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- PDB-1tjl: Crystal structure of transcription factor DksA from E. coli -

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Basic information

Entry
Database: PDB / ID: 1tjl
TitleCrystal structure of transcription factor DksA from E. coli
ComponentsDnaK suppressor protein
KeywordsTRANSCRIPTION / DksA / transcription factor / RNA polymerase / stringent response / ppGpp / RIKEN Structural Genomics/Proteomics Initiative / RSGI / Structural Genomics
Function / homology
Function and homology information


guanosine tetraphosphate binding / double-strand break repair / regulation of gene expression / zinc ion binding / cytoplasm / cytosol
Similarity search - Function
DksA, coiled-coil domain / : / DnaK suppressor protein DksA, N-terminal domain / RNA polymerase-binding transcription factor DksA / DksA, N-terminal domain superfamily / Zinc finger, DksA/TraR C4-type conserved site / Zinc finger, DksA/TraR C4-type, bacteria / Prokaryotic dksA C4-type zinc finger. / Zinc finger, DksA/TraR C4-type / Prokaryotic dksA/traR C4-type zinc finger ...DksA, coiled-coil domain / : / DnaK suppressor protein DksA, N-terminal domain / RNA polymerase-binding transcription factor DksA / DksA, N-terminal domain superfamily / Zinc finger, DksA/TraR C4-type conserved site / Zinc finger, DksA/TraR C4-type, bacteria / Prokaryotic dksA C4-type zinc finger. / Zinc finger, DksA/TraR C4-type / Prokaryotic dksA/traR C4-type zinc finger / Prokaryotic dksA C4-type zinc finger profiles. / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
RNA polymerase-binding transcription factor DksA
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å
AuthorsPerederina, A. / Svetlov, V. / Vassylyeva, M.N. / Artsimovitch, I. / Yokoyama, S. / Vassylyev, D.G. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: Cell(Cambridge,Mass.) / Year: 2004
Title: Regulation through the secondary channel--structural framework for ppGpp-DksA synergism during transcription
Authors: Perederina, A. / Svetlov, V. / Vassylyeva, M.N. / Tahirov, T.H. / Yokoyama, S. / Artsimovitch, I. / Vassylyev, D.G.
History
DepositionJun 6, 2004Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 7, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 16, 2014Group: Other
Revision 1.4Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: DnaK suppressor protein
B: DnaK suppressor protein
C: DnaK suppressor protein
D: DnaK suppressor protein
E: DnaK suppressor protein
F: DnaK suppressor protein
G: DnaK suppressor protein
H: DnaK suppressor protein
I: DnaK suppressor protein
J: DnaK suppressor protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)176,20220
Polymers175,54810
Non-polymers65410
Water18,4111022
1
A: DnaK suppressor protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,6202
Polymers17,5551
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: DnaK suppressor protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,6202
Polymers17,5551
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: DnaK suppressor protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,6202
Polymers17,5551
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: DnaK suppressor protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,6202
Polymers17,5551
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: DnaK suppressor protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,6202
Polymers17,5551
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: DnaK suppressor protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,6202
Polymers17,5551
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
G: DnaK suppressor protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,6202
Polymers17,5551
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
8
H: DnaK suppressor protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,6202
Polymers17,5551
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
9
I: DnaK suppressor protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,6202
Polymers17,5551
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
10
J: DnaK suppressor protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,6202
Polymers17,5551
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
11
A: DnaK suppressor protein
C: DnaK suppressor protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,2404
Polymers35,1102
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1990 Å2
ΔGint-9 kcal/mol
Surface area18250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.319, 96.593, 117.477
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe likely biological assembly is monomer. There are ten monomers of DksA in the asymmetric unit.

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Components

#1: Protein
DnaK suppressor protein / DksA / transcription factor


Mass: 17554.787 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: DksA / Plasmid: pVS11 / Production host: Escherichia coli (E. coli) / References: UniProt: P0ABS1
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1022 / 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: 3.05 Å3/Da / Density % sol: 58 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: PEG4000, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1.0, 1.28270, 1.28300
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jan 15, 2004
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
111
21.28271
31.2831
ReflectionResolution: 2→40 Å / Num. all: 137829 / Num. obs: 135624 / % possible obs: 98.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.1 % / Biso Wilson estimate: 21.1 Å2 / Rmerge(I) obs: 0.046 / Net I/σ(I): 28
Reflection shellResolution: 2→2.07 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 3.4 / Num. unique all: 13234 / % possible all: 96.2

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
MLPHAREphasing
RefinementMethod to determine structure: MAD / Resolution: 2→38.95 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 2378304.89 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.268 6619 4.9 %RANDOM
Rwork0.228 ---
all0.233 137829 --
obs0.228 134935 97.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 82.2456 Å2 / ksol: 0.348578 e/Å3
Displacement parametersBiso mean: 56 Å2
Baniso -1Baniso -2Baniso -3
1--0.32 Å20 Å20 Å2
2---3.03 Å20 Å2
3---3.35 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.32 Å0.29 Å
Luzzati d res low-5 Å
Luzzati sigma a0.23 Å0.34 Å
Refinement stepCycle: LAST / Resolution: 2→38.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11790 0 10 1022 12822
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d19.9
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.79
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.311.5
X-RAY DIFFRACTIONc_mcangle_it2.352
X-RAY DIFFRACTIONc_scbond_it1.62
X-RAY DIFFRACTIONc_scangle_it2.652.5
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.346 1121 5.3 %
Rwork0.321 20116 -
obs--93 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMTOPH19_1.ION
X-RAY DIFFRACTION3PARAM19.ION

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