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- PDB-6gz2: Crystal Structure of the LeuO Effector Binding Domain -

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Basic information

Entry
Database: PDB / ID: 6gz2
TitleCrystal Structure of the LeuO Effector Binding Domain
ComponentsHTH-type transcriptional regulator LeuO
KeywordsTRANSCRIPTION / LTTR / Transcription Factor
Function / homology
Function and homology information


protein-DNA complex / sequence-specific DNA binding / DNA-binding transcription factor activity / regulation of DNA-templated transcription
Similarity search - Function
LysR, substrate-binding / LysR substrate binding domain / LysR-type HTH domain profile. / Transcription regulator HTH, LysR / Bacterial regulatory helix-turn-helix protein, lysR family / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
MALONATE ION / HTH-type transcriptional regulator LeuO
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.94 Å
AuthorsFragel, S. / Montada, A.M. / Baumann, U. / Schacherl, M. / Schnetz, K.
Funding support Germany, 2items
OrganizationGrant numberCountry
German Research FoundationSCHN371/10-2 Germany
German Research FoundationSCHN371/11-1 Germany
CitationJournal: Nucleic Acids Res. / Year: 2019
Title: Characterization of the pleiotropic LysR-type transcription regulator LeuO of Escherichia coli.
Authors: Fragel, S.M. / Montada, A. / Heermann, R. / Baumann, U. / Schacherl, M. / Schnetz, K.
History
DepositionJul 2, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 5, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 26, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Aug 28, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HTH-type transcriptional regulator LeuO
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,0932
Polymers24,9911
Non-polymers1021
Water52229
1
A: HTH-type transcriptional regulator LeuO
hetero molecules

A: HTH-type transcriptional regulator LeuO
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,1874
Polymers49,9832
Non-polymers2042
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Buried area3210 Å2
ΔGint-15 kcal/mol
Surface area17540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.990, 88.770, 97.190
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z
#4: -x,-y,z
#5: x+1/2,y+1/2,z+1/2
#6: x+1/2,-y+1/2,-z+1/2
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2

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Components

#1: Protein HTH-type transcriptional regulator LeuO


Mass: 24991.340 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: LeuO Effector Binding Domain S120 D mutant orthorhombic form
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: leuO, b0076, JW0075 / Production host: Escherichia coli (E. coli) / References: UniProt: P10151
#2: Chemical ChemComp-MLI / MALONATE ION / Malonic acid


Mass: 102.046 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C3H2O4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 29 / 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: 2.8 Å3/Da / Density % sol: 56.15 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 1.4 M Sodium malonate pH 7.0, 0.1 M Bis-Tris propane pH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: May 25, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.94→54.028 Å / Num. obs: 21191 / % possible obs: 99.8 % / Redundancy: 12.7 % / Biso Wilson estimate: 35.2 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.082 / Rpim(I) all: 0.024 / Rrim(I) all: 0.086 / Net I/σ(I): 19.7
Reflection shellResolution: 1.94→1.97 Å / Redundancy: 11.7 % / Rmerge(I) obs: 1.67 / Num. unique obs: 1039 / CC1/2: 0.77 / Rpim(I) all: 0.505 / Rrim(I) all: 1.747 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.14_3211)refinement
DIALSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.94→54.02 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.44 / Phase error: 29.15
RfactorNum. reflection% reflectionSelection details
Rfree0.2332 1090 5.15 %RANDOM
Rwork0.2093 ---
obs0.2106 21174 99.9 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.94→54.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1643 0 7 29 1679
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051698
X-RAY DIFFRACTIONf_angle_d0.5652304
X-RAY DIFFRACTIONf_dihedral_angle_d12.2551020
X-RAY DIFFRACTIONf_chiral_restr0.044253
X-RAY DIFFRACTIONf_plane_restr0.003296
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9401-2.02840.3631360.35452471X-RAY DIFFRACTION100
2.0284-2.13530.33631340.31462457X-RAY DIFFRACTION100
2.1353-2.26910.29691120.26362504X-RAY DIFFRACTION100
2.2691-2.44430.27291470.24212483X-RAY DIFFRACTION100
2.4443-2.69030.21891330.23812496X-RAY DIFFRACTION100
2.6903-3.07960.27361290.23252519X-RAY DIFFRACTION100
3.0796-3.87980.21321560.19492510X-RAY DIFFRACTION100
3.8798-54.04540.20071430.16872644X-RAY DIFFRACTION100
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)
14.05641.09150.47665.76541.74843.41210.03760.199-1.25720.1130.223-0.61870.3871-0.0493-0.16860.3171-0.049-0.03340.32940.01790.805122.1818-13.361715.5313
24.90513.0111.07788.22735.04584.0917-0.63120.95420.2751-1.16770.44710.9436-0.6208-0.05960.06420.5352-0.0961-0.06670.53850.16390.554915.4529-3.38068.5343
34.9681-1.0131-0.70594.53230.38013.6226-0.03140.05710.8794-0.11240.1469-0.0799-0.3629-0.1331-0.08690.28430.00720.0380.2360.00550.556627.5512.629418.6434
42.54711.5738-0.43625.16271.32341.8703-0.276-0.08820.4717-0.31290.13880.9609-0.2732-0.31230.18310.28050.03070.02320.34080.07560.565917.81233.905618.9038
54.3279-0.3267-0.39097.42480.96244.8396-0.40330.1161-0.18050.13840.18350.94130.4255-0.24050.3110.4293-0.14550.07780.46230.06440.713410.7547-14.690616.1531
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 112 through 152 )
2X-RAY DIFFRACTION2chain 'A' and (resid 153 through 191 )
3X-RAY DIFFRACTION3chain 'A' and (resid 192 through 266 )
4X-RAY DIFFRACTION4chain 'A' and (resid 267 through 294 )
5X-RAY DIFFRACTION5chain 'A' and (resid 297 through 316 )

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