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- PDB-4ham: Crystal Structure of Transcriptional Antiterminator from Listeria... -

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Basic information

Entry
Database: PDB / ID: 4ham
TitleCrystal Structure of Transcriptional Antiterminator from Listeria monocytogenes EGD-e
ComponentsLmo2241 protein
KeywordsTRANSCRIPTION / Structural Genomics / PSI-Biology / Midwest Center for Structural Genomics / MCSG / winged helix-turn-helix / four helix bundle / transcriptional regulator
Function / homology
Function and homology information


DNA-binding transcription factor activity
Similarity search - Function
Helix Hairpins - #100 / 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 - #100 / 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
Biological speciesListeria monocytogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.905 Å
AuthorsKim, Y. / Chhor, G. / Endres, M. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal Structure of Transcriptional Antiterminator from Listeria monocytogenes EGD-e
Authors: Kim, Y. / Chhor, G. / Endres, M. / Joachimiak, A.
History
DepositionSep 27, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 17, 2012Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Lmo2241 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,6177
Polymers15,0561
Non-polymers5616
Water1,71195
1
A: Lmo2241 protein
hetero molecules

A: Lmo2241 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,23314
Polymers30,1122
Non-polymers1,12112
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_566x,-y+1,-z+11
Buried area6400 Å2
ΔGint-91 kcal/mol
Surface area15790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.122, 92.152, 91.999
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-367-

HOH

Detailsdimer is formed by: x,y,z and x,-y+1,-z+1

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Components

#1: Protein Lmo2241 protein / Transcriptional antiterminator BglG


Mass: 15056.078 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Listeria monocytogenes (bacteria) / Strain: EGD-e / Gene: lmo2241 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 magic / References: UniProt: Q8Y535
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 95 / 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: 2.61 Å3/Da / Density % sol: 52.92 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 2.0 M ammonium sulfate, 0.1 M HEPES pH 7.5, 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: 0.97935 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 18, 2012 / Details: mirrors
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97935 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. all: 12529 / Num. obs: 12529 / % possible obs: 98.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.6 % / Biso Wilson estimate: 28.4 Å2 / Rsym value: 0.087 / Net I/σ(I): 9.2
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 4.6 % / Mean I/σ(I) obs: 2.2 / Num. unique all: 607 / Rsym value: 0.561 / % possible all: 99.5

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
HKL-3000data collection
HKL-3000phasing
PHENIXmodel building
PHENIX(phenix.refine: 1.8.1_1161)refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.905→32.248 Å / SU ML: 0.19 / Isotropic thermal model: mixed / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 20.93 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.216 1221 9.97 %random
Rwork0.173 ---
all0.177 12249 --
obs0.177 12249 96.26 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 33.9 Å2
Refinement stepCycle: LAST / Resolution: 1.905→32.248 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1054 0 34 95 1183
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061180
X-RAY DIFFRACTIONf_angle_d0.8541596
X-RAY DIFFRACTIONf_dihedral_angle_d15.344465
X-RAY DIFFRACTIONf_chiral_restr0.061182
X-RAY DIFFRACTIONf_plane_restr0.003207
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
1.9051-1.98140.25411240.22181145126992
1.9814-2.07150.23111340.18621211134596
2.0715-2.18070.25221340.16911209134397
2.1807-2.31730.2271350.16581222135797
2.3173-2.49620.25241350.17241224135997
2.4962-2.74730.22051380.18011233137198
2.7473-3.14450.22921390.17681248138797
3.1445-3.96060.20091390.16441252139197
3.9606-32.2530.19291430.17011284142795
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)
13.61670.12840.46822.04712.12762.19160.2654-0.1750.0432-0.338-0.50050.15220.02210.5765-0.02260.3477-0.00190.03960.29130.0520.318736.517828.908744.148
23.13120.018-0.82390.55480.31310.61570.04370.17750.6054-0.13330.03830.052-0.1556-0.1145-0.07430.2086-0.02010.00720.19610.01990.206933.457832.369150.3781
32.1025-0.1058-0.00041.7504-0.46750.1225-0.0661-0.0892-0.00950.21380.1060.1817-0.04760.0296-0.04120.2519-0.01740.00230.2782-0.00820.189131.189723.320559.9162
42.82792.1133-1.34144.07240.28811.4695-0.1394-0.335-0.4655-0.1142-0.1006-0.02630.29480.32080.05660.1732-0.00180.00790.22280.03010.193643.625121.391150.1312
51.2436-2.1648-1.24963.74612.26891.6970.1415-0.33040.63980.05750.1245-0.5355-0.54970.4953-0.09730.2126-0.0267-0.03060.2601-0.02230.275943.272732.452455.4082
61.5994-0.8580.8043.2649-2.05561.969-0.1652-0.15320.39790.2409-0.0325-0.7592-0.05540.14610.08250.21470.01120.00630.278-0.01010.164938.57527.678864.283
70.3282-0.60670.57426.5356-1.15310.987-0.28970.15890.33941.875-0.44271.792-0.9068-1.3771-0.59140.69570.17070.24090.72190.0320.593827.18535.8965.7999
80.68310.43940.2591.7484-2.56554.8315-0.0849-0.09770.2240.4385-0.1588-0.3516-0.34510.33680.05150.25860.0001-0.01570.1587-0.01110.270728.863850.446848.6727
90.46530.4731-0.60863.0094-1.56521.1261-0.09750.3786-0.1527-0.55040.29980.55790.5298-0.5003-0.12690.27-0.041-0.05140.23450.01660.329518.817441.949541.3354
100.0285-0.00260.05410.112-0.08180.1104-0.2305-0.2654-0.45421.1258-0.0182-0.33641.03960.0440.13390.75120.0520.06840.36850.00180.521218.674420.556254.7818
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid -2 through 11 )
2X-RAY DIFFRACTION2chain 'A' and (resid 12 through 26 )
3X-RAY DIFFRACTION3chain 'A' and (resid 27 through 37 )
4X-RAY DIFFRACTION4chain 'A' and (resid 38 through 48 )
5X-RAY DIFFRACTION5chain 'A' and (resid 49 through 61 )
6X-RAY DIFFRACTION6chain 'A' and (resid 62 through 75 )
7X-RAY DIFFRACTION7chain 'A' and (resid 76 through 84 )
8X-RAY DIFFRACTION8chain 'A' and (resid 85 through 104 )
9X-RAY DIFFRACTION9chain 'A' and (resid 105 through 124 )
10X-RAY DIFFRACTION10chain 'A' and (resid 125 through 131 )

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