783.8324.085312.266-0.06850.4364-0.9724-0.0901-0.16340.08940.2214-0.34340.2319-0.2198-0.0339-0.1069-0.2229-0.1536-0.0104-25.603363.6127-18.9127
824.669521.9086-3.374928.2581-3.13122.54590.02670.23770.7232-0.51310.13630.9275-0.3241-0.2791-0.1629-0.15650.0358-0.0543-0.2024-0.1067-0.3769-31.422883.2606-10.2367
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA7 - 4110 - 44
2X-RAY DIFFRACTION2AA42 - 10745 - 110
3X-RAY DIFFRACTION3AA108 - 130111 - 133
4X-RAY DIFFRACTION4AA131 - 150134 - 153
5X-RAY DIFFRACTION5BB7 - 4110 - 44
6X-RAY DIFFRACTION6BB42 - 10745 - 110
7X-RAY DIFFRACTION7BB108 - 130111 - 133
8X-RAY DIFFRACTION8BB131 - 150134 - 153

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