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- PDB-4af5: Structure of the C. glutamicum AcnR Crystal Form I -

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Basic information

Entry
Database: PDB / ID: 4af5
TitleStructure of the C. glutamicum AcnR Crystal Form I
ComponentsHTH-TYPE TRANSCRIPTIONAL REPRESSOR ACNR COMPND 2
KeywordsTRANSCRIPTION / ACONITASE / TETR REPRESSOR
Function / homology
Function and homology information


transcription cis-regulatory region binding / DNA-binding transcription factor activity / regulation of DNA-templated transcription / magnesium ion binding / DNA binding
Similarity search - Function
: / 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. / Homeobox-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
CITRIC ACID / HTH-type transcriptional repressor AcnR
Similarity search - Component
Biological speciesCORYNEBACTERIUM GLUTAMICUM (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsGarcia-Nafria, J. / Baumgart, M. / Turkenburg, J.P. / Wilkinson, A.J. / Bott, M. / Wilson, K.S.
Citation
Journal: J.Biol.Chem. / Year: 2013
Title: Crystal and Solution Studies Reveal that the Transcriptional Regulator Acnr of Corynebacterium Glutamicum is Regulated by Citrate:Mg2+ Binding to a Non-Canonical Pocket.
Authors: Garcia-Nafria, J. / Baumgart, M. / Turkenburg, J.P. / Wilkinson, A.J. / Bott, M. / Wilson, K.S.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2010
Title: The Corynebacterium Glutamicum Aconitase Repressor: Scratching Around for Crystals.
Authors: Garcia-Nafria, J. / Baumgart, M. / Bott, M. / Wilkinson, A.J. / Wilson, K.S.
History
DepositionJan 17, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 23, 2013Provider: repository / Type: Initial release
Revision 1.1May 1, 2013Group: Database references / Structure summary
Revision 1.2Jun 19, 2013Group: Database references
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_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_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HTH-TYPE TRANSCRIPTIONAL REPRESSOR ACNR COMPND 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,6293
Polymers21,4121
Non-polymers2162
Water1,838102
1
A: HTH-TYPE TRANSCRIPTIONAL REPRESSOR ACNR COMPND 2
hetero molecules

A: HTH-TYPE TRANSCRIPTIONAL REPRESSOR ACNR COMPND 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,2576
Polymers42,8242
Non-polymers4334
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1,-y,z1
Buried area4190 Å2
ΔGint-39.3 kcal/mol
Surface area16480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)34.640, 72.730, 73.200
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein HTH-TYPE TRANSCRIPTIONAL REPRESSOR ACNR COMPND 2 / ACNR


Mass: 21412.209 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CORYNEBACTERIUM GLUTAMICUM (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q8NQ97
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 102 / 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: 2.34 Å3/Da / Density % sol: 42.9 % / Description: NONE
Crystal growpH: 4 / Details: 1 M AMMONIUM PHOSPHATE; 100 MM SODIUM CITRATE PH 4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.0332
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 18, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.9→31.31 Å / Num. obs: 15067 / % possible obs: 99.3 % / Observed criterion σ(I): 1 / Redundancy: 6 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 10
Reflection shellResolution: 1.9→2 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.66 / Mean I/σ(I) obs: 3.6 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.6.0119refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4AC6

4ac6


Resolution: 1.9→73.2 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.91 / SU B: 3.081 / SU ML: 0.093 / Cross valid method: THROUGHOUT / ESU R: 0.162 / ESU R Free: 0.156 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.24632 756 5 %RANDOM
Rwork0.19399 ---
obs0.19646 14286 98.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.792 Å2
Baniso -1Baniso -2Baniso -3
1-0.3 Å20 Å20 Å2
2---0.06 Å20 Å2
3----0.25 Å2
Refinement stepCycle: LAST / Resolution: 1.9→73.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1383 0 14 102 1499
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0191436
X-RAY DIFFRACTIONr_bond_other_d0.0010.021015
X-RAY DIFFRACTIONr_angle_refined_deg1.9561.9671936
X-RAY DIFFRACTIONr_angle_other_deg1.03932436
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5325179
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.13222.43274
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.78515262
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.9221520
X-RAY DIFFRACTIONr_chiral_restr0.2970.2215
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021614
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02318
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_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.264 64 -
Rwork0.223 911 -
obs--99.59 %

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