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- PDB-4o5a: The crystal structure of a LacI family transcriptional regulator ... -

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Basic information

Entry
Database: PDB / ID: 4o5a
TitleThe crystal structure of a LacI family transcriptional regulator from Bifidobacterium animalis subsp. lactis DSM 10140
ComponentsLacI family transcription regulator
KeywordsTRANSCRIPTION REGULATOR / structural genomics / PSI-Biology / protein structure initiative / midwest center for structural genomics / MCSG
Function / homologyResponse regulator / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / :
Function and homology information
Biological speciesBifidobacterium animalis subsp. lactis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.777 Å
AuthorsTan, K. / Li, H. / Endres, M. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The crystal structure of a LacI family transcriptional regulator from Bifidobacterium animalis subsp. lactis DSM 10140.
Authors: Tan, K. / Li, H. / Endres, M. / Joachimiak, A.
History
DepositionDec 19, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 15, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 26, 2025Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: LacI family transcription regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,2926
Polymers37,8241
Non-polymers4685
Water3,513195
1
A: LacI family transcription regulator
hetero molecules

A: LacI family transcription regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,58512
Polymers75,6482
Non-polymers93710
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area5030 Å2
ΔGint-61 kcal/mol
Surface area22350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.214, 88.913, 60.524
Angle α, β, γ (deg.)90.00, 94.65, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-504-

HOH

21A-673-

HOH

DetailsExperimentally unknown. It is predicted that the chain A and its symmetry-related molecule by an operator (-x+1,y,-z+1) form a dimer.

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Components

#1: Protein LacI family transcription regulator


Mass: 37823.988 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bifidobacterium animalis subsp. lactis (bacteria)
Strain: DSM 10140 / Gene: Balat_0153 / Plasmid: pMCSG68 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)magic / References: UniProt: C6AGK7
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 195 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.31 Å3/Da / Density % sol: 46.8 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2M Ammonium Sulfate, 0.1M Tris:HCl, 25% (w/v) PEG3350, pH 8.5, 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: 0.97921 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Nov 27, 2013 / Details: mirror
RadiationMonochromator: Si 111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97921 Å / Relative weight: 1
ReflectionResolution: 1.78→27 Å / Num. all: 32091 / Num. obs: 32091 / % possible obs: 97.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -5 / Redundancy: 4.7 % / Biso Wilson estimate: 23.31 Å2 / Rmerge(I) obs: 0.101 / Net I/σ(I): 33.4
Reflection shellResolution: 1.78→1.81 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.751 / Mean I/σ(I) obs: 2.5 / Num. unique all: 1576 / % possible all: 96.9

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
SHELXDphasing
MLPHAREphasing
DMmodel building
ARPmodel building
WARPmodel building
HKL-3000phasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
HKL-3000data reduction
HKL-3000data scaling
DMphasing
RefinementMethod to determine structure: SAD / Resolution: 1.777→26.967 Å / SU ML: 0.18 / σ(F): 1.36 / Phase error: 21.38 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1964 1616 5.04 %random
Rwork0.1655 ---
obs0.1671 32085 96.97 %-
all-32085 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.777→26.967 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2038 0 28 195 2261
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062150
X-RAY DIFFRACTIONf_angle_d1.0922930
X-RAY DIFFRACTIONf_dihedral_angle_d12.749804
X-RAY DIFFRACTIONf_chiral_restr0.074343
X-RAY DIFFRACTIONf_plane_restr0.005377
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7773-1.82960.33851180.25112441X-RAY DIFFRACTION94
1.8296-1.88870.27281350.22052526X-RAY DIFFRACTION96
1.8887-1.95610.2431270.18612530X-RAY DIFFRACTION97
1.9561-2.03440.21430.17072518X-RAY DIFFRACTION97
2.0344-2.1270.22711260.1732534X-RAY DIFFRACTION97
2.127-2.23910.20021330.17162530X-RAY DIFFRACTION97
2.2391-2.37930.19861450.17292546X-RAY DIFFRACTION98
2.3793-2.56290.23251410.1732564X-RAY DIFFRACTION98
2.5629-2.82050.19641320.17312559X-RAY DIFFRACTION98
2.8205-3.22810.21471410.17222602X-RAY DIFFRACTION98
3.2281-4.06480.15641430.14562578X-RAY DIFFRACTION99
4.0648-26.96980.17731320.14932541X-RAY DIFFRACTION95
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)
12.4404-0.4345-0.64823.16050.64543.9288-0.09480.32770.1167-0.29750.03670.4609-0.1666-0.5430.04890.1761-0.0299-0.030.23360.04640.240226.750865.772419.2812
22.0729-0.02770.0631.3247-0.58494.3184-0.05760.2073-0.0459-0.05090.00740.12490.007-0.17410.03550.1209-0.02820.00250.1289-0.03170.144124.391735.189714.8135
30.4955-0.1375-0.00595.5637-0.02790.2636-0.03950.12650.084-0.62180.0039-0.3029-0.07980.10740.03160.2545-0.04810.03950.22440.00610.167936.951350.870615.1787
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 63 through 171 )
2X-RAY DIFFRACTION2chain 'A' and (resid 172 through 289 )
3X-RAY DIFFRACTION3chain 'A' and (resid 290 through 341 )

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