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- PDB-5dxz: Crystal of AmtR from Corynebacterium glutamicum -

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Basic information

Entry
Database: PDB / ID: 5dxz
TitleCrystal of AmtR from Corynebacterium glutamicum
ComponentsTetR family transcriptional regulator
KeywordsDNA BINDING PROTEIN / TetR family regulator / Nitrogen master regulator / PII / GlnK / GlnB / TFR
Function / homologyBacterial regulatory proteins, tetR family / DNA-binding HTH domain, TetR-type / TetR-type HTH domain profile. / Homeobox-like domain superfamily / DNA binding / metal ion binding / TetR family transcriptional regulator
Function and homology information
Biological speciesCorynebacterium glutamicum ATCC 14067 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsPalanca, C. / Rubio, V.
CitationJournal: Febs J. / Year: 2016
Title: Structure of AmtR, the global nitrogen regulator of Corynebacterium glutamicum, in free and DNA-bound forms.
Authors: Palanca, C. / Rubio, V.
History
DepositionSep 24, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jan 13, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 20, 2016Group: Database references
Revision 1.2Mar 30, 2016Group: Database references
Revision 1.3Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TetR family transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,4466
Polymers26,9661
Non-polymers4805
Water63135
1
A: TetR family transcriptional regulator
hetero molecules

A: TetR family transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,89212
Polymers53,9312
Non-polymers96110
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_554x-y,-y,-z-2/31
Buried area3330 Å2
ΔGint-115 kcal/mol
Surface area17670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.310, 69.310, 92.720
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein TetR family transcriptional regulator


Mass: 26965.570 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Corynebacterium glutamicum ATCC 14067 (bacteria)
Gene: KIQ_008455 / Plasmid: pLIC-SGC1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A072Z681
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 35 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsStrain used is ATCC 13969. The only difference with the ATCC 14067 is the change of Val141 to Ile.

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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: 2.38 Å3/Da / Density % sol: 48.41 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / Details: 0.2 M Lithium Sulphate, 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 9, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873 Å / Relative weight: 1
ReflectionResolution: 2.25→36.69 Å / Num. obs: 12703 / % possible obs: 100 % / Redundancy: 11 % / CC1/2: 0.999 / Rmerge(I) obs: 0.066 / Rpim(I) all: 0.021 / Net I/σ(I): 22.5 / Num. measured all: 139352 / Scaling rejects: 81
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
2.25-2.3211.10.4226.51289011580.9580.132100
9-36.698.70.03239.520442340.9990.01198.4

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Processing

Software
NameVersionClassification
Aimless0.1.29data scaling
REFMAC5.7.0032refinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5DY1

5dy1


Resolution: 2.25→36.69 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.928 / WRfactor Rfree: 0.2496 / WRfactor Rwork: 0.2259 / FOM work R set: 0.8168 / SU B: 13.446 / SU ML: 0.16 / SU R Cruickshank DPI: 0.2656 / SU Rfree: 0.207 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.266 / ESU R Free: 0.207 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.249 619 4.9 %RANDOM
Rwork0.2195 ---
obs0.2209 12056 99.93 %-
Solvent computationIon probe radii: 1 Å / Shrinkage radii: 1 Å / VDW probe radii: 1.3 Å / Solvent model: MASK
Displacement parametersBiso max: 101.54 Å2 / Biso mean: 44.905 Å2 / Biso min: 24.2 Å2
Baniso -1Baniso -2Baniso -3
1--0.25 Å2-0.25 Å20 Å2
2---0.25 Å20 Å2
3---0.81 Å2
Refinement stepCycle: final / Resolution: 2.25→36.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1519 0 25 35 1579
Biso mean--74.85 42.84 -
Num. residues----199
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0191582
X-RAY DIFFRACTIONr_bond_other_d0.0010.021484
X-RAY DIFFRACTIONr_angle_refined_deg1.5041.9862163
X-RAY DIFFRACTIONr_angle_other_deg0.81533411
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0985201
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.17823.84665
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.02815250
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.4131511
X-RAY DIFFRACTIONr_chiral_restr0.0790.2260
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211768
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02337
X-RAY DIFFRACTIONr_mcbond_it2.3032.737804
X-RAY DIFFRACTIONr_mcbond_other2.2972.732803
X-RAY DIFFRACTIONr_mcangle_it3.3574.0861005
LS refinement shellResolution: 2.25→2.309 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.326 50 -
Rwork0.258 894 -
all-944 -
obs--99.79 %
Refinement TLS params.Method: refined / Origin x: 36.755 Å / Origin y: -4.019 Å / Origin z: -19.107 Å
111213212223313233
T0.1756 Å2-0.0796 Å2-0.0124 Å2-0.1974 Å2-0.012 Å2--0.0475 Å2
L2.6609 °2-0.5737 °20.3862 °2-0.3951 °2-0.4062 °2--0.4712 °2
S0.0239 Å °-0.1217 Å °-0.1083 Å °0.0667 Å °0.0138 Å °0.0314 Å °-0.0217 Å °-0.0614 Å °-0.0377 Å °

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