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- PDB-3bil: Crystal structure of a probable LacI family transcriptional regul... -

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Basic information

Entry
Database: PDB / ID: 3bil
TitleCrystal structure of a probable LacI family transcriptional regulator from Corynebacterium glutamicum
ComponentsProbable LacI-family transcriptional regulator
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / PSI-2 / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC / DNA-binding / Transcription / Transcription regulation
Function / homology
Function and homology information


regulation of DNA-templated transcription / DNA binding
Similarity search - Function
LacI-type HTH domain / Bacterial regulatory proteins, lacI family / LacI-type HTH domain profile. / helix_turn _helix lactose operon repressor / Periplasmic binding protein / Periplasmic binding protein domain / Lambda repressor-like, DNA-binding domain superfamily / Response regulator / Periplasmic binding protein-like I / Rossmann fold ...LacI-type HTH domain / Bacterial regulatory proteins, lacI family / LacI-type HTH domain profile. / helix_turn _helix lactose operon repressor / Periplasmic binding protein / Periplasmic binding protein domain / 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
Transcriptional regulators
Similarity search - Component
Biological speciesCorynebacterium glutamicum ATCC 13032 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.5 Å
AuthorsBonanno, J.B. / Freeman, J. / Bain, K.T. / Mendoza, M. / Ozyurt, S. / Smith, D. / Wasserman, S. / Sauder, J.M. / Burley, S.K. / Almo, S.C. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Crystal structure of a probable LacI family transcriptional regulator from Corynebacterium glutamicum.
Authors: Bonanno, J.B. / Freeman, J. / Bain, K.T. / Mendoza, M. / Ozyurt, S. / Smith, D. / Wasserman, S. / Sauder, J.M. / Burley, S.K. / Almo, S.C.
History
DepositionNov 30, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 11, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Nov 14, 2018Group: Data collection / Structure summary / Category: audit_author / Item: _audit_author.identifier_ORCID
Revision 1.4Feb 3, 2021Group: Database references / Structure summary
Category: audit_author / citation_author / struct_ref_seq_dif
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _struct_ref_seq_dif.details
Revision 1.5Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Probable LacI-family transcriptional regulator
B: Probable LacI-family transcriptional regulator


Theoretical massNumber of molelcules
Total (without water)73,9862
Polymers73,9862
Non-polymers00
Water36020
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.209, 54.338, 78.650
Angle α, β, γ (deg.)90.000, 94.190, 90.000
Int Tables number4
Space group name H-MP1211
DetailsAUTHORS STATE THAT THE DIMERIC ASSEMBLY OF THE BIOLOGICAL UNIT THAT IS SHOWN IN REMARK 350 IS PUTATIVE AT THE TIME OF DEPOSITION.

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Components

#1: Protein Probable LacI-family transcriptional regulator


Mass: 36992.832 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Corynebacterium glutamicum ATCC 13032 (bacteria)
Species: Corynebacterium glutamicum / Strain: DSM 20300 / JCM 1318 / LMG 3730 / NCIMB 10025 / Gene: ccpA1, Cgl1367, cg1547 / Plasmid: modified pET26 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q8NQQ9
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 20 / 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: 2.17 Å3/Da / Density % sol: 43.22 %
Crystal growTemperature: 294 K / Method: vapor diffusion / pH: 7
Details: 30% PEG 3350, 150mM Ammonium fluoride, pH 7.0, VAPOR DIFFUSION, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.97958 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Nov 17, 2007
RadiationMonochromator: diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97958 Å / Relative weight: 1
ReflectionResolution: 2.5→29.922 Å / Num. all: 22200 / Num. obs: 22200 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.1 % / Biso Wilson estimate: 55.9 Å2 / Rmerge(I) obs: 0.13 / Rsym value: 0.13 / Net I/σ(I): 16.6
Reflection shellResolution: 2.5→2.64 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.616 / Mean I/σ(I) obs: 2.3 / Num. unique all: 3201 / Rsym value: 0.616 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
SCALAdata scaling
REFMACrefinement
PDB_EXTRACT3.004data extraction
MAR345CCDdata collection
MOSFLMdata reduction
SHELXCDphasing
SHELXEmodel building
RefinementMethod to determine structure: SAD / Resolution: 2.5→20 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.892 / SU B: 9.696 / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.457 / ESU R Free: 0.302 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.278 1116 5 %RANDOM
Rwork0.218 ---
obs0.221 22149 99.96 %-
all-22149 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 47.336 Å2
Baniso -1Baniso -2Baniso -3
1-3.94 Å20 Å20.13 Å2
2---1.95 Å20 Å2
3----1.97 Å2
Refinement stepCycle: LAST / Resolution: 2.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3822 0 0 20 3842
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0223880
X-RAY DIFFRACTIONr_angle_refined_deg1.6981.9715280
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.855510
X-RAY DIFFRACTIONr_dihedral_angle_2_deg44.58426.184152
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.34415644
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.2141510
X-RAY DIFFRACTIONr_chiral_restr0.1120.2650
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022858
X-RAY DIFFRACTIONr_nbd_refined0.2350.21669
X-RAY DIFFRACTIONr_nbtor_refined0.3070.22681
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1680.2132
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2020.212
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0170.21
X-RAY DIFFRACTIONr_mcbond_it3.06222603
X-RAY DIFFRACTIONr_mcangle_it4.62234126
X-RAY DIFFRACTIONr_scbond_it3.15321370
X-RAY DIFFRACTIONr_scangle_it4.70531152
LS refinement shellResolution: 2.5→2.564 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.401 68 -
Rwork0.302 1515 -
all-1583 -
obs-1515 100 %

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