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- PDB-5ufh: The crystal structure of a LacI-type transcription regulator from... -

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Basic information

Entry
Database: PDB / ID: 5ufh
TitleThe crystal structure of a LacI-type transcription regulator from Bifidobacterium animalis subsp. lactis DSM 10140
ComponentsLacI-type transcriptional regulator
KeywordsTRANSCRIPTION / Human Microbiome / structural genomics / PSI-Biology / protein structure initiative / midwest center for structural genomics / MC SG / MCSG
Function / homology
Function and homology information


regulation of DNA-templated transcription / DNA binding
Similarity search - Function
Periplasmic binding protein-like domain / LacI-type HTH domain / Bacterial regulatory proteins, lacI family / LacI-type HTH domain profile. / helix_turn _helix lactose operon repressor / Lambda repressor-like, DNA-binding domain superfamily / Response regulator / Periplasmic binding protein-like I / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NITRATE ION / LacI-type transcriptional regulator
Similarity search - Component
Biological speciesBifidobacterium animalis subsp. lactis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.45 Å
AuthorsTan, K. / Li, H. / Endres, M. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM115586 United States
CitationJournal: To Be Published
Title: The crystal structure of a LacI-type transcription regulator from Bifidobacterium animalis subsp. lactis DSM 10140
Authors: Tan, K. / Li, H. / Endres, M. / Joachimiak, A.
History
DepositionJan 4, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 18, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: LacI-type transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,17424
Polymers38,7181
Non-polymers1,45623
Water3,351186
1
A: LacI-type transcriptional regulator
hetero molecules

A: LacI-type transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,34948
Polymers77,4362
Non-polymers2,91246
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area10830 Å2
ΔGint45 kcal/mol
Surface area20400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.326, 60.171, 67.188
Angle α, β, γ (deg.)90.00, 109.22, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein LacI-type transcriptional regulator


Mass: 38718.133 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bifidobacterium animalis subsp. lactis (strain AD011) (bacteria)
Strain: AD011 / Gene: BLA_0054 / Plasmid: pMCSG73 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)magic / References: UniProt: B8DV56
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical...
ChemComp-NO3 / NITRATE ION / Nitrate


Mass: 62.005 Da / Num. of mol.: 22 / Source method: obtained synthetically / Formula: NO3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 186 / 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: 1.82 Å3/Da / Density % sol: 32.26 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 0.1M Tris:HCl, 6 M Ammonium Nitrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97919 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Oct 5, 2016 / Details: mirror
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97919 Å / Relative weight: 1
ReflectionResolution: 1.45→22.574 Å / Num. obs: 46714 / % possible obs: 96.8 % / Observed criterion σ(I): -3 / Redundancy: 4.9 % / Biso Wilson estimate: 16.3 Å2 / Rmerge(I) obs: 0.088 / Net I/σ(I): 38.9
Reflection shellResolution: 1.45→1.48 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.699 / Mean I/σ(I) obs: 2.1 / CC1/2: 0.74 / % possible all: 93.8

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
RefinementMethod to determine structure: SAD / Resolution: 1.45→22.574 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.51 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1843 2333 5 %
Rwork0.1647 --
obs0.1657 46658 96.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.45→22.574 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2133 0 94 186 2413
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012285
X-RAY DIFFRACTIONf_angle_d1.133083
X-RAY DIFFRACTIONf_dihedral_angle_d15.465795
X-RAY DIFFRACTIONf_chiral_restr0.094334
X-RAY DIFFRACTIONf_plane_restr0.007424
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.45-1.47960.27971200.26862475X-RAY DIFFRACTION92
1.4796-1.51180.23361380.24432540X-RAY DIFFRACTION95
1.5118-1.5470.24591430.22332558X-RAY DIFFRACTION96
1.547-1.58560.24381290.20562565X-RAY DIFFRACTION96
1.5856-1.62850.2321450.20042593X-RAY DIFFRACTION96
1.6285-1.67640.20891350.18962569X-RAY DIFFRACTION96
1.6764-1.73050.19191590.18142568X-RAY DIFFRACTION96
1.7305-1.79230.22051300.17732604X-RAY DIFFRACTION97
1.7923-1.8640.2091170.17172634X-RAY DIFFRACTION97
1.864-1.94880.18291380.1682616X-RAY DIFFRACTION97
1.9488-2.05150.20091530.1582611X-RAY DIFFRACTION97
2.0515-2.17990.16761460.15032605X-RAY DIFFRACTION98
2.1799-2.34810.17671470.15612647X-RAY DIFFRACTION98
2.3481-2.58410.17681350.15882662X-RAY DIFFRACTION98
2.5841-2.95730.17571510.16282665X-RAY DIFFRACTION99
2.9573-3.72320.16981230.14912701X-RAY DIFFRACTION99
3.7232-22.57650.16441240.15682712X-RAY DIFFRACTION97
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)
12.1162-0.24981.2143.4321.25573.39040.0835-0.0302-0.1192-0.07330.2608-0.35590.25950.3414-0.28680.2065-0.0086-0.0380.20890.00120.179723.530427.739921.4684
21.37411.10710.29011.07820.2781.4237-0.10040.09290.0202-0.10480.02150.0235-0.0106-0.00680.07170.1338-0.00250.00340.14610.01830.106622.565349.22846.6563
31.16910.74180.55491.58310.07191.29120.006-0.050.04640.011-0.0449-0.0063-0.0248-0.02910.04890.09760.01050.01160.12570.010.105422.736149.278818.4219
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 63 through 155 )
2X-RAY DIFFRACTION2chain 'A' and (resid 156 through 217 )
3X-RAY DIFFRACTION3chain 'A' and (resid 218 through 344 )

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