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- PDB-3u2r: Crystal structure of MarR transcription factor from Planctomyces ... -

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Basic information

Entry
Database: PDB / ID: 3u2r
TitleCrystal structure of MarR transcription factor from Planctomyces limnophilus
ComponentsRegulatory protein MarR
Keywordstranscription regulator / Structural Genomics / PSI-Biology / Midwest Center for Structural Genomics / MCSG / helix-turn-helix
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
Regulatory protein MarR
Similarity search - Component
Biological speciesPlanctomyces limnophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 Å
AuthorsMichalska, K. / Li, H. / Bearden, J. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal structure of MarR transcription factor from Planctomyces limnophilus
Authors: Michalska, K. / Li, H. / Bearden, J. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
History
DepositionOct 4, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 19, 2011Provider: repository / Type: Initial release
Revision 1.1Oct 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: Regulatory protein MarR


Theoretical massNumber of molelcules
Total (without water)19,8971
Polymers19,8971
Non-polymers00
Water36020
1
A: Regulatory protein MarR

A: Regulatory protein MarR

A: Regulatory protein MarR

A: Regulatory protein MarR


Theoretical massNumber of molelcules
Total (without water)79,5884
Polymers79,5884
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation7_555y,x,-z1
crystal symmetry operation8_665-y+1,-x+1,-z1
Buried area9530 Å2
ΔGint-88 kcal/mol
Surface area29610 Å2
MethodPISA
2
A: Regulatory protein MarR

A: Regulatory protein MarR


Theoretical massNumber of molelcules
Total (without water)39,7942
Polymers39,7942
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
Buried area3550 Å2
ΔGint-29 kcal/mol
Surface area16020 Å2
MethodPISA
3
A: Regulatory protein MarR

A: Regulatory protein MarR


Theoretical massNumber of molelcules
Total (without water)39,7942
Polymers39,7942
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z1
Buried area1020 Å2
ΔGint-11 kcal/mol
Surface area18550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.970, 64.970, 87.260
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212

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Components

#1: Protein Regulatory protein MarR / MarR transcription factor


Mass: 19897.035 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Planctomyces limnophilus (bacteria) / Strain: DSM 3776 / Gene: Plim_0262 / Plasmid: PMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) Magic / References: UniProt: D5SNV8
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 20 / 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: 2.31 Å3/Da / Density % sol: 46.84 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.64 M malonic acid, 0.0875 M monoammonium malate, 0.14 M sodium acetate, 0.175 M sodium formate, 0.056 M ammonium tartrate, pH 7.0, 0.1 M Bis-Tris propane:NaOH, pH 7.0, VAPOR DIFFUSION, ...Details: 0.64 M malonic acid, 0.0875 M monoammonium malate, 0.14 M sodium acetate, 0.175 M sodium formate, 0.056 M ammonium tartrate, pH 7.0, 0.1 M Bis-Tris propane:NaOH, 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: 0.97929 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 3, 2011 / Details: mirrors
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97929 Å / Relative weight: 1
ReflectionResolution: 2.2→40 Å / Num. all: 10039 / Num. obs: 9939 / % possible obs: 99 % / Observed criterion σ(I): -3 / Redundancy: 5.9 % / Biso Wilson estimate: 48.26 Å2 / Rmerge(I) obs: 0.111 / Net I/σ(I): 13.4
Reflection shellResolution: 2.2→2.24 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.619 / Mean I/σ(I) obs: 2.8 / Num. unique all: 993 / % possible all: 100

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
SHELXmodel building
MLPHAREphasing
DMmodel building
ARP/wARPmodel building
Cootmodel building
BUSTER2.10.0refinement
HKL-3000data reduction
HKL-3000data scaling
SHELXphasing
DMphasing
RefinementMethod to determine structure: SAD / Resolution: 2.2→32.48 Å / Cor.coef. Fo:Fc: 0.9335 / Cor.coef. Fo:Fc free: 0.8937 / SU R Cruickshank DPI: 0.511 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ML
Details: HYDROGEN ATOMS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2533 993 10.03 %RANDOM
Rwork0.2012 ---
all0.2062 9900 --
obs0.2062 9900 99.01 %-
Displacement parametersBiso mean: 60.3 Å2
Baniso -1Baniso -2Baniso -3
1--5.1149 Å20 Å20 Å2
2---5.1149 Å20 Å2
3---10.2298 Å2
Refine analyzeLuzzati coordinate error obs: 0.303 Å
Refinement stepCycle: LAST / Resolution: 2.2→32.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1113 0 0 20 1133
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0142256HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.154081HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d656SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes34HARMONIC2
X-RAY DIFFRACTIONt_gen_planes326HARMONIC5
X-RAY DIFFRACTIONt_it2256HARMONIC20
X-RAY DIFFRACTIONt_omega_torsion3.62
X-RAY DIFFRACTIONt_other_torsion3.23
X-RAY DIFFRACTIONt_chiral_improper_torsion144SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact2530SEMIHARMONIC4
LS refinement shellResolution: 2.2→2.46 Å / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.2301 297 10.84 %
Rwork0.1847 2443 -
all0.19 2740 -
obs-2740 99.01 %
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)
14.41510.6965-2.91043.6832-1.22593.32270.1911-0.54420.34470.3984-0.0557-0.1573-0.30390.2407-0.1354-0.02290.04190.0116-0.0489-0.0256-0.079730.743636.231417.7741
22.67740.5546-0.20975.3999-2.91046.35050.1520.0288-0.05940.342-0.20760.0224-0.22930.26740.0556-0.0939-0.10330.0357-0.03220.0293-0.048119.126816.262923.7424
34.32821.2362.63352.87740.11016.85750.2003-0.54420.22980.4385-0.14230.0306-0.16180.0764-0.058-0.0276-0.12390.075-0.0208-0.0239-0.080615.291112.972432.7917
42.5622.7983-1.80815.3229-2.65733.1426-0.06710.15760.1005-0.10260.21830.25850.1627-0.3003-0.1512-0.0641-0.00550.0025-0.01920.0067-0.136325.349628.84267.1204
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{A|9 - A|32}A9 - 32
2X-RAY DIFFRACTION2{A|33 - A|67}A33 - 67
3X-RAY DIFFRACTION3{A|68 - A|110}A68 - 110
4X-RAY DIFFRACTION4{A|111 - A|146}A111 - 146

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