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- PDB-6bog: Crystal structure of RapA, a Swi2/Snf2 protein that recycles RNA ... -

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Basic information

Entry
Database: PDB / ID: 6bog
TitleCrystal structure of RapA, a Swi2/Snf2 protein that recycles RNA polymerase during transcription
ComponentsRNA polymerase-associated protein RapA
KeywordsTRANSCRIPTION / hydrolase
Function / homology
Function and homology information


hydrolase activity, acting on acid anhydrides / ATP-dependent chromatin remodeler activity => GO:0140658 / helicase activity / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / regulation of DNA-templated transcription / DNA binding / ATP binding
Similarity search - Function
SH3 type barrels. - #930 / Dihydrodipicolinate Reductase; domain 2 - #80 / Helix Hairpins - #1500 / Helix Hairpins - #2230 / Tandem AAA-ATPase domain / RNA polymerase recycling, bacterial, C-terminal / RNA polymerase-associated protein RapA / RapA, N-terminal Tudor like domain 1 / RapA, N-terminal Tudor-like domain 2 / RNA polymerase recycling family C-terminal ...SH3 type barrels. - #930 / Dihydrodipicolinate Reductase; domain 2 - #80 / Helix Hairpins - #1500 / Helix Hairpins - #2230 / Tandem AAA-ATPase domain / RNA polymerase recycling, bacterial, C-terminal / RNA polymerase-associated protein RapA / RapA, N-terminal Tudor like domain 1 / RapA, N-terminal Tudor-like domain 2 / RNA polymerase recycling family C-terminal / RapA N-terminal Tudor like domain / RapA N-terminal Tudor like domain 1 / SH3 type barrels. - #140 / SNF2-like, N-terminal domain superfamily / SNF2, N-terminal / SNF2-related domain / Helix Hairpins / Dihydrodipicolinate Reductase; domain 2 / Helix non-globular / Helicase conserved C-terminal domain / Special / SH3 type barrels. / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / P-loop containing nucleotide triphosphate hydrolases / Roll / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
RNA polymerase-associated protein RapA
Similarity search - Component
Biological speciesEscherichia coli O45:K1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 3.205 Å
Model detailsRNA polymerase-dependent ATPase
AuthorsShaw, G.X. / Gan, J. / Zhou, Y.N. / Zhang, R. / Joachimiak, A. / Jin, D.J. / Ji, X.
Citation
Journal: Structure / Year: 2008
Title: Structure of RapA, a Swi2/Snf2 protein that recycles RNA polymerase during transcription.
Authors: Shaw, G. / Gan, J. / Zhou, Y.N. / Zhi, H. / Subburaman, P. / Zhang, R. / Joachimiak, A. / Jin, D.J. / Ji, X.
#1: Journal: J. Biol. Chem. / Year: 2015
Title: Allosteric Activation of Bacterial Swi2/Snf2 (Switch/Sucrose Non-fermentable) Protein RapA by RNA Polymerase: BIOCHEMICAL AND STRUCTURAL STUDIES.
Authors: Kakar, S. / Fang, X. / Lubkowska, L. / Zhou, Y.N. / Shaw, G.X. / Wang, Y.X. / Jin, D.J. / Kashlev, M. / Ji, X.
History
DepositionNov 20, 2017Deposition site: RCSB / Processing site: RCSB
SupersessionDec 13, 2017ID: 3DMQ
Revision 1.0Dec 13, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2018Group: Database references / Category: citation / citation_author
Revision 1.2Aug 30, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation_author / database_2
Item: _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RNA polymerase-associated protein RapA
B: RNA polymerase-associated protein RapA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)222,7199
Polymers222,0472
Non-polymers6727
Water00
1
A: RNA polymerase-associated protein RapA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,3124
Polymers111,0231
Non-polymers2883
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: RNA polymerase-associated protein RapA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,4085
Polymers111,0231
Non-polymers3844
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)123.856, 123.856, 187.994
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number78
Space group name H-MP43

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Components

#1: Protein RNA polymerase-associated protein RapA / ATP-dependent helicase HepA


Mass: 111023.414 Da / Num. of mol.: 2 / Fragment: Full-length
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli O45:K1 (bacteria) / Strain: S88 / ExPEC / Gene: rapA, ECS88_0062 / Plasmid: pQE80L / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: B7MAI2, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4

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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: 62.18 % / Mosaicity: 1.203 °
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Ammonium sulfate, 1,4-Dioxane, Ethylene glycol, MES

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97935,0.97951
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 4, 2007 / Details: Mirrors
RadiationMonochromator: Double crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979351
20.979511
Reflection twinOperator: h,-k,-l / Fraction: 0.5
ReflectionResolution: 3.2→30 Å / Num. obs: 45885 / % possible obs: 99 % / Redundancy: 4.4 % / Rmerge(I) obs: 0.123 / Rpim(I) all: 0.064 / Rrim(I) all: 0.139 / Χ2: 0.982 / Net I/σ(I): 10.5 / Num. measured all: 203007
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
3.2-3.313.80.96645340.4260.5391.1120.92998.5
3.31-3.454.20.68246210.650.3650.7770.93799.5
3.45-3.64.40.43945590.8110.230.4980.96499.4
3.6-3.794.50.29746170.9130.1550.3360.97399.7
3.79-4.034.60.20146040.9570.1040.2270.9799.6
4.03-4.344.60.12745990.9830.0660.1440.99299.6
4.34-4.784.60.09146400.9890.0470.1031.0299.5
4.78-5.464.60.08345810.9910.0420.0931.01299.3
5.46-6.874.50.08546150.990.0440.0961.02999.1
6.87-304.50.06145150.9950.0320.0690.98595.9

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Processing

Software
NameClassification
SCALEPACKdata scaling
PHENIXrefinement
HKL-2000data collection
HKL-2000data reduction
SHELXDphasing
RefinementMethod to determine structure: MAD / Resolution: 3.205→29.193 Å / Cross valid method: FREE R-VALUE / Phase error: 29.63
Details: CNS refinement version 1.1 was used for early stage refinement.
RfactorNum. reflection% reflection
Rfree0.2789 995 2.17 %
Rwork0.2437 --
obs0.25 45884 98.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 267.96 Å2 / Biso mean: 105.3952 Å2 / Biso min: 37.36 Å2
Refinement stepCycle: final / Resolution: 3.205→29.193 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15438 0 35 0 15473
Biso mean--93.59 --
Num. residues----1934
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00515754
X-RAY DIFFRACTIONf_angle_d0.921346
X-RAY DIFFRACTIONf_chiral_restr0.052366
X-RAY DIFFRACTIONf_plane_restr0.0042838
X-RAY DIFFRACTIONf_dihedral_angle_d19.1275910
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.2085-3.37740.35821400.33666359649996
3.3774-3.58870.3611390.31576383652298
3.5887-3.86520.36541440.28916417656198
3.8652-4.2530.30741420.27476458660098
4.253-4.86590.25511420.24446411655397
4.8659-6.12090.25181420.24286437657997
6.1209-28.84850.24021450.19546340648595

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