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- PDB-4r9n: DeoR family transcriptional regulator from Listeria monocytogenes. -

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Basic information

Entry
Database: PDB / ID: 4r9n
TitleDeoR family transcriptional regulator from Listeria monocytogenes.
ComponentsLmo0547 protein
KeywordsTRANSCRIPTION / structural genomics / APC106822 / DeoR family / transcriptional regulator / sugar-binding / PSI-Biology / Midwest Center for Structural Genomics / MCSG
Function / homologySugar-binding domain, putative / Putative sugar-binding domain / Rossmann fold - #1360 / NagB/RpiA transferase-like / carbohydrate binding / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / Lmo0547 protein
Function and homology information
Biological speciesListeria monocytogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.869 Å
AuthorsOsipiuk, J. / Wu, R. / Clancy, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: DeoR family transcriptional regulator from Listeria monocytogenes.
Authors: Osipiuk, J. / Wu, R. / Clancy, S. / Joachimiak, A.
History
DepositionSep 5, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 17, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Lmo0547 protein


Theoretical massNumber of molelcules
Total (without water)28,6091
Polymers28,6091
Non-polymers00
Water2,522140
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)52.818, 52.818, 172.283
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Lmo0547 protein


Mass: 28608.670 Da / Num. of mol.: 1 / Fragment: Putative sugar-binding domain / Mutation: 61..311 protein fragment
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Listeria monocytogenes (bacteria) / Strain: ATCC BAA-679 / EGD-e / Gene: lmo0547 / Plasmid: pMCSG68 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8Y9I1
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 140 / 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: 2.1 Å3/Da / Density % sol: 41.43 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 0.2 M sodium chloride, 0.1 M sodium acetate buffer, 20% PEG-8000, pH 4.5, 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: 0.9792 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 20, 2013
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: 1.869→39 Å / Num. all: 21169 / Num. obs: 21169 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9 % / Biso Wilson estimate: 33.1 Å2 / Rmerge(I) obs: 0.114 / Χ2: 1.493 / Net I/σ(I): 8.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allΧ2% possible all
1.869-1.97.30.8862.3310210.833100
1.9-1.948.20.73410280.858100
1.94-1.979.10.67610200.869100
1.97-2.019.60.61310340.925100
2.01-2.069.50.48110290.961100
2.06-2.119.50.39310601.024100
2.11-2.169.50.36110151.027100
2.16-2.229.50.29610471.111100
2.22-2.289.60.25110391.141100
2.28-2.369.40.2110471.226100
2.36-2.449.50.18410351.236100
2.44-2.549.50.16310731.39100
2.54-2.659.40.13810501.511100
2.65-2.799.40.12910571.658100
2.79-2.979.30.10810551.818100
2.97-3.29.20.09510621.95100
3.2-3.528.80.08110941.998100
3.52-4.038.30.07310812.28599.7
4.03-5.078.10.05711142.64799.5
5.07-507.50.06312083.53997.7

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.8.0073refinement
PDB_EXTRACT3.15data extraction
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
SHELXCDphasing
SHELXDphasing
MLPHAREphasing
DMphasing
SOLVEphasing
RESOLVEphasing
HKL-3000phasing
RefinementMethod to determine structure: SAD / Resolution: 1.869→39 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.936 / SU B: 6.714 / SU ML: 0.099 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.153 / ESU R Free: 0.146 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2312 1061 5 %RANDOM
Rwork0.1815 ---
all0.1839 20024 --
obs0.1839 20024 99.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 84.77 Å2 / Biso mean: 31.016 Å2 / Biso min: 13.4 Å2
Baniso -1Baniso -2Baniso -3
1-0.61 Å2-0 Å2-0 Å2
2--0.61 Å20 Å2
3----1.23 Å2
Refinement stepCycle: LAST / Resolution: 1.869→39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1937 0 0 140 2077
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0192105
X-RAY DIFFRACTIONr_bond_other_d0.0010.022073
X-RAY DIFFRACTIONr_angle_refined_deg1.8311.9882871
X-RAY DIFFRACTIONr_angle_other_deg0.90234824
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1015283
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.44925.93896
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.57815395
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.987157
X-RAY DIFFRACTIONr_chiral_restr0.1120.2334
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022377
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02434
X-RAY DIFFRACTIONr_mcbond_it2.0442.0911028
X-RAY DIFFRACTIONr_mcbond_other2.0412.0891027
X-RAY DIFFRACTIONr_mcangle_it3.0343.1151291
LS refinement shellResolution: 1.869→1.917 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.27 79 -
Rwork0.229 1423 -
all-1502 -
obs-1502 99.47 %
Refinement TLS params.Method: refined / Origin x: 1.2996 Å / Origin y: 23.3118 Å / Origin z: 11.2123 Å
111213212223313233
T0.0306 Å2-0.0106 Å20.0151 Å2-0.0224 Å2-0.0096 Å2--0.0169 Å2
L0.5899 °2-0.3977 °20.2326 °2-0.5438 °2-0.1129 °2--2.1447 °2
S-0.0032 Å °0.0483 Å °0.0361 Å °-0.014 Å °0.0296 Å °-0.0728 Å °-0.1626 Å °0.1109 Å °-0.0264 Å °

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