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

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Basic information

Entry
Database: PDB / ID: 9guk
TitleCrystal structure of transcription factor NtcA from Synechococcus elongatus in complex with its transcriptional co- activator PipX and its target DNA (Crystal I)
Components
  • DNA (30-MER)
  • Global nitrogen regulator
  • PipX
KeywordsDNA BINDING PROTEIN / DNA binding protein. Transcriptional regulation / NtcA / nitrogen regulation / cyanobacteria / CRP / PipX
Function / homology
Function and homology information


DNA-binding transcription factor activity / DNA binding / cytosol
Similarity search - Function
PII-interacting protein X, cyanobacteria / PII-interacting protein X / 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 ...PII-interacting protein X, cyanobacteria / PII-interacting protein X / 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 / PipX
Similarity search - Component
Biological speciesSynechococcus elongatus PCC 7942 = FACHB-805 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.8 Å
AuthorsForcada-Nadal, A. / Llacer, J.L. / 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
D: Global nitrogen regulator
F: Global nitrogen regulator
G: DNA (30-MER)
I: DNA (30-MER)
J: PipX
H: PipX
A: Global nitrogen regulator
B: Global nitrogen regulator
C: DNA (30-MER)
K: DNA (30-MER)
L: PipX
E: PipX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)180,22916
Polymers179,64512
Non-polymers5844
Water00
1
D: Global nitrogen regulator
F: Global nitrogen regulator
G: DNA (30-MER)
I: DNA (30-MER)
J: PipX
H: PipX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,1158
Polymers89,8226
Non-polymers2922
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15460 Å2
ΔGint-72 kcal/mol
Surface area33670 Å2
MethodPISA
2
A: Global nitrogen regulator
B: Global nitrogen regulator
C: DNA (30-MER)
K: DNA (30-MER)
L: PipX
E: PipX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,1158
Polymers89,8226
Non-polymers2922
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15610 Å2
ΔGint-67 kcal/mol
Surface area33430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.260, 68.180, 126.250
Angle α, β, γ (deg.)90.00, 115.07, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Global nitrogen regulator


Mass: 24862.053 Da / Num. of mol.: 4
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 (30-MER)


Mass: 9508.181 Da / Num. of mol.: 4 / Source method: obtained synthetically
Source: (synth.) Synechococcus elongatus PCC 7942 = FACHB-805 (bacteria)
#3: Protein
PipX


Mass: 10540.987 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechococcus elongatus PCC 7942 = FACHB-805 (bacteria)
Gene: Synpcc7942_2061 / Plasmid: pTrc99A / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta / References: UniProt: Q7X386
#4: Chemical
ChemComp-AKG / 2-OXOGLUTARIC ACID


Mass: 146.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C5H6O5 / Feature type: SUBJECT OF INVESTIGATION
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: 2.46 Å3/Da / Density % sol: 49.96 %
Crystal growTemperature: 294.15 K / Method: vapor diffusion, sitting drop
Details: PipX-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 ...Details: PipX-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: 0,2M MgSO4 and 20% PEG3350. Cryo protectant: 39% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9173 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Mar 10, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9173 Å / Relative weight: 1
ReflectionResolution: 3.8→114.4 Å / Num. obs: 16087 / % possible obs: 92.2 % / Redundancy: 2.8 % / Rsym value: 0.193 / Net I/σ(I): 3
Reflection shellResolution: 3.8→4.01 Å / Num. unique obs: 16087 / Rsym value: 0.398

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Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
SCALAdata scaling
MOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.8→64.14 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.867 / SU B: 188.698 / SU ML: 1.129 / Cross valid method: THROUGHOUT / ESU R Free: 1.251 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.35385 811 5 %RANDOM
Rwork0.3154 ---
obs0.31739 15269 91.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 69.248 Å2
Baniso -1Baniso -2Baniso -3
1--2.83 Å2-0 Å21.75 Å2
2--1.38 Å2-0 Å2
3----0.13 Å2
Refinement stepCycle: 1 / Resolution: 3.8→64.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9543 2460 40 0 12043
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.01112511
X-RAY DIFFRACTIONr_bond_other_d0.0190.01610589
X-RAY DIFFRACTIONr_angle_refined_deg1.7581.68317393
X-RAY DIFFRACTIONr_angle_other_deg0.6681.54724650
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.47751177
X-RAY DIFFRACTIONr_dihedral_angle_2_deg10.4075104
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.204101754
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1150.21987
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212491
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022409
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_it2.4263.5344750
X-RAY DIFFRACTIONr_mcbond_other2.4263.5344750
X-RAY DIFFRACTIONr_mcangle_it4.015.35913
X-RAY DIFFRACTIONr_mcangle_other4.015.35914
X-RAY DIFFRACTIONr_scbond_it1.9343.7027761
X-RAY DIFFRACTIONr_scbond_other1.9333.7027760
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.3165.52411481
X-RAY DIFFRACTIONr_long_range_B_refined7.665201909
X-RAY DIFFRACTIONr_long_range_B_other7.665201910
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.8→3.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.525 47 -
Rwork0.451 1086 -
obs--89.28 %
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)
12.1013-0.34650.25162.74160.61512.43920.04970.42850.0198-0.246-0.0225-0.0433-0.14210.0596-0.02720.35320.0854-0.11380.11140.00940.3538-2.4957-11.7887-37.9051
22.6353-0.79360.52222.7159-0.72922.3781-0.0336-0.1660.1493-0.2003-0.0585-0.2445-0.2030.15740.09210.22480.0051-0.00350.0512-0.03790.38050.4587-0.2411-17.8308
30.36880.5930.8332.62232.32544.65010.1482-0.06770.0320.0646-0.14980.03770.2473-0.31290.00160.1293-0.0038-0.02310.3270.10640.4623-11.6378-24.9053-16.4359
40.9860.4891-0.01462.24532.32644.79680.15510.0005-0.12790.153-0.13570.00340.4016-0.5456-0.01940.23330.0408-0.1050.26510.10410.503-11.6326-24.0196-15.041
56.3379-3.931.30233.4486-0.18982.31120.1588-0.33250.1483-0.36030.1838-0.55410.02260.3073-0.34260.40270.05870.0230.25510.1170.468226.0298-11.0002-18.4484
67.4227-0.48010.35073.79211.43963.48710.36980.45730.10010.0823-0.36190.1092-0.1164-0.4412-0.00790.4240.0807-0.04260.1750.01790.3188-25.01974.6714-41.1393
73.14670.33450.41061.71850.45132.3977-0.0240.1240.13770.1757-0.01410.1733-0.1248-0.11240.0380.2477-0.0004-0.06120.02230.06540.3963-3.6541-0.2644-96.3344
82.75-0.31650.41042.9886-0.85311.7723-0.1147-0.3511-0.04090.33560.1089-0.0034-0.26620.05370.00580.3788-0.0924-0.07750.0969-0.01830.3034-0.4618-11.8919-76.4007
91.0089-0.2858-0.22782.2048-2.40995.24870.17230.0147-0.1606-0.2142-0.03960.05350.45810.3813-0.13280.2224-0.0505-0.09340.2476-0.12540.50758.4703-24.0236-99.2873
100.3381-0.59241.16693.7036-3.23155.74990.06740.10240.0143-0.1699-0.0939-0.02890.39710.15360.02650.15870.0216-0.03780.3018-0.11580.61718.4174-24.8683-97.9135
116.284-0.3537-0.33371.9056-1.92143.50610.0783-0.2542-0.01360.2002-0.10750.0376-0.2460.25750.02920.3872-0.0539-0.05720.1875-0.05640.307121.77954.6719-73.0006
125.42542.68980.56932.287-0.52823.86970.09440.11640.4230.26360.07340.22810.0307-0.4918-0.16780.3823-0.0101-0.01330.25-0.07660.3742-29.1984-11.1705-95.5223
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1D7 - 222
2X-RAY DIFFRACTION2F6 - 222
3X-RAY DIFFRACTION3G2 - 31
4X-RAY DIFFRACTION4I2 - 31
5X-RAY DIFFRACTION5J4 - 88
6X-RAY DIFFRACTION6H4 - 89
7X-RAY DIFFRACTION7A7 - 222
8X-RAY DIFFRACTION8B6 - 222
9X-RAY DIFFRACTION9C2 - 31
10X-RAY DIFFRACTION10K2 - 31
11X-RAY DIFFRACTION11L4 - 88
12X-RAY DIFFRACTION12E4 - 89

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