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- PDB-3e3m: Crystal structure of a LacI family transcriptional regulator from... -

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Basic information

Entry
Database: PDB / ID: 3e3m
TitleCrystal structure of a LacI family transcriptional regulator from Silicibacter pomeroyi
ComponentsTranscriptional regulator, LacI family
KeywordsTRANSCRIPTION / STRUCTURAL GENOMICS / DNA-binding / Plasmid / Transcription regulation / PSI-2 / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC
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
Transcriptional regulator, LacI family
Similarity search - Component
Biological speciesSilicibacter pomeroyi (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.6 Å
AuthorsBonanno, J.B. / Freeman, J. / Bain, K.T. / Iizuka, 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 LacI family transcriptional regulator from Silicibacter pomeroyi
Authors: Bonanno, J.B. / Freeman, J. / Bain, K.T. / Iizuka, M. / Ozyurt, S. / Smith, D. / Wasserman, S. / Sauder, J.M. / Burley, S.K. / Almo, S.C.
History
DepositionAug 7, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 26, 2008Provider: 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 10, 2021Group: Database references / Structure summary / Category: audit_author / citation_author
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID
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: Transcriptional regulator, LacI family
B: Transcriptional regulator, LacI family
C: Transcriptional regulator, LacI family
D: Transcriptional regulator, LacI family


Theoretical massNumber of molelcules
Total (without water)157,6084
Polymers157,6084
Non-polymers00
Water18,6641036
1
A: Transcriptional regulator, LacI family
B: Transcriptional regulator, LacI family


Theoretical massNumber of molelcules
Total (without water)78,8042
Polymers78,8042
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3180 Å2
ΔGint-12 kcal/mol
Surface area20800 Å2
MethodPISA
2
C: Transcriptional regulator, LacI family
D: Transcriptional regulator, LacI family


Theoretical massNumber of molelcules
Total (without water)78,8042
Polymers78,8042
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3220 Å2
ΔGint-12 kcal/mol
Surface area21050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.400, 60.443, 90.766
Angle α, β, γ (deg.)82.910, 76.960, 87.220
Int Tables number1
Space group name H-MP1
Detailsauthors state that the biological unit is probable dimer

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Components

#1: Protein
Transcriptional regulator, LacI family


Mass: 39402.051 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Silicibacter pomeroyi (bacteria) / Gene: SPOA0242 / Plasmid: modified pET26 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q5LKY7
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1036 / 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: 2.03 Å3/Da / Density % sol: 39.47 %
Crystal growTemperature: 294 K / Method: vapor diffusion / pH: 7
Details: 100mM Hepes pH 7.0, 20% PEG 3350, 200mM sodium chloride, 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: Jul 26, 2008
RadiationMonochromator: diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97958 Å / Relative weight: 1
ReflectionResolution: 1.6→87.833 Å / Num. all: 163765 / Num. obs: 156396 / % possible obs: 95.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Biso Wilson estimate: 16.3 Å2 / Rmerge(I) obs: 0.091 / Rsym value: 0.091 / Net I/σ(I): 12.1
Reflection shellResolution: 1.6→1.69 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.502 / Mean I/σ(I) obs: 2.1 / Num. measured all: 88241 / Num. unique all: 22479 / Rsym value: 0.502 / % possible all: 93.8

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Processing

Software
NameVersionClassificationNB
SCALA3.2.19data scaling
REFMACrefinement
PDB_EXTRACT3.006data extraction
MAR345CCDdata collection
MOSFLMdata reduction
SHELXCDphasing
SHELXEmodel building
RefinementMethod to determine structure: SAD / Resolution: 1.6→15 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.94 / WRfactor Rfree: 0.216 / WRfactor Rwork: 0.185 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.879 / SU B: 1.601 / SU ML: 0.057 / SU R Cruickshank DPI: 0.089 / SU Rfree: 0.09 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.089 / ESU R Free: 0.09 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.215 7876 5 %RANDOM
Rwork0.184 ---
obs0.185 156311 95.56 %-
all-163574 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 56.37 Å2 / Biso mean: 22.032 Å2 / Biso min: 6.81 Å2
Baniso -1Baniso -2Baniso -3
1--0.16 Å20.1 Å2-0.11 Å2
2---0.29 Å20.03 Å2
3---0.48 Å2
Refinement stepCycle: LAST / Resolution: 1.6→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8441 0 0 1036 9477
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0228616
X-RAY DIFFRACTIONr_angle_refined_deg1.2931.98211704
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.08551092
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.64323.232393
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.309151458
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.5231585
X-RAY DIFFRACTIONr_chiral_restr0.0810.21333
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.026573
X-RAY DIFFRACTIONr_nbd_refined0.1950.24308
X-RAY DIFFRACTIONr_nbtor_refined0.3110.25954
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1230.2808
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1410.268
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1460.237
X-RAY DIFFRACTIONr_mcbond_it0.7811.55553
X-RAY DIFFRACTIONr_mcangle_it1.2628725
X-RAY DIFFRACTIONr_scbond_it2.18233373
X-RAY DIFFRACTIONr_scangle_it3.3214.52968
LS refinement shellResolution: 1.6→1.641 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.268 581 -
Rwork0.228 10613 -
all-11194 -
obs-10613 93.58 %

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