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- PDB-4ac6: Corynebacterium glutamicum AcnR AU derivative structure -

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Basic information

Entry
Database: PDB / ID: 4ac6
TitleCorynebacterium glutamicum AcnR AU derivative structure
ComponentsHTH-TYPE TRANSCRIPTIONAL REPRESSOR ACNR
KeywordsTRANSCRIPTION / ACONITASE / CITRATE / TETR SUPERFAMILY
Function / homology
Function and homology information


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
: / HTH-type transcriptional repressor AcnR
Similarity search - Component
Biological speciesCORYNEBACTERIUM GLUTAMICUM (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.54 Å
AuthorsGarcia-Nafria, J. / Baumgart, M. / Turkenburg, J.P. / Wilkinson, A.J. / Bott, M. / Wilson, K.S.
CitationJournal: 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.
History
DepositionDec 14, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 26, 2012Provider: repository / Type: Initial release
Revision 1.1May 1, 2013Group: Database references / Other / Structure summary
Revision 1.2Jun 19, 2013Group: Database references
Revision 1.3May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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 / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,2995
Polymers21,5111
Non-polymers7884
Water88349
1
A: HTH-TYPE TRANSCRIPTIONAL REPRESSOR ACNR
hetero molecules

A: HTH-TYPE TRANSCRIPTIONAL REPRESSOR ACNR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,59810
Polymers43,0232
Non-polymers1,5768
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1,-y,z1
Buried area4100 Å2
ΔGint-53.9 kcal/mol
Surface area16160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)34.142, 72.886, 73.250
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


Mass: 21511.338 Da / Num. of mol.: 1 / Fragment: RESIDUES 2-188
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-AU / GOLD ION


Mass: 196.967 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Au
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 49 / 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: 2.29 Å3/Da / Density % sol: 46 % / Description: NONE
Crystal growpH: 4
Details: 1 M AMMONIUM PHOSPHATE, 100 MM SODIUM CITRATE PH 5.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.9334
DetectorType: ADSC CCD / Detector: CCD / Date: Apr 17, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9334 Å / Relative weight: 1
ReflectionResolution: 2.54→73.25 Å / Num. obs: 6461 / % possible obs: 100 % / Observed criterion σ(I): 1 / Redundancy: 8.8 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 47.9
Reflection shellResolution: 2.54→2.58 Å / Redundancy: 8.4 % / Rmerge(I) obs: 0.15 / Mean I/σ(I) obs: 21.9 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.6.0116refinement
HKL-2000data reduction
SCALEPACKdata scaling
SHELXCDEphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 2.54→73.25 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.88 / SU B: 11.151 / SU ML: 0.248 / Cross valid method: THROUGHOUT / ESU R: 1.046 / ESU R Free: 0.33 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.26336 301 4.7 %RANDOM
Rwork0.19454 ---
obs0.19792 6151 99.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.191 Å2
Baniso -1Baniso -2Baniso -3
1-0.88 Å20 Å20 Å2
2---1 Å20 Å2
3---0.12 Å2
Refinement stepCycle: LAST / Resolution: 2.54→73.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1401 0 4 49 1454
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0211421
X-RAY DIFFRACTIONr_bond_other_d0.0010.02999
X-RAY DIFFRACTIONr_angle_refined_deg1.3551.9561912
X-RAY DIFFRACTIONr_angle_other_deg0.9332400
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9835175
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.0322.70374
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.53615260
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.2881519
X-RAY DIFFRACTIONr_chiral_restr0.0740.2213
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021594
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02311
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: 2.539→2.605 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.352 21 -
Rwork0.192 388 -
obs--99.03 %

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