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- PDB-9gui: Crystal structure of transcription factor NtcA from Synechococcus... -

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Basic information

Entry
Database: PDB / ID: 9gui
TitleCrystal structure of transcription factor NtcA from Synechococcus elongatus in complex with its target DNA.
Components
  • DNA (5'-D(P*AP*GP*CP*TP*GP*AP*TP*AP*CP*AP*TP*AP*AP*AP*AP*AP*T)-3')
  • DNA (5'-D(P*AP*TP*TP*TP*TP*TP*AP*TP*GP*TP*AP*TP*C)-3')
  • Global 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
2-OXOGLUTARIC ACID / DNA / DNA (> 10) / Global nitrogen regulator
Similarity search - Component
Biological speciesSynechococcus elongatus PCC 7942 = FACHB-805 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 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
C: DNA (5'-D(P*AP*TP*TP*TP*TP*TP*AP*TP*GP*TP*AP*TP*C)-3')
D: DNA (5'-D(P*AP*GP*CP*TP*GP*AP*TP*AP*CP*AP*TP*AP*AP*AP*AP*AP*T)-3')
E: DNA (5'-D(P*AP*TP*TP*TP*TP*TP*AP*TP*GP*TP*AP*TP*C)-3')
F: DNA (5'-D(P*AP*GP*CP*TP*GP*AP*TP*AP*CP*AP*TP*AP*AP*AP*AP*AP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,9438
Polymers68,6516
Non-polymers2922
Water724
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11240 Å2
ΔGint-63 kcal/mol
Surface area26930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)119.854, 46.935, 139.737
Angle α, β, γ (deg.)90.00, 98.62, 90.00
Int Tables number5
Space group name H-MC121

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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: DNA chain DNA (5'-D(P*AP*TP*TP*TP*TP*TP*AP*TP*GP*TP*AP*TP*C)-3')


Mass: 4235.774 Da / Num. of mol.: 2 / Source method: obtained synthetically
Source: (synth.) Synechococcus elongatus PCC 7942 = FACHB-805 (bacteria)
#3: DNA chain DNA (5'-D(P*AP*GP*CP*TP*GP*AP*TP*AP*CP*AP*TP*AP*AP*AP*AP*AP*T)-3')


Mass: 5227.451 Da / Num. of mol.: 2 / Source method: obtained synthetically
Source: (synth.) Synechococcus elongatus PCC 7942 = FACHB-805 (bacteria)
#4: Chemical ChemComp-AKG / 2-OXOGLUTARIC ACID


Mass: 146.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H6O5 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.83 Å3/Da / Density % sol: 56.54 %
Crystal growTemperature: 294.15 K / Method: vapor diffusion, sitting drop
Details: NTCA-DNA complex was 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 and 10mM 2-oxoglutarate. CRYSTALLIZATION SOLUTION: ...Details: NTCA-DNA complex was 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 and 10mM 2-oxoglutarate. CRYSTALLIZATION SOLUTION: 0,1M Bis-Tris, pH 6,5, 28% PEG monomethyl ether 2K. Cryo protectant: 38% PEG monomethyl ether

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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: 3→24.2 Å / Num. obs: 15466 / % possible obs: 98.5 % / Redundancy: 2.7 % / Rsym value: 0.085 / Net I/σ(I): 7.9
Reflection shellResolution: 3→3.16 Å / Num. unique obs: 15466 / Rsym value: 0.429

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Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
SCALAdata scaling
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→24.17 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.881 / SU B: 49.329 / SU ML: 0.389 / Cross valid method: THROUGHOUT / ESU R Free: 0.433 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2525 767 5 %RANDOM
Rwork0.2138 ---
obs0.21585 14688 97.54 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 67.789 Å2
Baniso -1Baniso -2Baniso -3
1--3.64 Å2-0 Å20.91 Å2
2---4.99 Å20 Å2
3---7.99 Å2
Refinement stepCycle: 1 / Resolution: 3→24.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3305 1230 20 4 4559
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0124770
X-RAY DIFFRACTIONr_bond_other_d0.0010.0163994
X-RAY DIFFRACTIONr_angle_refined_deg1.6681.6896700
X-RAY DIFFRACTIONr_angle_other_deg0.4251.5459312
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5885427
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.704533
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.66710616
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0980.2785
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024527
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02855
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_it2.673.6451705
X-RAY DIFFRACTIONr_mcbond_other2.673.6451705
X-RAY DIFFRACTIONr_mcangle_it4.3885.462127
X-RAY DIFFRACTIONr_mcangle_other4.3895.4632128
X-RAY DIFFRACTIONr_scbond_it3.0264.2923065
X-RAY DIFFRACTIONr_scbond_other3.0254.2923066
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.9116.4044572
X-RAY DIFFRACTIONr_long_range_B_refined10.24171565
X-RAY DIFFRACTIONr_long_range_B_other10.24171566
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3→3.075 Å
RfactorNum. reflection% reflection
Rfree0.309 56 -
Rwork0.318 1026 -
obs--92.4 %
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)
13.06650.4328-1.13252.4145-0.03534.72010.1541-0.04590.2525-0.1078-0.0629-0.146-0.13640.3141-0.09120.0286-0.016-0.00520.03410.02730.0957-19.48464.9955-54.3682
23.83160.677-0.37672.6743-0.37634.0593-0.0192-0.3447-0.04240.1203-0.1616-0.48620.05330.36130.18080.05120.0447-0.1060.33030.03260.2879-3.2228-4.3535-40.3787
36.3072-1.57021.95620.7940.13742.0064-0.0737-0.3070.05210.23770.0869-0.0032-0.07760.0158-0.01310.5026-0.04470.02140.40520.03060.2556-7.6786-8.1098-12.7837
44.3994-0.76642.25493.9523-2.96627.43530.1762-0.1142-0.32010.0160.2550.51730.0374-0.1239-0.43120.07560.0351-0.00490.1545-0.02430.1947-41.7046-0.6995-42.6059
55.5756-0.46121.03445.1704-2.52527.45160.05660.2341-0.4433-0.17620.06060.65970.2734-0.4964-0.11720.04280.0008-0.07770.2530.01480.2685-46.6380.6568-48.1849
68.1917-1.16992.94960.9042-0.12771.6542-0.235-0.2897-0.15460.37350.1924-0.0313-0.0597-0.05380.04250.4967-0.0196-0.01290.4740.05530.218-13.4975-6.7786-17.0418
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A6 - 500
2X-RAY DIFFRACTION2B7 - 500
3X-RAY DIFFRACTION3C2 - 14
4X-RAY DIFFRACTION4D15 - 31
5X-RAY DIFFRACTION5E2 - 14
6X-RAY DIFFRACTION6F15 - 31

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