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- PDB-3g85: Crystal structure of LacI family transcription regulator from Clo... -

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Basic information

Entry
Database: PDB / ID: 3g85
TitleCrystal structure of LacI family transcription regulator from Clostridium acetobutylicum
ComponentsTranscriptional regulator (LacI family)
KeywordsTRANSCRIPTION REGULATOR / PSI-II / 11230o / Structural Genomics / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC / New York Structural GenomiX Research Consortium / DNA-binding / Transcription / Transcription regulation
Function / homology
Function and homology information


transcription cis-regulatory region binding / DNA-binding transcription factor activity
Similarity search - Function
LacI-type HTH domain signature. / Transcriptional regulator LacI/GalR-like, sensor domain / 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 ...LacI-type HTH domain signature. / Transcriptional regulator LacI/GalR-like, sensor domain / 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 speciesClostridium acetobutylicum ATCC 824 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.84 Å
AuthorsBagaria, A. / Burley, S.K. / Swaminathan, S. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Crystal structure of LacI family transcription regulator from Clostridium acetobutylicum
Authors: Bagaria, A. / Burley, S.K. / Swaminathan, S.
History
DepositionFeb 11, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 24, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Feb 10, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / struct_conn / struct_ref_seq_dif / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _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
Revision 1.3Oct 16, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: Transcriptional regulator (LacI family)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,7092
Polymers32,6161
Non-polymers921
Water3,855214
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Transcriptional regulator (LacI family)
hetero molecules

A: Transcriptional regulator (LacI family)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,4174
Polymers65,2332
Non-polymers1842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_566x,-y+1,-z+11
Buried area2820 Å2
ΔGint-20.7 kcal/mol
Surface area23110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.024, 96.058, 99.976
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-575-

HOH

21A-673-

HOH

31A-706-

HOH

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Components

#1: Protein Transcriptional regulator (LacI family)


Mass: 32616.432 Da / Num. of mol.: 1 / Fragment: UNP residues 58-335
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium acetobutylicum ATCC 824 (bacteria)
Strain: DSM 792 / JCM 1419 / LMG 5710 / VKM B-1787 / Gene: CA_C3553 / Plasmid: pSGX3(BC) / Production host: Escherichia coli (E. coli) / References: UniProt: Q97DC5
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 214 / 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: 2.58 Å3/Da / Density % sol: 52.27 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1M Bis-Tris pH 6.5, 28% w/v PEG MME 2000, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 4, 2009 / Details: Mirrors
RadiationMonochromator: Si(111) channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.84→28.3 Å / Num. all: 26906 / Num. obs: 26906 / Observed criterion σ(I): 0 / Redundancy: 11.5 % / Biso Wilson estimate: 32 Å2 / Rmerge(I) obs: 0.081 / Net I/σ(I): 16.3
Reflection shellResolution: 1.84→1.92 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.403 / Mean I/σ(I) obs: 2.89 / Num. unique all: 2113 / % possible all: 72.3

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Processing

Software
NameVersionClassification
CBASSdata collection
SHELXDphasing
SHARPphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 1.84→28.3 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.939 / SU B: 2.999 / SU ML: 0.091 / Cross valid method: THROUGHOUT / ESU R: 0.127 / ESU R Free: 0.129 / Stereochemistry target values: Engh & Huber
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. Residues listed as missing in Remark 465 are due to lack of electron density. Residues with missing atoms listed in Remark 470 are due to ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. Residues listed as missing in Remark 465 are due to lack of electron density. Residues with missing atoms listed in Remark 470 are due to lack of electron density for side chains and modeled as alanines.
RfactorNum. reflection% reflectionSelection details
Rfree0.23035 1446 5.1 %RANDOM
Rwork0.1839 ---
obs0.18623 26906 96.33 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.961 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20 Å20 Å2
2---0.02 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.84→28.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2111 0 6 214 2331
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0222150
X-RAY DIFFRACTIONr_angle_refined_deg1.4741.9782906
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2275269
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.22825.44490
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.32415403
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.401159
X-RAY DIFFRACTIONr_chiral_restr0.0940.2341
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021567
X-RAY DIFFRACTIONr_nbd_refined0.2160.21057
X-RAY DIFFRACTIONr_nbtor_refined0.3080.21524
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1810.2188
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3080.250
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3030.226
X-RAY DIFFRACTIONr_mcbond_it1.2571.51393
X-RAY DIFFRACTIONr_mcangle_it1.81422192
X-RAY DIFFRACTIONr_scbond_it3.0563853
X-RAY DIFFRACTIONr_scangle_it4.5194.5714
LS refinement shellResolution: 1.84→1.89 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.307 70 -
Rwork0.268 1441 -
obs--71.21 %

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