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- PDB-1ojl: Crystal structure of a sigma54-activator suggests the mechanism f... -

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Basic information

Entry
Database: PDB / ID: 1ojl
TitleCrystal structure of a sigma54-activator suggests the mechanism for the conformational switch necessary for sigma54 binding
ComponentsTRANSCRIPTIONAL REGULATORY PROTEIN ZRAR
KeywordsRESPONSE REGULATOR / TWO COMPONENT SYSTEM / AAA DOMAIN / NTRC FAMILY / DNA-BINDING / TRANSCRIPTION REGULATION
Function / homology
Function and homology information


DNA-binding transcription activator activity / phosphorelay signal transduction system / cis-regulatory region sequence-specific DNA binding / protein-DNA complex / positive regulation of DNA-templated transcription / ATP hydrolysis activity / ATP binding / cytoplasm
Similarity search - Function
Sigma-54 interaction domain ATP-binding region A signature. / Sigma-54 interaction domain, conserved site / Sigma-54 interaction domain C-terminal part signature. / Sigma-54 interaction domain, ATP-binding site 1 / Sigma-54 interaction domain, ATP-binding site 2 / Sigma-54 interaction domain ATP-binding region B signature. / Sigma-54 interaction domain profile. / Sigma-54 interaction domain / RNA polymerase sigma factor 54 interaction domain / DNA binding HTH domain, Fis-type ...Sigma-54 interaction domain ATP-binding region A signature. / Sigma-54 interaction domain, conserved site / Sigma-54 interaction domain C-terminal part signature. / Sigma-54 interaction domain, ATP-binding site 1 / Sigma-54 interaction domain, ATP-binding site 2 / Sigma-54 interaction domain ATP-binding region B signature. / Sigma-54 interaction domain profile. / Sigma-54 interaction domain / RNA polymerase sigma factor 54 interaction domain / DNA binding HTH domain, Fis-type / Bacterial regulatory protein, Fis family / Helicase, Ruva Protein; domain 3 - #60 / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. / Homeodomain-like / CheY-like superfamily / Helicase, Ruva Protein; domain 3 / Homeobox-like domain superfamily / Arc Repressor Mutant, subunit A / P-loop containing nucleotide triphosphate hydrolases / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / PHOSPHATE ION / Transcriptional regulatory protein ZraR
Similarity search - Component
Biological speciesSALMONELLA TYPHIMURIUM (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 3 Å
AuthorsSallai, L. / Tucker, P.A.
CitationJournal: J. Struct. Biol. / Year: 2005
Title: Crystal structure of the central and C-terminal domain of the sigma(54)-activator ZraR.
Authors: Sallai, L. / Tucker, P.A.
History
DepositionJul 10, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 19, 2005Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 13, 2018Group: Data collection / Database references / Category: citation / diffrn_radiation
Item: _citation.journal_abbrev / _citation.page_last ..._citation.journal_abbrev / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _diffrn_radiation.pdbx_diffrn_protocol
Revision 1.4May 8, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.method
Revision 1.5May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TRANSCRIPTIONAL REGULATORY PROTEIN ZRAR
B: TRANSCRIPTIONAL REGULATORY PROTEIN ZRAR
C: TRANSCRIPTIONAL REGULATORY PROTEIN ZRAR
D: TRANSCRIPTIONAL REGULATORY PROTEIN ZRAR
E: TRANSCRIPTIONAL REGULATORY PROTEIN ZRAR
F: TRANSCRIPTIONAL REGULATORY PROTEIN ZRAR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)203,41412
Polymers202,4326
Non-polymers9826
Water1,838102
1
A: TRANSCRIPTIONAL REGULATORY PROTEIN ZRAR
B: TRANSCRIPTIONAL REGULATORY PROTEIN ZRAR
C: TRANSCRIPTIONAL REGULATORY PROTEIN ZRAR
hetero molecules

A: TRANSCRIPTIONAL REGULATORY PROTEIN ZRAR
B: TRANSCRIPTIONAL REGULATORY PROTEIN ZRAR
C: TRANSCRIPTIONAL REGULATORY PROTEIN ZRAR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)203,00112
Polymers202,4326
Non-polymers5706
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
MethodPQS
2
D: TRANSCRIPTIONAL REGULATORY PROTEIN ZRAR
E: TRANSCRIPTIONAL REGULATORY PROTEIN ZRAR
F: TRANSCRIPTIONAL REGULATORY PROTEIN ZRAR
hetero molecules

D: TRANSCRIPTIONAL REGULATORY PROTEIN ZRAR
E: TRANSCRIPTIONAL REGULATORY PROTEIN ZRAR
F: TRANSCRIPTIONAL REGULATORY PROTEIN ZRAR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)203,82612
Polymers202,4326
Non-polymers1,3946
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_454-x-1,y,-z-1/21
MethodPQS
Unit cell
Length a, b, c (Å)107.440, 114.740, 187.260
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number17
Space group name H-MP2221
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.01748, -0.72577, -0.68771), (0.67163, 0.51805, -0.52965), (0.74068, -0.45263, 0.49651)-29.60146, -15.92121, 15.51326
2given(-0.06139, -0.75914, 0.64802), (0.6834, -0.50516, -0.52704), (0.72746, 0.4105, 0.54981)32.20237, -33.45885, 34.52425
3given(-0.98746, 0.07013, -0.14141), (0.07173, 0.9974, -0.00623), (0.14061, -0.0163, -0.98993)-56.45045, 9.842, 7.73447
4given(-0.62958, -0.18706, 0.75408), (-0.05856, 0.97925, 0.19402), (-0.77473, 0.078, -0.62747)-2.86014, 7.12358, -22.07212
5given(0.35725, -0.08985, 0.92968), (-0.0573, 0.99138, 0.11784), (-0.93225, -0.09537, 0.34903)61.41856, 6.83556, 9.65586
6given(-0.49283, -0.08406, -0.86606), (-0.08795, 0.99504, -0.04653), (0.86567, 0.05324, -0.49778)38.60946, -1.93878, 70.81321
7given(0.5506, -0.12315, -0.82564), (0.04778, 0.99209, -0.11612), (0.8334, 0.02449, 0.55212)37.67504, 2.80946, 21.62971
8given(-0.98507, 0.09239, -0.14528), (0.09801, 0.99467, -0.03205), (0.14154, -0.04581, -0.98887)-56.31959, 10.99685, 7.55039
9given(-0.62393, -0.09184, 0.77606), (-0.02414, 0.99486, 0.09833), (-0.7811, 0.04261, -0.62294)0.02741, 7.44891, -22.632
10given(0.42684, -0.15815, 0.89039), (-0.04876, 0.97913, 0.19729), (-0.90301, -0.12762, 0.41022)58.81954, 10.16251, 12.08483
11given(-0.51139, -0.06681, -0.85675), (0.037, 0.99434, -0.09963), (0.85855, -0.08265, -0.50602)37.72173, 4.47624, 67.75424
12given(0.48458, -0.11637, -0.86697), (0.07403, 0.99301, -0.09192), (0.87161, -0.01964, 0.48981)36.74771, 2.98881, 22.723

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Components

#1: Protein
TRANSCRIPTIONAL REGULATORY PROTEIN ZRAR / HYDG / ZRAR / STM4174 / STMF1.27


Mass: 33738.598 Da / Num. of mol.: 6
Fragment: ATPASE (AAA) AND DNA BINDING DOMAINS, RESIDUES 141-441
Source method: isolated from a genetically manipulated source
Details: N-TERMINAL(RECEIVER) DOMAIN DELETED / Source: (gene. exp.) SALMONELLA TYPHIMURIUM (bacteria) / Plasmid: PET28 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): B834 / References: UniProt: P25852
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 102 / Source method: isolated from a natural source / Formula: H2O
Compound detailsMEMBER OF THE TWO-COMPONENT REGULATORY SYSTEM ZRAS/ZRAR. ACTIVATED BY ZRAS AND ACTS IN CONJUNCTION ...MEMBER OF THE TWO-COMPONENT REGULATORY SYSTEM ZRAS/ZRAR. ACTIVATED BY ZRAS AND ACTS IN CONJUNCTION WITH SIGMA-54 TO REGULATE THE EXPRESSION OF ZRAP.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 3

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Sample preparation

CrystalDensity Matthews: 2.91 Å3/Da / Density % sol: 57 %
Crystal growMethod: vapor diffusion, sitting drop / pH: 8
Details: SITTING DROP VAPOUR DIFFUSION, WELL:100MM HEPES PH8.2 9% ISOPROPANOL, 3% METHANOL, 200MM NACL PROTEIN: 10-12MG/ML ,20MM CHES PH9.5,2MM DTT ,0.1MM EDTA. DROP 1:0.6 PROTEIN:WELL, pH 8.00

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.802
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 21, 2002 / Details: MIRRORS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.802 Å / Relative weight: 1
ReflectionResolution: 3→30 Å / Num. obs: 46186 / % possible obs: 97.5 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 10.9
Reflection shellResolution: 3→3.11 Å / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 2.6 / % possible all: 87.8

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
SHELXDphasing
SOLVEphasing
REFMACrefinement
RefinementMethod to determine structure: SIRAS / Resolution: 3→20 Å / SU B: 22.041 / SU ML: 0.415 / Cross valid method: THROUGHOUT / ESU R Free: 0.505
RfactorNum. reflection% reflectionSelection details
Rfree0.30833 2290 5 %RANDOM
Rwork0.25179 ---
obs0.25457 43710 97.5 %-
Displacement parametersBiso mean: 58.433 Å2
Baniso -1Baniso -2Baniso -3
1--6.68 Å20 Å20 Å2
2--14.59 Å20 Å2
3----7.91 Å2
Refinement stepCycle: LAST / Resolution: 3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12436 0 56 102 12594

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