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- PDB-3f8l: Crystal Structure of the Effector Domain of PhnF from Mycobacteri... -

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Basic information

Entry
Database: PDB / ID: 3f8l
TitleCrystal Structure of the Effector Domain of PhnF from Mycobacterium smegmatis
ComponentsHTH-type transcriptional repressor phnF
KeywordsTRANSCRIPTION / PhnF / GntR / HutC / regulator / UTRA / DNA-binding / Transcription regulation
Function / homology
Function and homology information


DNA-binding transcription factor activity / DNA binding / cytoplasm
Similarity search - Function
UTRA / UbiC transcription regulator-associated / UTRA domain / : / Chorismate lyase / Chorismate lyase-like / Chorismate pyruvate-lyase/UbiC transcription regulator-associated domain superfamily / Transcription regulator HTH, GntR / Bacterial regulatory proteins, gntR family / GntR-type HTH domain profile. ...UTRA / UbiC transcription regulator-associated / UTRA domain / : / Chorismate lyase / Chorismate lyase-like / Chorismate pyruvate-lyase/UbiC transcription regulator-associated domain superfamily / Transcription regulator HTH, GntR / Bacterial regulatory proteins, gntR family / GntR-type HTH domain profile. / helix_turn_helix gluconate operon transcriptional repressor / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
HTH-type transcriptional repressor PhnF
Similarity search - Component
Biological speciesMycobacterium smegmatis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 Å
AuthorsBusby, J.N. / Gebhard, S. / Cook, G.M. / Baker, E.N. / Lott, S.J. / Money, V.A.
CitationJournal: To be Published
Title: Crystal structure of PhnF, a GntR-family transcription regulator in Mycobacterium smegmatis
Authors: Busby, J.N. / Gebhard, S. / Cook, G.M. / Baker, E.N. / Lott, S.J. / Money, V.A.
History
DepositionNov 12, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 17, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HTH-type transcriptional repressor phnF
B: HTH-type transcriptional repressor phnF
C: HTH-type transcriptional repressor phnF
D: HTH-type transcriptional repressor phnF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,75716
Polymers88,6124
Non-polymers1,14512
Water11,367631
1
A: HTH-type transcriptional repressor phnF
C: HTH-type transcriptional repressor phnF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,9709
Polymers44,3062
Non-polymers6657
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3700 Å2
ΔGint-97.7 kcal/mol
Surface area14150 Å2
MethodPISA
2
B: HTH-type transcriptional repressor phnF
D: HTH-type transcriptional repressor phnF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,7867
Polymers44,3062
Non-polymers4805
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3360 Å2
ΔGint-95.8 kcal/mol
Surface area14660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.558, 78.172, 120.514
Angle α, β, γ (deg.)90.00, 125.42, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Refine code: 4 / Label seq-ID: 1 - 162

Dom-IDAuth asym-IDLabel asym-IDAuth seq-ID
1AA77 - 238
2BB76 - 245

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Components

#1: Protein
HTH-type transcriptional repressor phnF


Mass: 22152.977 Da / Num. of mol.: 4 / Fragment: UNP residues 82-250
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium smegmatis (bacteria) / Strain: Mc2155 / Gene: MSMEG_0650, phnF / Plasmid: pDEST17 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0QQ72
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 631 / 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: 2.48 Å3/Da / Density % sol: 50.43 % / Mosaicity: 0.565 °
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: Micro-seeded into 0.65M ammonium sulfate, 0.1M lithium sulfate, 0.1M tris, pH8.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54179 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Mar 4, 2008
RadiationMonochromator: Ni FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54179 Å / Relative weight: 1
ReflectionResolution: 1.9→25.28 Å / Num. all: 68334 / Num. obs: 68334 / % possible obs: 100 % / Redundancy: 6.8 % / Biso Wilson estimate: 26.8 Å2 / Rmerge(I) obs: 0.069 / Net I/σ(I): 8.5
Reflection shellResolution: 1.9→2 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.491 / Mean I/σ(I) obs: 1.6 / Num. unique all: 9909 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.3.3data scaling
REFMACrefinement
PDB_EXTRACT3.006data extraction
MAR345dtbdata collection
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2P19

2p19


Resolution: 1.9→25.1 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.953 / WRfactor Rfree: 0.196 / WRfactor Rwork: 0.184 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.901 / SU B: 2.381 / SU ML: 0.07 / SU R Cruickshank DPI: 0.13 / SU Rfree: 0.112 / Cross valid method: THROUGHOUT / ESU R: 0.13 / ESU R Free: 0.112 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1959 3456 5.1 %RANDOM
Rwork0.1818 ---
all-68333 --
obs-64877 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 93.52 Å2 / Biso mean: 30.244 Å2 / Biso min: 4.87 Å2
Baniso -1Baniso -2Baniso -3
1-1.23 Å20 Å20.78 Å2
2---0.56 Å20 Å2
3---0.24 Å2
Refinement stepCycle: LAST / Resolution: 1.9→25.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4967 0 62 631 5660
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0225157
X-RAY DIFFRACTIONr_angle_refined_deg1.5971.9857015
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5275666
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.06721.93228
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.95115845
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.2391568
X-RAY DIFFRACTIONr_chiral_restr0.1050.2820
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213876
X-RAY DIFFRACTIONr_mcbond_it0.9131.53260
X-RAY DIFFRACTIONr_mcangle_it1.625224
X-RAY DIFFRACTIONr_scbond_it2.52231897
X-RAY DIFFRACTIONr_scangle_it4.0154.51782
Refine LS restraints NCS

Ens-ID: 1 / Number: 1205 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1AMEDIUM POSITIONAL0.320.5
2BMEDIUM THERMAL1.622
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.277 259 -
Rwork0.255 4751 -
all-5010 -
obs-4751 100 %

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