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- PDB-4r1h: GntR family transcriptional regulator from Listeria monocytogenes -

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Basic information

Entry
Database: PDB / ID: 4r1h
TitleGntR family transcriptional regulator from Listeria monocytogenes
ComponentsLmo0741 protein
KeywordsTRANSCRIPTION REGULATOR / structural genomics / APC106832 / Winged helix-turn-helix / DNA-binding / GntR family / transcriptional regulator / PSI-Biology / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


DNA-binding transcription factor activity
Similarity search - Function
Helix Hairpins - #2110 / GntR-type HTH domain profile. / helix_turn_helix gluconate operon transcriptional repressor / Transcription regulator HTH, GntR / Bacterial regulatory proteins, gntR family / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Helix Hairpins / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily ...Helix Hairpins - #2110 / GntR-type HTH domain profile. / helix_turn_helix gluconate operon transcriptional repressor / Transcription regulator HTH, GntR / Bacterial regulatory proteins, gntR family / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Helix Hairpins / 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
ACETATE ION / Lmo0741 protein
Similarity search - Component
Biological speciesListeria monocytogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.76 Å
AuthorsOsipiuk, J. / Mack, J. / Clancy, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: GntR family transcriptional regulator from Listeria monocytogenes
Authors: Osipiuk, J. / Mack, J. / Clancy, S. / Joachimiak, A.
History
DepositionAug 5, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 20, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Lmo0741 protein
B: Lmo0741 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,7614
Polymers29,6432
Non-polymers1182
Water3,621201
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3060 Å2
ΔGint-28 kcal/mol
Surface area13820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.032, 68.398, 84.016
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Lmo0741 protein


Mass: 14821.556 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Listeria monocytogenes (bacteria) / Strain: EGD-e / Gene: lmo0741 / Plasmid: pMCSG73 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8Y901
#2: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 201 / 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: 2.62 Å3/Da / Density % sol: 53.03 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.17 M sodium acetate, 0.085 M Tris-HCl buffer, 25.5% PEG 4000, 15% glycerol, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 297K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 2, 2014
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.76→31.7 Å / Num. all: 31502 / Num. obs: 31502 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.5 % / Biso Wilson estimate: 37.2 Å2 / Rmerge(I) obs: 0.069 / Χ2: 1.595 / Net I/σ(I): 11.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allΧ2% possible all
1.76-1.796.20.7812.0615510.77100
1.79-1.826.70.62715590.78100
1.82-1.867.40.50615690.819100
1.86-1.97.70.42115290.9100
1.9-1.947.70.33415520.962100
1.94-1.987.70.2815501.032100
1.98-2.037.70.22615491.1100
2.03-2.097.70.19515651.203100
2.09-2.157.80.15615521.422100
2.15-2.227.70.13715641.507100
2.22-2.37.70.11515531.641100
2.3-2.397.70.10115641.682100
2.39-2.57.70.09515721.818100
2.5-2.637.70.08615962.022100
2.63-2.797.70.07315532.079100
2.79-3.017.60.06716042.184100
3.01-3.317.50.06415772.165100
3.31-3.797.30.0616191.988100
3.79-4.787.20.04616232.084100
4.78-506.90.04317013.50597.9

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.8.0073refinement
PDB_EXTRACT3.14data extraction
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
SHELXCDphasing
SHELXDphasing
MLPHAREphasing
DMphasing
ARP/wARPmodel building
HKL-3000phasing
RefinementMethod to determine structure: SAD / Resolution: 1.76→31.7 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.953 / SU B: 4.175 / SU ML: 0.067 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.098 / ESU R Free: 0.101 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2088 1541 4.9 %RANDOM
Rwork0.17 ---
obs0.172 31447 99.85 %-
all-31447 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 112.45 Å2 / Biso mean: 35.67 Å2 / Biso min: 16.71 Å2
Baniso -1Baniso -2Baniso -3
1--0.47 Å2-0 Å20 Å2
2--1.09 Å20 Å2
3----0.62 Å2
Refinement stepCycle: LAST / Resolution: 1.76→31.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1880 0 8 201 2089
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0192024
X-RAY DIFFRACTIONr_bond_other_d0.0010.022035
X-RAY DIFFRACTIONr_angle_refined_deg1.7651.982750
X-RAY DIFFRACTIONr_angle_other_deg0.85734716
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0815260
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.48624.89898
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.33315414
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.6691514
X-RAY DIFFRACTIONr_chiral_restr0.1110.2322
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022242
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02428
X-RAY DIFFRACTIONr_mcbond_it2.3682.431952
X-RAY DIFFRACTIONr_mcbond_other2.3322.422949
X-RAY DIFFRACTIONr_mcangle_it3.4893.6121192
LS refinement shellResolution: 1.762→1.807 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.27 113 -
Rwork0.25 2190 -
all-2303 -
obs-2303 99.57 %
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)
11.9638-0.0258-2.58320.14060.09393.5321-0.0636-0.0664-0.099-0.05570.00370.02670.07550.12940.05990.0371-0.0142-0.02290.064-0.01930.070234.2912.030923.7057
22.96271.6201-0.28671.0108-0.00630.2795-0.06090.0996-0.1958-0.04930.0358-0.0740.0181-0.01450.02510.02820.01580.00780.0158-0.00230.089712.90621.683939.3574
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 118
2X-RAY DIFFRACTION2B3 - 116

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