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- PDB-9gug: Crystal structure of NtcA from S. elongatus in apo form A1 -

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Basic information

Entry
Database: PDB / ID: 9gug
TitleCrystal structure of NtcA from S. elongatus in apo form A1
ComponentsGlobal nitrogen regulator
KeywordsDNA BINDING PROTEIN / Transcriptional regulation / NtcA / nitrogen regulation / cyanobacteria / CRP
Function / homology
Function and homology information


DNA-binding transcription factor activity / DNA binding / cytosol
Similarity search - Function
Transcription regulator, NtcA / helix_turn_helix, cAMP Regulatory protein / Transcription regulator HTH, Crp-type, conserved site / Crp-type HTH domain signature. / : / Crp-like helix-turn-helix domain / Crp-type HTH domain profile. / Crp-type HTH domain / Cyclic nucleotide-monophosphate binding domain / Cyclic nucleotide-binding domain ...Transcription regulator, NtcA / helix_turn_helix, cAMP Regulatory protein / Transcription regulator HTH, Crp-type, conserved site / Crp-type HTH domain signature. / : / Crp-like helix-turn-helix domain / Crp-type HTH domain profile. / Crp-type HTH domain / Cyclic nucleotide-monophosphate binding domain / Cyclic nucleotide-binding domain / cAMP/cGMP binding motif profile. / Cyclic nucleotide-binding domain / Cyclic nucleotide-binding domain superfamily / RmlC-like jelly roll fold / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
Global nitrogen regulator
Similarity search - Component
Biological speciesSynechococcus elongatus PCC 7942 = FACHB-805 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsLlacer, J.L. / Forcada-Nadal, A. / Rubio, V.
Funding support Spain, 2items
OrganizationGrant numberCountry
Spanish Ministry of Science, Innovation, and UniversitiesPID2020-116880GB-I00 Spain
Spanish Ministry of Economy and CompetitivenessBFU2017-84264-P Spain
CitationJournal: Nucleic Acids Res. / Year: 2025
Title: Structures of the cyanobacterial nitrogen regulators NtcA and PipX complexed to DNA shed light on DNA binding by NtcA and implicate PipX in the recruitment of RNA polymerase.
Authors: Forcada-Nadal, A. / Bibak, S. / Salinas, P. / Contreras, A. / Rubio, V. / Llacer, J.L.
History
DepositionSep 19, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 12, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Global nitrogen regulator
B: Global nitrogen regulator


Theoretical massNumber of molelcules
Total (without water)49,7242
Polymers49,7242
Non-polymers00
Water905
1
A: Global nitrogen regulator

A: Global nitrogen regulator


Theoretical massNumber of molelcules
Total (without water)49,7242
Polymers49,7242
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-1/21
Buried area2980 Å2
ΔGint-24 kcal/mol
Surface area17890 Å2
2
B: Global nitrogen regulator

B: Global nitrogen regulator


Theoretical massNumber of molelcules
Total (without water)49,7242
Polymers49,7242
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area2990 Å2
ΔGint-25 kcal/mol
Surface area17300 Å2
Unit cell
Length a, b, c (Å)95.167, 95.487, 160.788
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Global nitrogen regulator


Mass: 24862.053 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechococcus elongatus PCC 7942 = FACHB-805 (bacteria)
Gene: ntcA, Synpcc7942_0127 / Plasmid: pET15b / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta / References: UniProt: P29283
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 3.67 Å3/Da / Density % sol: 66.51 %
Crystal growTemperature: 294.15 K / Method: vapor diffusion, sitting drop
Details: NtcA protein was at 6,1 mg/ml IN 50 mM sodium citrate pH 6.5, 0.5 M NaCl, 5 mM magnesium cloride, 50 mM arginine hydrocloride, 50 mM Na L-glutamate. CRYSTALLIZATION SOLUTION: 0.1M Na acetate pH 4.5, 40% PEG 200

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.977 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 17, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.977 Å / Relative weight: 1
ReflectionResolution: 2.65→80.4 Å / Num. obs: 21137 / % possible obs: 98 % / Redundancy: 3.5 % / Rsym value: 0.057 / Net I/σ(I): 5.8
Reflection shellResolution: 2.65→2.79 Å / Redundancy: 3.3 % / Num. unique obs: 21137 / Rsym value: 0.408 / % possible all: 98

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
SCALAdata scaling
MOSFLMdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→47.79 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.893 / SU B: 25.832 / SU ML: 0.235 / Cross valid method: THROUGHOUT / ESU R: 0.411 / ESU R Free: 0.298 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27709 1026 5.1 %RANDOM
Rwork0.24117 ---
obs0.24295 18944 97.23 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 82.01 Å2
Baniso -1Baniso -2Baniso -3
1-0.32 Å20 Å2-0 Å2
2--4.88 Å20 Å2
3----5.2 Å2
Refinement stepCycle: 1 / Resolution: 2.7→47.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2830 0 0 5 2835
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0122887
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162772
X-RAY DIFFRACTIONr_angle_refined_deg1.7761.8143926
X-RAY DIFFRACTIONr_angle_other_deg0.5951.7146307
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9535380
X-RAY DIFFRACTIONr_dihedral_angle_2_deg10.721521
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.44810444
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.080.2490
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023366
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02646
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_it5.7366.0281543
X-RAY DIFFRACTIONr_mcbond_other5.7366.0281543
X-RAY DIFFRACTIONr_mcangle_it8.70610.8251918
X-RAY DIFFRACTIONr_mcangle_other8.70510.8271919
X-RAY DIFFRACTIONr_scbond_it5.3516.2011344
X-RAY DIFFRACTIONr_scbond_other5.3496.2031345
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other8.18111.3632009
X-RAY DIFFRACTIONr_long_range_B_refined11.68155.63039
X-RAY DIFFRACTIONr_long_range_B_other11.68155.613040
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.7→2.768 Å
RfactorNum. reflection% reflection
Rfree0.297 70 -
Rwork0.351 1336 -
obs--95.84 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.063-1.87880.14773.19020.76233.2749-0.1031-0.3233-0.23090.30490.40170.25810.8934-0.3561-0.29860.42840.0057-0.05760.19350.09120.0637-4.144-31.739-28.326
22.9488-1.80680.21222.67970.58442.98410.32920.16420.118-0.2876-0.0469-0.2282-0.26980.9247-0.28230.28510.00560.05630.3456-0.06640.0395-15.6134.104-11.85
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A21 - 221
2X-RAY DIFFRACTION2B23 - 220

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