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- PDB-2xgx: Crystal structure of transcription factor NtcA from Synechococcus... -

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Basic information

Entry
Database: PDB / ID: 2xgx
TitleCrystal structure of transcription factor NtcA from Synechococcus elongatus (mercury derivative)
ComponentsGLOBAL NITROGEN REGULATOR
KeywordsTRANSCRIPTION / NITROGEN ASSIMILATION / CRP/FNR SUPERFAMILY / CYANOBACTERIA / 2-OXOGLUTARATE
Function / homologyCyclic nucleotide-binding domain / Crp-type HTH domain / RmlC-like jelly roll fold / Transcription regulator HTH, Crp-type, conserved site / Cyclic nucleotide-binding-like / Transcription regulator, NtcA / Winged helix-like DNA-binding domain superfamily / Winged helix DNA-binding domain superfamily / Cyclic nucleotide-binding domain / Crp-like helix-turn-helix domain ...Cyclic nucleotide-binding domain / Crp-type HTH domain / RmlC-like jelly roll fold / Transcription regulator HTH, Crp-type, conserved site / Cyclic nucleotide-binding-like / Transcription regulator, NtcA / Winged helix-like DNA-binding domain superfamily / Winged helix DNA-binding domain superfamily / Cyclic nucleotide-binding domain / Crp-like helix-turn-helix domain / Crp-type HTH domain signature. / cAMP/cGMP binding motif profile. / Crp-type HTH domain profile. / DNA-binding transcription factor activity / DNA binding / Global nitrogen regulator
Function and homology information
Specimen sourceSYNECHOCOCCUS ELONGATUS (Cyanobacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / 2.85 Å resolution
AuthorsLlacer, J.L. / Castells, M.A. / Rubio, V.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2010
Title: Structural Basis for the Regulation of Ntca-Dependent Transcription by Proteins Pipx and Pii.
Authors: Llacer, J.L. / Espinosa, J. / Castells, M.A. / Contreras, A. / Forchhammer, K. / Rubio, V.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Jun 8, 2010 / Release: Aug 18, 2010
RevisionDateData content typeGroupProviderType
1.0Aug 18, 2010Structure modelrepositoryInitial release
1.1May 8, 2011Structure modelVersion format compliance
1.2Jul 13, 2011Structure modelVersion format compliance

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: GLOBAL NITROGEN REGULATOR
B: GLOBAL NITROGEN REGULATOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,6277
Polyers49,7242
Non-polymers9035
Water1629
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area (Å2)5190
ΔGint (kcal/M)-61.3
Surface area (Å2)18790
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)67.393, 69.973, 149.002
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP 21 21 21

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Components

#1: Protein/peptide GLOBAL NITROGEN REGULATOR / NTCA


Mass: 24862.053 Da / Num. of mol.: 2
Details: AN HG ATOM BOUND TO EACH CYS 156 OF THE NTCA DIMER.
Source: (gene. exp.) SYNECHOCOCCUS ELONGATUS (Cyanobacteria)
Strain: PCC 7942 / Plasmid name: PET15B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): ROSETTA / References: UniProt: P29283
#2: Chemical ChemComp-AKG / 2-OXOGLUTARIC ACID


Mass: 146.098 Da / Num. of mol.: 2 / Formula: C5H6O5 / Alpha-Ketoglutaric acid
#3: Chemical ChemComp-HG / MERCURY (II) ION


Mass: 200.590 Da / Num. of mol.: 2 / Formula: Hg / Mercury
#4: Chemical ChemComp-BTB / 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / BIS-TRIS BUFFER


Mass: 209.240 Da / Num. of mol.: 1 / Formula: C8H19NO5
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 9 / Formula: H2O / Water

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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: 3.25 / Density percent sol: 62.2 % / Description: NONE
Crystal growpH: 6.5
Details: NTCA PROTEIN WAS AT 4.7 MG/ML IN 50 MM SODIUM CITRATE PH 6.5, 0.5 M NACL, 5 MM MAGNESIUM CHLORIDE, 50 MM ARGININE HYDROCHLORIDE, 50 MM NA L-GLUTAMATE AND 10 MM 2- OXOGLUTARATE (2OG). CRISTALLIZATION SOLUTION: 0.1 M BIS-TRIS PH 6.5, 36 % PEG 400. THEN, SOAKED IN THE SAME SOLUTION CONTAINING ALSO 10MM 2OG AND 2 MM HGCL2.

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Data collection

DiffractionMean temperature: 100 kelvins
SourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM16 / Wavelength: 1.007
DetectorType: ADSC CCD / Detector: CCD / Collection date: Feb 26, 2009
RadiationDiffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.007 Å / Relative weight: 1
ReflectionB iso Wilson estimate: 74.73 Å2 / D resolution high: 2.85 Å / D resolution low: 74.5 Å / Number obs: 16626 / Observed criterion sigma I: 1.9 / Rmerge I obs: 0.08 / NetI over sigmaI: 8 / Redundancy: 6.6 % / Percent possible obs: 97.3
Reflection shellRmerge I obs: 0.46 / Highest resolution: 2.85 Å / Lowest resolution: 3 Å / MeanI over sigI obs: 1.9 / Redundancy: 6.6 % / Percent possible all: 97.3

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Processing

Software
NameVersionClassification
REFMAC5.5.0072refinement
MOSFLMdata reduction
SCALAdata scaling
SHELXSOFTWARE PACKAGEphasing
RefineMethod to determine structure: SAD
Starting model: NONE

Correlation coeff Fo to Fc: 0.939 / Correlation coeff Fo to Fc free: 0.909
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS
Overall SU B: 28.068 / Overall SU ML: 0.251 / R Free selection details: RANDOM / Cross valid method: THROUGHOUT / Overall ESU R: 0.745 / Overall ESU R Free: 0.332 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Solvent computationSolvent ion probe radii: 0.8 Å / Solvent shrinkage radii: 0.8 Å / Solvent vdw probe radii: 1.2 Å / Solvent model details: MASK
Displacement parametersB iso mean: 65.129 Å2 / Aniso B11: 0.47 Å2 / Aniso B12: 0 Å2 / Aniso B13: 0 Å2 / Aniso B22: 0.16 Å2 / Aniso B23: 0 Å2 / Aniso B33: -0.63 Å2
Least-squares processR factor R free: 0.2453 / R factor R work: 0.21067 / R factor obs: 0.21236 / Highest resolution: 2.85 Å / Lowest resolution: 5 Å / Number reflection R free: 837 / Number reflection obs: 15751 / Percent reflection R free: 5 / Percent reflection obs: 97.07
Refine hist #LASTHighest resolution: 2.85 Å / Lowest resolution: 5 Å
Number of atoms included #LASTProtein: 3302 / Nucleic acid: 0 / Ligand: 36 / Solvent: 9 / Total: 3347
Refine LS restraints
Refine IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0100.0223405
X-RAY DIFFRACTIONr_bond_other_d0.0030.0202346
X-RAY DIFFRACTIONr_angle_refined_deg1.2981.9864602
X-RAY DIFFRACTIONr_angle_other_deg0.8983.0005704
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0585.000425
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.35722.786140
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.51915.000601
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.86315.00030
X-RAY DIFFRACTIONr_chiral_restr0.0810.200550
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0213707
X-RAY DIFFRACTIONr_gen_planes_other0.0020.020699
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_it0.2891.5002123
X-RAY DIFFRACTIONr_mcbond_other0.0611.500857
X-RAY DIFFRACTIONr_mcangle_it0.5672.0003431
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.9003.0001282
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.5414.5001169
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
Refine LS restraints ncs

Ens ID: 1 / Refine ID: X-RAY DIFFRACTION

Dom IDAuth asym IDNumberTypeRms dev positionWeight position
1A2361tight positional0.040.05
2B2361tight positional0.040.05
1A281medium positional0.020.50
2B281medium positional0.020.50
1A10loose positional0.035.00
2B10loose positional0.035.00
1A2361tight thermal0.050.50
2B2361tight thermal0.050.50
1A281medium thermal0.032.00
2B281medium thermal0.032.00
1A10loose thermal0.0310.00
2B10loose thermal0.0310.00
Refine LS shellHighest resolution: 2.85 Å / R factor R free: 0.429 / R factor R work: 0.342 / Lowest resolution: 2.924 Å / Number reflection R free: 58 / Number reflection R work: 1104 / Total number of bins used: 20 / Percent reflection obs: 92.44
Refine TLS

Method: refined / Refine ID: X-RAY DIFFRACTION

IDL11L12L13L22L23L33S11S12S13S21S22S23S31S32S33T11T12T13T22T23T33Origin xOrigin yOrigin z
14.79740.5262-0.13111.9784-1.27744.62630.1110-0.28880.72260.1284-0.09420.1931-0.8396-0.2590-0.01670.16210.04870.00760.1561-0.04560.1184-2.5050-4.1550-6.1360
26.7083-1.18321.24447.49100.07332.0584-0.07860.29950.6564-0.4451-0.0405-0.7307-0.39990.48630.11910.1046-0.07980.02680.31670.03720.116518.7490-12.0170-7.9560
33.68740.0632-0.09136.4341-0.74904.44600.04060.49180.6979-0.3014-0.14540.2916-0.7183-0.26820.10490.19570.0679-0.04410.30220.09270.1539-5.9580-2.7580-26.4210
410.1165-0.56661.24888.14273.31853.66330.30550.3042-0.9564-0.4559-0.33761.01450.7665-0.35070.03200.4430-0.0225-0.18950.3549-0.03410.2341-7.2300-25.3750-29.7750
Refine TLS group

Refine ID: X-RAY DIFFRACTION

IDBeg auth asym IDBeg auth seq IDEnd auth asym IDEnd auth seq IDRefine TLS ID
1A6A1561
2A157A2222
3B6B1563
4B157B2224

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