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- PDB-5k7h: Crystal structure of AibR in complex with the effector molecule i... -

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Basic information

Entry
Database: PDB / ID: 5k7h
TitleCrystal structure of AibR in complex with the effector molecule isovaleryl coenzyme A
ComponentsTranscriptional regulator, TetR family
KeywordsTRANSCRIPTION / TetR like regulator / isovaleryl coenzyme A / regulation
Function / homology
Function and homology information


transcription cis-regulatory region binding / DNA-binding transcription factor activity
Similarity search - Function
HTH-type transcriptional repressor KstR2, C-terminal / Tetracyclin repressor-like, C-terminal 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. / Homeodomain-like ...HTH-type transcriptional repressor KstR2, C-terminal / Tetracyclin repressor-like, C-terminal 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. / Homeodomain-like / Homeobox-like domain superfamily / Arc Repressor Mutant, subunit A / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Isovaleryl-coenzyme A / NICKEL (II) ION / Transcriptional regulator, TetR family
Similarity search - Component
Biological speciesMyxococcus xanthus DK 1622 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsBock, T. / Volz, C. / Mueller, R. / Blankenfeldt, W.
CitationJournal: Nucleic Acids Res. / Year: 2017
Title: The AibR-isovaleryl coenzyme A regulator and its DNA binding site - a model for the regulation of alternative de novo isovaleryl coenzyme A biosynthesis in Myxococcus xanthus.
Authors: Bock, T. / Volz, C. / Hering, V. / Scrima, A. / Muller, R. / Blankenfeldt, W.
History
DepositionMay 26, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Dec 21, 2016Provider: repository / Type: Initial release
Revision 1.1May 3, 2017Group: Database references
Revision 1.2Jan 10, 2024Group: 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 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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.ptnr1_symmetry / _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_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)53,2739
Polymers51,3692
Non-polymers1,9047
Water50428
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4580 Å2
ΔGint-77 kcal/mol
Surface area16180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.780, 89.780, 132.118
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61

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Components

#1: Protein Transcriptional regulator, TetR family


Mass: 25684.354 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Myxococcus xanthus DK 1622 (bacteria) / Gene: MXAN_4263 / Details (production host): pET28a / Production host: Escherichia coli (E. coli) / References: UniProt: Q1D4I5
#2: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-IVC / Isovaleryl-coenzyme A / S-[2-[3-[[(2R)-4-[[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-4-oxidanyl-3-phosphonooxy-oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-3,3-dimethyl-2-oxidanyl-butanoyl]amino]propanoylamino]ethyl] 3-methylbutanethioate


Mass: 851.651 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C26H44N7O17P3S
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 28 / 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: 2.99 Å3/Da / Density % sol: 58.89 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1 M sodium acetate pH 4.6, 2 M sodium chloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9762 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 8, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 2.35→44.89 Å / Num. obs: 25158 / % possible obs: 99.9 % / Redundancy: 9.2 % / Biso Wilson estimate: 47.61 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.072 / Rpim(I) all: 0.025 / Rrim(I) all: 0.076 / Net I/σ(I): 19.9 / Num. measured all: 230876 / Scaling rejects: 8
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique allCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.35-2.438.20.7651998424510.8070.2830.8172.999.6
9.1-44.898.10.03936834540.9980.0140.04250.299.4

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
Aimless0.5.7data scaling
PDB_EXTRACT3.2data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5K7F

5k7f


Resolution: 2.35→44.89 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 24.21 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2346 1231 4.9 %
Rwork0.192 23877 -
obs0.194 25108 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 142.11 Å2 / Biso mean: 64.0344 Å2 / Biso min: 31.46 Å2
Refinement stepCycle: final / Resolution: 2.35→44.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2873 0 193 28 3094
Biso mean--59.32 49.86 -
Num. residues----368
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023056
X-RAY DIFFRACTIONf_angle_d0.5124152
X-RAY DIFFRACTIONf_chiral_restr0.035455
X-RAY DIFFRACTIONf_plane_restr0.002518
X-RAY DIFFRACTIONf_dihedral_angle_d14.6651780
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.3501-2.44420.30681410.270226172758
2.4442-2.55550.24951230.235726622785
2.5555-2.69020.24961340.227826472781
2.6902-2.85870.23171220.228426682790
2.8587-3.07940.28691400.236926372777
3.0794-3.38920.25671670.231126202787
3.3892-3.87930.22681390.187726632802
3.8793-4.88660.18221300.152126592789
4.8866-44.89820.23981350.165927042839

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