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- PDB-4i76: Crystal structure of transcriptional regulator TM1030 with octanol -

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Basic information

Entry
Database: PDB / ID: 4i76
TitleCrystal structure of transcriptional regulator TM1030 with octanol
ComponentsTranscriptional regulator, TetR familyTranscriptional regulation
KeywordsTranscription Regulator / Structural Genomics / PSI-Biology / Midwest Center for Structural Genomics / MCSG / PFAM TetR_N / helix-turn-helix / Transcriptional regulator / DNA Binding
Function / homology
Function and homology information


transcription cis-regulatory region binding / DNA-binding transcription factor activity / regulation of DNA-templated transcription
Similarity search - Function
: / Tetracyclin repressor-like, C-terminal domain / DNA-binding HTH domain, TetR-type, conserved site / TetR-type HTH domain signature. / Tetracycline Repressor, domain 2 / Tetracyclin repressor-like, C-terminal domain superfamily / Tetracycline Repressor; domain 2 / Bacterial regulatory proteins, tetR family / DNA-binding HTH domain, TetR-type / TetR-type HTH domain profile. ...: / Tetracyclin repressor-like, C-terminal domain / DNA-binding HTH domain, TetR-type, conserved site / TetR-type HTH domain signature. / Tetracycline Repressor, domain 2 / Tetracyclin repressor-like, C-terminal domain superfamily / Tetracycline Repressor; domain 2 / Bacterial regulatory proteins, tetR family / DNA-binding HTH domain, TetR-type / TetR-type HTH domain profile. / Homeodomain-like / Homeobox-like domain superfamily / Arc Repressor Mutant, subunit A / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
OCTAN-1-OL / Transcriptional regulator, TetR family
Similarity search - Component
Biological speciesThermotoga maritima MSB8 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsKoclega, K.D. / Chruszcz, M. / Cooper, D.R. / Petkowski, J.J. / Tkaczuk, K.L. / Joachimiak, A. / Minor, W. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal structure of transcriptional regulator TM1030 with octanol
Authors: Koclega, K.D. / Chruszcz, M. / Cooper, D.R. / Petkowski, J.J. / Tkaczuk, K.L. / Joachimiak, A. / Minor, W.
History
DepositionNov 30, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 2, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software
Revision 1.2Apr 13, 2022Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / database_2 / 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 / _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
Revision 1.3Sep 20, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.4Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Transcriptional regulator, TetR family
B: Transcriptional regulator, TetR family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,2657
Polymers48,8182
Non-polymers4475
Water3,711206
1
A: Transcriptional regulator, TetR family
hetero molecules

A: Transcriptional regulator, TetR family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,58710
Polymers48,8182
Non-polymers7698
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area4850 Å2
ΔGint-32 kcal/mol
Surface area20280 Å2
MethodPISA
2
B: Transcriptional regulator, TetR family
hetero molecules

B: Transcriptional regulator, TetR family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,9424
Polymers48,8182
Non-polymers1242
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area2580 Å2
ΔGint-10 kcal/mol
Surface area21660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.911, 50.429, 88.098
Angle α, β, γ (deg.)90.000, 129.150, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: THR / End label comp-ID: THR / Refine code: 0 / Auth seq-ID: 3 - 199 / Label seq-ID: 5 - 201

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
DetailsEach monomer in the ASU is one half of two distinct dimers

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Components

#1: Protein Transcriptional regulator, TetR family / Transcriptional regulation


Mass: 24409.078 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima MSB8 (bacteria) / Strain: ATCC 43589 / MSB8 / DSM 3109 / JCM 10099 / Gene: TM1030, TM_1030 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-GOLD (DE3) / References: UniProt: Q9X0C0
#2: Chemical ChemComp-OC9 / OCTAN-1-OL / 1-Octanol


Mass: 130.228 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 206 / 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: 2.15 Å3/Da / Density % sol: 42.82 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7.5
Details: 30%w/v PEG 2K MME, 0.1M KSCN, 6%v/v octanol, pH 7.5, VAPOR DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 23321 / % possible obs: 95.5 % / Redundancy: 4.5 % / Rmerge(I) obs: 0.12 / Χ2: 2.301 / Net I/σ(I): 7.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.1-2.183.30.37817680.882173.5
2.18-2.263.60.33121420.956187.8
2.26-2.374.10.32123390.985196.1
2.37-2.494.50.27623951.203199.3
2.49-2.654.80.24424241.2671100
2.65-2.8550.19224121.4581100
2.85-3.1450.14724591.879199.8
3.14-3.594.90.11224242.716199.4
3.59-4.524.80.08424393.57199.6
4.52-504.80.08425196.265199.2

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.11data extraction
Blu-IceIcedata collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2ID6

2id6


Resolution: 2.1→26.99 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.908 / WRfactor Rfree: 0.2412 / WRfactor Rwork: 0.1844 / Occupancy max: 1 / Occupancy min: 0.41 / FOM work R set: 0.833 / SU B: 6.033 / SU ML: 0.16 / SU R Cruickshank DPI: 0.2858 / SU Rfree: 0.2244 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.286 / ESU R Free: 0.224 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2562 1200 5.1 %RANDOM
Rwork0.1931 ---
obs0.1963 23318 95.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 105.95 Å2 / Biso mean: 30.2997 Å2 / Biso min: 11.07 Å2
Baniso -1Baniso -2Baniso -3
1-0.95 Å20 Å2-0.14 Å2
2--0.14 Å20 Å2
3----0.42 Å2
Refinement stepCycle: LAST / Resolution: 2.1→26.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3293 0 30 206 3529
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0193455
X-RAY DIFFRACTIONr_bond_other_d0.0050.023373
X-RAY DIFFRACTIONr_angle_refined_deg1.6371.994631
X-RAY DIFFRACTIONr_angle_other_deg1.17237776
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5365412
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.7124.211171
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.71815630
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.9461521
X-RAY DIFFRACTIONr_chiral_restr0.1010.2496
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023803
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02794
Refine LS restraints NCS

Ens-ID: 1 / Number: 11437 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.16 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.101→2.156 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.341 71 -
Rwork0.254 1196 -
all-1267 -
obs--70.43 %

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