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- PDB-2xgx: Crystal structure of transcription factor NtcA from Synechococcus... -

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Basic information

Entry
Database: PDB / ID: 2xgx
TitleCrystal structure of transcription factor NtcA from Synechococcus elongatus (mercury derivative)
ComponentsGLOBAL NITROGEN REGULATOR
KeywordsTRANSCRIPTION / NITROGEN ASSIMILATION / CRP/FNR SUPERFAMILY / CYANOBACTERIA / 2-OXOGLUTARATE
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 / 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-OXOGLUTARIC ACID / : / Global nitrogen regulator
Similarity search - Component
Biological speciesSYNECHOCOCCUS ELONGATUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.85 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
DepositionJun 8, 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 1.3May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_conn / 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_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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

Downloads & links

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Assembly

Deposited unit
A: GLOBAL NITROGEN REGULATOR
B: GLOBAL NITROGEN REGULATOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,6277
Polymers49,7242
Non-polymers9035
Water1629
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5190 Å2
ΔGint-61.3 kcal/mol
Surface area18790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.393, 69.973, 149.002
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1112A1 - 20
2112B1 - 20
1211A21 - 22
2211B21 - 22
1312A61
2312B61
1411A62 - 80
2411B62 - 80
1515A81 - 85
2515B81 - 85
1611A86 - 102
2611B86 - 102
1712A103 - 105
2712B103 - 105
1811A107 - 112
2811B107 - 112
1914A113 - 117
2914B113 - 117
11011A118 - 141
21011B118 - 141
11112A142
21112B142
11211A143 - 162
21211B143 - 162
11312A186
21312B186
11411A187 - 190
21411B187 - 190
11512A191
21512B191
11611A192 - 197
21611B192 - 197
11712A199
21712B199
11811A200 - 204
21811B200 - 204
11912A205 - 206
21912B205 - 206
12011A207 - 222
22011B207 - 222
12112A163 - 166
22112B163 - 166
12211A167 - 185
22211B167 - 185
12312A31
22312B31
12411A32 - 60
22411B32 - 60
12511A24 - 30
22511B24 - 30
12612A23
22612B23

NCS oper: (Code: given
Matrix: (-0.4064, -0.9017, -0.1476), (-0.8989, 0.3656, 0.2416), (-0.1639, 0.2309, -0.9591)
Vector: -11.324, -2.0908, -31.8786)

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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
Details: AN HG ATOM BOUND TO EACH CYS 156 OF THE NTCA DIMER.
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: Chemical ChemComp-AKG / 2-OXOGLUTARIC ACID


Mass: 146.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H6O5
#3: Chemical ChemComp-HG / MERCURY (II) ION


Mass: 200.590 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Hg
#4: Chemical ChemComp-BTB / 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / BIS-TRIS BUFFER


Mass: 209.240 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H19NO5 / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 9 / 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: 3.25 Å3/Da / Density % sol: 62.2 % / Description: NONE
Crystal growpH: 6.5
Details: NTCA PROTEIN WAS AT 4.7 MG/ML 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 (2OG). ...Details: NTCA PROTEIN WAS AT 4.7 MG/ML 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 (2OG). CRISTALLIZATION SOLUTION: 0.1 M BIS-TRIS PH 6.5, 36 % PEG 400. THEN, SOAKED IN THE SAME SOLUTION CONTAINING ALSO 10MM 2OG AND 2 MM HGCL2.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM16 / Wavelength: 1.007
DetectorType: ADSC CCD / 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: 2.85→74.5 Å / Num. obs: 16626 / % possible obs: 97.3 % / Observed criterion σ(I): 1.9 / Redundancy: 6.6 % / Biso Wilson estimate: 74.73 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 8
Reflection shellResolution: 2.85→3 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 1.9 / % possible all: 97.3

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Processing

Software
NameVersionClassification
REFMAC5.5.0072refinement
MOSFLMdata reduction
SCALAdata scaling
SHELXSOFTWARE PACKAGEphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 2.85→50 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.909 / SU B: 28.068 / SU ML: 0.251 / Cross valid method: THROUGHOUT / ESU R: 0.745 / ESU R Free: 0.332 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS
RfactorNum. reflection% reflectionSelection details
Rfree0.2453 837 5 %RANDOM
Rwork0.21067 ---
obs0.21236 15751 97.07 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 65.129 Å2
Baniso -1Baniso -2Baniso -3
1-0.47 Å20 Å20 Å2
2--0.16 Å20 Å2
3----0.63 Å2
Refinement stepCycle: LAST / Resolution: 2.85→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3302 0 36 9 3347
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0223405
X-RAY DIFFRACTIONr_bond_other_d0.0030.022346
X-RAY DIFFRACTIONr_angle_refined_deg1.2981.9864602
X-RAY DIFFRACTIONr_angle_other_deg0.89835704
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0585425
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.35722.786140
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.51915601
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.8631530
X-RAY DIFFRACTIONr_chiral_restr0.0810.2550
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0213707
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02699
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_it0.2891.52123
X-RAY DIFFRACTIONr_mcbond_other0.0611.5857
X-RAY DIFFRACTIONr_mcangle_it0.56723431
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.931282
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.5414.51169
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

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A2361tight positional0.040.05
2B2361tight positional0.040.05
1A281medium positional0.020.5
2B281medium positional0.020.5
1A10loose positional0.035
2B10loose positional0.035
1A2361tight thermal0.050.5
2B2361tight thermal0.050.5
1A281medium thermal0.032
2B281medium thermal0.032
1A10loose thermal0.0310
2B10loose thermal0.0310
LS refinement shellResolution: 2.85→2.924 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.429 58 -
Rwork0.342 1104 -
obs--92.44 %
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)
14.79740.5262-0.13111.9784-1.27744.62630.111-0.28880.72260.1284-0.09420.1931-0.8396-0.259-0.01670.16210.04870.00760.1561-0.04560.1184-2.505-4.155-6.136
26.7083-1.18321.24447.4910.07332.0584-0.07860.29950.6564-0.4451-0.0405-0.7307-0.39990.48630.11910.1046-0.07980.02680.31670.03720.116518.749-12.017-7.956
33.68740.0632-0.09136.4341-0.7494.4460.04060.49180.6979-0.3014-0.14540.2916-0.7183-0.26820.10490.19570.0679-0.04410.30220.09270.1539-5.958-2.758-26.421
410.1165-0.56661.24888.14273.31853.66330.30550.3042-0.9564-0.4559-0.33761.01450.7665-0.35070.0320.443-0.0225-0.18950.3549-0.03410.2341-7.23-25.375-29.775
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A6 - 156
2X-RAY DIFFRACTION2A157 - 222
3X-RAY DIFFRACTION3B6 - 156
4X-RAY DIFFRACTION4B157 - 222

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