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- PDB-3jvd: Crystal structure of putative transcription regulation repressor ... -

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Basic information

Entry
Database: PDB / ID: 3jvd
TitleCrystal structure of putative transcription regulation repressor (LACI family) FROM Corynebacterium glutamicum
ComponentsTranscriptional regulators
KeywordsTRANSCRIPTION REGULATOR / STRUCTURAL GENOMICS / PSI-2 / SUGAR BINDING PROTEIN / TRANSCRIPTION REGULATION / PROTEIN STRUCTURE INITIATIVE / NEW YORK SGX RESEARCH CENTER FOR STRUCTURAL GENOMICS / NYSGXRC / DNA-binding / Transcription / UNCHARACTERIZED PROTEIN
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 regulators
Similarity search - Component
Biological speciesCorynebacterium glutamicum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 Å
AuthorsPatskovsky, Y. / Ramagopal, U. / Toro, R. / Foti, R. / Freeman, J. / Do, J. / 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 LACI family protein from Corynebacterium glutamicum
Authors: Patskovsky, Y. / Ramagopal, U. / Toro, R. / Foti, R. / Freeman, J. / Do, J. / Sauder, J.M. / Burley, S.K. / Almo, S.C.
History
DepositionSep 16, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 22, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Nov 21, 2018Group: Data collection / Structure summary / Category: audit_author / Item: _audit_author.identifier_ORCID
Revision 1.3Feb 10, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / struct_ref_seq_dif / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Feb 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 regulators
B: Transcriptional regulators
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,8556
Polymers71,4752
Non-polymers3804
Water1,33374
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3190 Å2
ΔGint-50 kcal/mol
Surface area21280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.970, 91.970, 285.453
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22B
13A
23B
/ NCS ensembles :
ID
1
2
3

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Components

#1: Protein Transcriptional regulators / LACI family protein


Mass: 35737.316 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Corynebacterium glutamicum (bacteria) / Gene: Cgl2044, ycza / Plasmid: MODIFIED PET26 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8NNY3
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 74 / 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: 2.45 Å3/Da / Density % sol: 49.82 %
Crystal growMethod: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1M SODIUM CACODYLATE, PH 6.5, 2M AMMONIUM SULFATE, 200MM SODIUM CHLORIDE, 10% GLYCEROL, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 294K

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9789
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 24, 2009 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 2.3→40 Å / Num. obs: 32657 / % possible obs: 100 % / Observed criterion σ(I): -5 / Redundancy: 11.7 % / Biso Wilson estimate: 50.208 Å2 / Rsym value: 0.104 / Net I/σ(I): 5.1
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 11.6 % / Rmerge(I) obs: 0.95 / Mean I/σ(I) obs: 1 / % possible all: 100

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Processing

Software
NameVersionClassification
SHELXmodel building
REFMAC5.3.0034refinement
HKL-2000data reduction
HKL-2000data scaling
SHELXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.3→20 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.913 / SU B: 7.524 / SU ML: 0.184 / Cross valid method: THROUGHOUT / ESU R: 0.265 / ESU R Free: 0.235 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28353 1032 3.2 %RANDOM
Rwork0.22425 ---
obs0.22604 31506 99.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 60.047 Å2
Baniso -1Baniso -2Baniso -3
1-2.42 Å21.21 Å20 Å2
2--2.42 Å20 Å2
3----3.62 Å2
Refinement stepCycle: LAST / Resolution: 2.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3858 0 21 74 3953
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0223991
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.131.9655439
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2395525
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.59324.855173
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.90515631
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.8961520
X-RAY DIFFRACTIONr_chiral_restr0.0740.2629
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.023032
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1360.31784
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2920.52744
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1430.5236
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1360.335
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.130.59
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.74222631
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it6.7734139
X-RAY DIFFRACTIONr_scbond_it9.17141500
X-RAY DIFFRACTIONr_scangle_it12.60461292
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Refine-ID: X-RAY DIFFRACTION

Ens-IDNumberTypeRms dev position (Å)Weight position
1473tight positional0.350.3
21085tight positional0.560.3
3101tight positional0.260.3
1473tight thermal6.928
21085tight thermal7.838
3101tight thermal3.898
LS refinement shellResolution: 2.303→2.362 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.353 78 -
Rwork0.272 2226 -
obs--99.48 %

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