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- PDB-3la3: Crystal structure of NtcA in complex with 2,2-difluoropentanedioi... -

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Basic information

Entry
Database: PDB / ID: 3la3
TitleCrystal structure of NtcA in complex with 2,2-difluoropentanedioic acid
ComponentsGlobal nitrogen regulator
KeywordsTRANSCRIPTION / nitrogen regulator / Activator / DNA-binding / Transcription regulation
Function / homology
Function and homology information


DNA-binding transcription factor activity / DNA binding / cytosol
Similarity search - Function
Transcription regulator, NtcA / Transcription regulator HTH, Crp-type, conserved site / Crp-type HTH domain signature. / helix_turn_helix, cAMP Regulatory protein / Crp-type HTH domain profile. / Crp-like helix-turn-helix domain / Crp-type HTH domain / Cyclic nucleotide-monophosphate binding domain / Cyclic nucleotide-binding domain / cAMP/cGMP binding motif profile. ...Transcription regulator, NtcA / Transcription regulator HTH, Crp-type, conserved site / Crp-type HTH domain signature. / helix_turn_helix, cAMP Regulatory protein / Crp-type HTH domain profile. / Crp-like helix-turn-helix domain / 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 / Jelly Rolls / RmlC-like jelly roll fold / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / 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
2,2-difluoropentanedioic acid / Global nitrogen regulator
Similarity search - Component
Biological speciesAnabaena (bacteria)
MethodX-RAY DIFFRACTION / MAD / Resolution: 2.4 Å
AuthorsZhao, M.X. / Jiang, Y.L. / He, Y.X. / Chen, Y.F. / Teng, Y.B. / Chen, Y.X. / Zhang, C.C. / Zhou, C.Z.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2010
Title: Structural basis for the allosteric control of the global transcription factor NtcA by the nitrogen starvation signal 2-oxoglutarate.
Authors: Zhao, M.X. / Jiang, Y.L. / He, Y.X. / Chen, Y.F. / Teng, Y.B. / Chen, Y.X. / Zhang, C.C. / Zhou, C.Z.
History
DepositionJan 6, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 14, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)54,5814
Polymers54,2452
Non-polymers3362
Water2,882160
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3960 Å2
ΔGint-32 kcal/mol
Surface area18620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.030, 70.080, 149.730
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 / DNA-binding protein VF1 / Nitrogen-responsive regulatory protein


Mass: 27122.645 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Anabaena (bacteria) / Strain: PCC 7120 / Gene: alr4392, bifA, ntcA / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P0A4U6
#2: Chemical ChemComp-2FT / 2,2-difluoropentanedioic acid


Mass: 168.096 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H6F2O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 160 / 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: 3.29 Å3/Da / Density % sol: 62.61 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: 0.05M (NH4)2SO4, 25% pentaerythritol ethoxylate (3/4, EO/OH), pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418, 0.9792, 0.9795, 0.9700
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Dec 28, 2008
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.54181
20.97921
30.97951
40.971
ReflectionResolution: 2.4→149.07 Å / Num. obs: 27164 / % possible obs: 94.7 % / Redundancy: 3.6 % / Biso Wilson estimate: 58.3 Å2 / Rmerge(I) obs: 0.041 / Net I/σ(I): 18.4
Reflection shellResolution: 2.4→2.53 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.342 / Mean I/σ(I) obs: 3.1 / Num. unique all: 3632 / % possible all: 88.3

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
SHELXDphasing
REFMAC5.5.0066refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MAD / Resolution: 2.4→20.45 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.92 / SU B: 13.472 / SU ML: 0.144 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.269 / ESU R Free: 0.225 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25267 1373 5.1 %RANDOM
Rwork0.21119 ---
obs0.21328 25791 94.28 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 50.242 Å2
Baniso -1Baniso -2Baniso -3
1-0.58 Å20 Å20 Å2
2--0.9 Å20 Å2
3----1.47 Å2
Refinement stepCycle: LAST / Resolution: 2.4→20.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3109 0 22 160 3291
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0223208
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3022.0024326
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7055397
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.50622.891128
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.94215611
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8561528
X-RAY DIFFRACTIONr_chiral_restr0.0820.2524
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212277
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.691.51971
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.29723200
X-RAY DIFFRACTIONr_scbond_it1.89631237
X-RAY DIFFRACTIONr_scangle_it3.2184.51124
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.398 91 -
Rwork0.288 1717 -
obs--86.63 %
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)
10.73170.1762-0.05762.84080.03941.54420.0761-0.02270.03760.1407-0.0478-0.1793-0.05230.1539-0.02840.0885-0.0238-0.02520.1379-0.00720.02235.43224.39927.6
22.47220.6006-0.0611.17730.17461.04790.04860.09980.1212-0.0531-0.0260.0325-0.1405-0.0077-0.02250.05230.0188-0.00360.14460.02240.012-3.92827.1336.722
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A25 - 115
2X-RAY DIFFRACTION1A116 - 141
3X-RAY DIFFRACTION1A142 - 220
4X-RAY DIFFRACTION2B25 - 115
5X-RAY DIFFRACTION2B116 - 141
6X-RAY DIFFRACTION2B142 - 220

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