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- PDB-2xko: Crystal structure of the complex of NtcA with its transcriptional... -

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Basic information

Entry
Database: PDB / ID: 2xko
TitleCrystal structure of the complex of NtcA with its transcriptional co- activator PipX
Components
  • GLOBAL NITROGEN REGULATOR
  • PIPX
KeywordsTRANSCRIPTION / NITROGEN ASSIMILATION / CRP/FNR SUPERFAMILY / 2-OXOGLUTARATE / GLOBAL NITROGEN CONTROLLER
Function / homology
Function and homology information


DNA-binding transcription factor activity / DNA binding / cytosol
Similarity search - Function
Protein of unknown function (DUF3539) / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #870 / 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 ...Protein of unknown function (DUF3539) / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #870 / 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 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Cyclic nucleotide-monophosphate binding domain / Cyclic nucleotide-binding domain / cAMP/cGMP binding motif profile. / Cyclic nucleotide-binding domain / Cyclic nucleotide-binding domain superfamily / Jelly Rolls / RmlC-like jelly roll fold / Helix non-globular / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Special / SH3 type barrels. / Arc Repressor Mutant, subunit A / Roll / Winged helix DNA-binding domain superfamily / Jelly Rolls / Winged helix-like DNA-binding domain superfamily / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
2-OXOGLUTARIC ACID / Global nitrogen regulator / PipX
Similarity search - Component
Biological speciesSYNECHOCOCCUS ELONGATUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
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.
History
DepositionJul 11, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 18, 2010Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.
Remark 700 SHEET DETERMINATION METHOD: AUTHOR PROVIDED.

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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: PIPX
D: PIPX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,0986
Polymers70,8064
Non-polymers2922
Water1,802100
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9610 Å2
ΔGint-44.7 kcal/mol
Surface area27310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.020, 52.020, 227.730
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12C
22D

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1111A1 - 222
2111B1 - 222
1121C1 - 89
2121D1 - 89

NCS ensembles :
ID
1
2

NCS oper:
IDCodeMatrixVector
1given(0.0004, 1), (1, 0.0004, 0.0007), (0.0007, -1)-26.0092, 26.0024, 0.0727
2given(0.001, 1, 0.0007), (1, 0.001, 0.0005), (0.0005, 0.0007, -1)-25.9893, 25.9983, 0.0873

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Components

#1: Protein GLOBAL NITROGEN REGULATOR / NTCA


Mass: 24862.053 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SYNECHOCOCCUS ELONGATUS (bacteria) / Strain: PCC 7942 / Plasmid: PET15B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): ROSETTA / References: UniProt: P29283
#2: Protein PIPX


Mass: 10540.987 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SYNECHOCOCCUS ELONGATUS (bacteria) / Strain: PCC 7942 / Plasmid: PTRC99A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q7X386
#3: Chemical ChemComp-AKG / 2-OXOGLUTARIC ACID


Mass: 146.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H6O5
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 100 / Source method: isolated from a natural source / Formula: H2O

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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 Å3/Da / Density % sol: 43.5 % / Description: NONE
Crystal growpH: 5.5
Details: NTCA-PIPX COMPLEX WAS 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. CRYSTALLIZATION ...Details: NTCA-PIPX COMPLEX WAS 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. CRYSTALLIZATION SOLUTION: 50 MM MES PH 5.5, 1M SODIUM MALONATE 10 MM MANGANESE CHLORIDE, 2% MPD, 5% DMSO.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM16 / Wavelength: 1.007
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Feb 26, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.007 Å / Relative weight: 1
ReflectionResolution: 2.25→56.89 Å / Num. obs: 28245 / % possible obs: 98.9 % / Observed criterion σ(I): 2 / Redundancy: 6.9 % / Biso Wilson estimate: 36.2 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 7.1
Reflection shellResolution: 2.25→2.37 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 2 / % possible all: 98.9

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Processing

Software
NameVersionClassification
REFMAC5.5.0072refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2XHK

2xhk


Resolution: 2.25→25 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.917 / SU B: 15.998 / SU ML: 0.177 / Cross valid method: THROUGHOUT / ESU R: 0.412 / ESU R Free: 0.242 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ATOM RECORDS CONTAINS SUM OF TLS AND RESIDUAL B FACTORS
RfactorNum. reflection% reflectionSelection details
Rfree0.24533 1420 5 %RANDOM
Rwork0.21413 ---
obs0.2157 26813 98.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.677 Å2
Baniso -1Baniso -2Baniso -3
1--0.17 Å20 Å20 Å2
2---0.17 Å20 Å2
3---0.34 Å2
Refinement stepCycle: LAST / Resolution: 2.25→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4744 0 20 100 4864
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0224936
X-RAY DIFFRACTIONr_bond_other_d0.0010.023484
X-RAY DIFFRACTIONr_angle_refined_deg1.4191.9746668
X-RAY DIFFRACTIONr_angle_other_deg0.89638424
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7935610
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.47422.773238
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.91115898
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.1871552
X-RAY DIFFRACTIONr_chiral_restr0.080.2758
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0215452
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021076
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_it0.6171.52986
X-RAY DIFFRACTIONr_mcbond_other0.1321.51210
X-RAY DIFFRACTIONr_mcangle_it1.17124822
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.81331950
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.9994.51834
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

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A2884tight positional0.010.05
12B2884tight positional0.010.05
21C1258tight positional0.010.05
22D1258tight positional0.010.05
11A2884tight thermal0.050.5
12B2884tight thermal0.050.5
21C1258tight thermal0.050.5
22D1258tight thermal0.050.5
LS refinement shellResolution: 2.25→2.308 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.466 76 -
Rwork0.426 1755 -
obs--88.03 %
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)
13.28250.4544-0.98461.6162-0.06562.1374-0.07240.1134-0.0662-0.1008-0.09020.1589-0.0122-0.21060.16260.15020.0241-0.01720.0694-0.05790.061-4.20827.206-10.773
24.651-2.7466-2.08364.02391.63322.8032-0.1381-0.0007-0.51760.19190.00710.27450.23910.00590.13110.1099-0.03990.00220.2578-0.08010.1761-21.19437.36417.753
31.58620.43310.24753.2021.07342.216-0.0774-0.1025-0.15560.1174-0.0810.05110.2075-0.0090.15840.07160.02330.0630.1590.0190.0611.20121.80210.796
44.0877-2.7-1.57674.40881.98352.6452-0.02120.1825-0.3042-0.0091-0.14580.4963-0.0077-0.29030.16690.2578-0.03540.06660.1209-0.00560.170811.2154.806-17.691
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A11 - 222
2X-RAY DIFFRACTION2C4 - 89
3X-RAY DIFFRACTION3B11 - 222
4X-RAY DIFFRACTION4D4 - 89

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