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- PDB-4kwa: Crystal structure of a putative transcriptional regulator from Sa... -

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Basic information

Entry
Database: PDB / ID: 4kwa
TitleCrystal structure of a putative transcriptional regulator from Saccharomonospora viridis in complex with choline
ComponentsTranscriptional regulator
KeywordsTRANSCRIPTION REGULATOR / Structural Genomics / PSI-Biology / Midwest Center for Structural Genomics / MCSG / TetR family
Function / homology
Function and homology information


transcription cis-regulatory region binding / DNA-binding transcription factor activity
Similarity search - Function
BetI-type transcriptional repressor, C-terminal / BetI-type transcriptional repressor, C-terminal / : / Cro/C1-type HTH domain profile. / Cro/C1-type helix-turn-helix domain / 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 ...BetI-type transcriptional repressor, C-terminal / BetI-type transcriptional repressor, C-terminal / : / Cro/C1-type HTH domain profile. / Cro/C1-type helix-turn-helix domain / 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. / Lambda repressor-like, DNA-binding domain superfamily / Homeobox-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
BETA-MERCAPTOETHANOL / CHOLINE ION / Transcriptional regulator
Similarity search - Component
Biological speciesSaccharomonospora viridis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsFilippova, E.V. / Minasov, G. / Shuvalova, L. / Kiryukhina, O. / Endres, M. / Joachimiak, A. / Anderson, W.F. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal structure of a putative transcriptional regulator from Saccharomonospora viridis in complex with choline
Authors: Filippova, E.V. / Minasov, G. / Shuvalova, L. / Kiryukhina, O. / Endres, M. / Joachimiak, A. / Anderson, W.F. / Midwest Center for Structural Genomics (MCSG)
History
DepositionMay 23, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 12, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.2Sep 20, 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_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Dec 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
B: Transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,2247
Polymers45,7972
Non-polymers4275
Water3,351186
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4620 Å2
ΔGint4 kcal/mol
Surface area17720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.901, 77.355, 109.830
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Transcriptional regulator


Mass: 22898.748 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomonospora viridis (bacteria) / Strain: DSM 43017 / Gene: Svir_16270 / Plasmid: pMCSG68 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)magic / References: UniProt: C7MT25
#2: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-CHT / CHOLINE ION


Mass: 104.171 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H14NO
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 186 / 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: 1.99 Å3/Da / Density % sol: 38.18 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2 M Sodium iodide, 0.1 M Bis Tris propane, 20% w/v PEG 3350, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.987856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 22, 2013 / Details: MIRROR
RadiationMonochromator: SI-CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987856 Å / Relative weight: 1
ReflectionResolution: 1.8→40 Å / Num. all: 34150 / Num. obs: 34150 / % possible obs: 98.7 % / Observed criterion σ(I): -3 / Redundancy: 5.2 % / Biso Wilson estimate: 41.5 Å2 / Rmerge(I) obs: 0.052 / Net I/σ(I): 41.05
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.63 / Mean I/σ(I) obs: 3.1 / Num. unique all: 1689 / % possible all: 100

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Processing

Software
NameVersionClassification
Blu-IceMaxdata collection
PHASERphasing
REFMAC5.7.0032refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ICH

4ich


Resolution: 1.8→33.83 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.936 / SU B: 7.333 / SU ML: 0.104 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.157 / ESU R Free: 0.155 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25946 1711 5 %RANDOM
Rwork0.19946 ---
obs0.20236 32382 98.56 %-
all-32382 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 38.855 Å2
Baniso -1Baniso -2Baniso -3
1-1.38 Å2-0 Å2-0 Å2
2--0.61 Å20 Å2
3----2 Å2
Refine analyzeLuzzati coordinate error obs: 0.2 Å
Refinement stepCycle: LAST / Resolution: 1.8→33.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3171 0 26 186 3383
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0193284
X-RAY DIFFRACTIONr_bond_other_d0.0010.023216
X-RAY DIFFRACTIONr_angle_refined_deg2.0181.9454442
X-RAY DIFFRACTIONr_angle_other_deg0.98237309
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.0345389
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.41222.273176
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.31915573
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.0061546
X-RAY DIFFRACTIONr_chiral_restr0.1410.2492
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.023705
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02837
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.802→1.849 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.28 120 -
Rwork0.232 2332 -
obs--97.61 %
Refinement TLS params.Method: refined / Origin x: -21.7108 Å / Origin y: 0.3596 Å / Origin z: -13.5555 Å
111213212223313233
T0.05 Å20.0163 Å2-0.0008 Å2-0.0117 Å20.0048 Å2--0.0246 Å2
L0.5044 °20.0225 °20.0487 °2-0.2195 °2-0.0119 °2--0.5701 °2
S0.1006 Å °-0.0061 Å °-0.0297 Å °-0.0076 Å °-0.0234 Å °-0.0216 Å °-0.0169 Å °-0.007 Å °-0.0772 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1B401 - 482
2X-RAY DIFFRACTION1A401 - 504
3X-RAY DIFFRACTION1B301 - 302
4X-RAY DIFFRACTION1A301 - 303
5X-RAY DIFFRACTION1B94 - 285
6X-RAY DIFFRACTION1A93 - 285

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