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- PDB-9gqu: Crystal structure of NtcA from S. elongatus in apo form A2 -

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Basic information

Entry
Database: PDB / ID: 9gqu
TitleCrystal structure of NtcA from S. elongatus in apo form A2
ComponentsGlobal nitrogen regulator
KeywordsDNA BINDING PROTEIN / DNA 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: 2.85 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 9, 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
Water27015
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3050 Å2
ΔGint-21 kcal/mol
Surface area18540 Å2
Unit cell
Length a, b, c (Å)66.502, 88.845, 99.689
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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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.: 15 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.96 Å3/Da / Density % sol: 58.46 %
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 HEPES ...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 HEPES pH 6.5, 20,5% PEG 4000. CRYO PROTECTANT: 25% PEG 400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM16 / Wavelength: 0.9797 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Sep 6, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9797 Å / Relative weight: 1
ReflectionResolution: 2.85→66.3 Å / Num. obs: 14209 / % possible obs: 99 % / Redundancy: 4.6 % / Rsym value: 0.056 / Net I/σ(I): 12.1
Reflection shellResolution: 2.85→3 Å / Redundancy: 3.6 % / Num. unique obs: 14209 / Rsym value: 0.341

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Processing

Software
NameVersionClassification
PHENIX(1.21.1_5286: ???)refinement
SCALAdata scaling
MOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.85→23.78 Å / SU ML: 0.39 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 27.32 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2588 712 5.03 %RANDOM
Rwork0.213 ---
obs0.2152 14161 99.03 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.85→23.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2977 0 0 15 2992
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.009
X-RAY DIFFRACTIONf_angle_d1.131
X-RAY DIFFRACTIONf_dihedral_angle_d21.1671086
X-RAY DIFFRACTIONf_chiral_restr0.062509
X-RAY DIFFRACTIONf_plane_restr0.01525
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.85-3.070.35231600.29312537X-RAY DIFFRACTION97
3.07-3.380.30791620.27032652X-RAY DIFFRACTION100
3.38-3.860.2741270.23062719X-RAY DIFFRACTION100
3.86-4.860.24061270.18462721X-RAY DIFFRACTION100
4.86-23.780.22691360.19552820X-RAY DIFFRACTION99
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)
12.32251.0542-0.37325.24470.23323.12340.176-0.0053-0.5795-0.38390.1266-0.08390.2278-0.07170.00410.31120.0401-0.02340.41560.00290.498526.9998-19.8598-11.0971
24.1569-1.4633-2.75834.1725-0.03282.1820.3526-0.35830.0158-0.0812-0.008-0.3438-0.32420.004-0.00050.4476-0.0390.03390.60350.04110.455624.5353-12.209-7.19
30.93040.71120.06844.29030.41062.13840.38040.47340.0508-0.6519-0.14890.056-0.32510.1531-0.00060.5720.04140.08990.64830.07580.455426.7056-9.5024-17.1537
45.28921.0058-1.14772.3583-1.30753.59020.22591.1230.2022-0.73180.40210.362-0.404-0.33480.00740.4958-0.03260.0320.76140.14720.58484.1109-13.9615-10.4708
53.88261.1117-1.68044.5648-0.83453.61930.22950.48280.2972-0.03640.04160.4968-0.0781-0.3860.00080.41550.070.09330.63630.14640.63310.1164-15.9698-3.8091
62.3781-0.05780.56730.3421-0.67911.41220.67131.1307-1.05320.884-0.5418-0.41981.4156-0.26690.11841.0813-0.24640.10210.47380.24910.926734.162615.8896-25.5675
71.92650.6353-0.46942.3196-0.19573.20680.26660.43671.0999-0.07720.50831.386-0.9314-0.43630.04320.8419-0.01860.22950.54740.24350.812417.562110.4108-13.825
82.08663.67267.22191.52822.62225.1173-0.8237-2.55391.274-1.1918-0.23660.13810.1001-0.0588-1.33551.4486-0.14180.17870.42360.19880.649922.68465.609-18.1138
91.63293.0341-1.74295.8802-1.57731.77350.0974-0.2922-0.0222-0.4021-0.0055-0.0817-0.67790.80070.02710.6091-0.06910.21420.44880.01370.490626.39234.842-15.3535
100.82561.0043-0.09943.5304-0.1292.67070.6365-0.56520.91091.4388-0.35350.6059-0.99070.1816-0.01081.3126-0.25440.39810.7249-0.14930.961720.094510.8735.8877
112.95143.0939-0.65614.2861-1.98612.29230.7339-0.20871.43111.9454-0.76221.8143-0.32520.0613-0.18961.677-0.19280.22970.9263-0.19140.821425.327710.947612.6792
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 19 through 56 )
2X-RAY DIFFRACTION2chain 'A' and (resid 57 through 96 )
3X-RAY DIFFRACTION3chain 'A' and (resid 97 through 141 )
4X-RAY DIFFRACTION4chain 'A' and (resid 142 through 174 )
5X-RAY DIFFRACTION5chain 'A' and (resid 175 through 220 )
6X-RAY DIFFRACTION6chain 'B' and (resid 10 through 27 )
7X-RAY DIFFRACTION7chain 'B' and (resid 28 through 68 )
8X-RAY DIFFRACTION8chain 'B' and (resid 69 through 88 )
9X-RAY DIFFRACTION9chain 'B' and (resid 89 through 141 )
10X-RAY DIFFRACTION10chain 'B' and (resid 142 through 198 )
11X-RAY DIFFRACTION11chain 'B' and (resid 199 through 220 )

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