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- PDB-3nbx: Crystal structure of E. coli RavA (Regulatory ATPase variant A) i... -

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Basic information

Entry
Database: PDB / ID: 3nbx
TitleCrystal structure of E. coli RavA (Regulatory ATPase variant A) in complex with ADP
ComponentsATPase ravA
KeywordsHYDROLASE / AAA+ ATPase / alpha-beta-alpha structure / Rossmann fold
Function / homology
Function and homology information


Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to catalyse transmembrane movement of substances / ATP hydrolysis activity / ATP binding / identical protein binding / cytosol / cytoplasm
Similarity search - Function
Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #1510 / Lipocalin - #430 / : / ATPase, RavA, C-terminal / ATPase RavA / ATPase RavA-like, AAA lid domain / MoxR domain / ATPase RavA, LARA domain / ATPase RavA, LARA domain superfamily / ATPase, RavA, C-terminal ...Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #1510 / Lipocalin - #430 / : / ATPase, RavA, C-terminal / ATPase RavA / ATPase RavA-like, AAA lid domain / MoxR domain / ATPase RavA, LARA domain / ATPase RavA, LARA domain superfamily / ATPase, RavA, C-terminal / AAA lid domain / MoxR domain in the MoxR-vWA-beta-propeller ternary systems / ATPase, RavA, LARA domain / AAA domain (dynein-related subfamily) / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Lipocalin / P-loop containing nucleotide triphosphate hydrolases / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Up-down Bundle / Beta Barrel / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / ATPase RavA
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 2.91 Å
AuthorsEl Bakkouri, M.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2010
Title: Structure of RavA MoxR AAA+ protein reveals the design principles of a molecular cage modulating the inducible lysine decarboxylase activity
Authors: El Bakkouri, M. / Gutsche, I. / Kanjee, U. / Zhao, B. / Yu, M. / Goret, G. / Schoehn, G. / Burmeister, W.P. / Houry, W.A.
History
DepositionJun 4, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 12, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 12, 2014Group: Structure summary
Revision 1.3Feb 21, 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

Downloads & links

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Assembly

Deposited unit
X: ATPase ravA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,1663
Polymers56,6431
Non-polymers5232
Water79344
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)162.232, 162.232, 55.316
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65
DetailsAUTHOR STATES THAT THE BIOLOGICAL ASSEMBLY IS A HEXAMER AND CAN BE GENERATED USING THE FOLLOWING MATRIX. 1.000000 0.000000 0.000000 -0.00000 0.000000 1.000000 0.000000 0.00000 0.000000 0.000000 1.000000 0.00000 0.519950 -0.829970 0.201980 -13.57312 0.788100 0.557320 0.261340 -13.64050 -0.329470 0.023300 0.943880 1.85240 -0.461170 -0.884830 0.066300 -8.33842 0.735400 -0.339340 0.586540 -32.81131 -0.496490 0.319260 0.807200 9.92959 -0.958100 -0.112630 -0.263350 10.26787 -0.081610 -0.773990 0.627920 -37.96370 -0.274550 0.623100 0.732370 14.40234 -0.453740 0.726710 -0.515760 25.73058 -0.888740 -0.326650 0.321620 -21.89569 0.065250 0.604310 0.794080 12.19125 0.511830 0.781950 -0.355780 19.18100 -0.828960 0.558250 0.034410 -4.21656 0.225520 0.277320 0.933940 5.02638

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Components

#1: Protein ATPase ravA / Regulatory ATPase variant A


Mass: 56642.836 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: 6His tag followed by TEV cleavage site / Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 MG1655 / Gene: b3746, JW3725, ravA, yieN / Plasmid: p11 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) pLysS
References: UniProt: P31473, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to catalyse transmembrane movement of substances
#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 44 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.71 Å3/Da / Density % sol: 66.84 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1 M MES pH 6.5, 2 mM ATP, 10 mM MgCl2, 0.1-0.6 M ammonium sulfate, 10-20% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 1.004 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jun 25, 2007
Details: 1 collimating mirror, 1 focusing toroidal mirror Si(111) double crystal monochromator
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.004 Å / Relative weight: 1
ReflectionResolution: 2.91→29.7 Å / Num. all: 18552 / Num. obs: 18402 / % possible obs: 99.19 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.7 % / Biso Wilson estimate: 88 Å2 / Rmerge(I) obs: 0.065 / Rsym value: 0.065 / Net I/σ(I): 25
Reflection shellResolution: 2.91→3.04 Å / Redundancy: 3.4 % / Mean I/σ(I) obs: 2.9 / Num. unique all: 2268 / % possible all: 95.6

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Processing

Software
NameVersionClassification
DNAdata collection
SHARPphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SIRAS / Resolution: 2.91→29.7 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.881 / SU B: 15.524 / SU ML: 0.295 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.379 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26923 939 5.1 %RANDOM
Rwork0.22345 ---
obs0.22574 17463 99.31 %-
all-18552 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 74.216 Å2
Baniso -1Baniso -2Baniso -3
1--2.31 Å2-1.16 Å20 Å2
2---2.31 Å20 Å2
3---3.47 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.379 Å0.55 Å
Refinement stepCycle: LAST / Resolution: 2.91→29.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3847 0 32 44 3923
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0223949
X-RAY DIFFRACTIONr_angle_refined_deg0.971.9795348
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.5795478
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.43324.18189
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.85115712
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9911532
X-RAY DIFFRACTIONr_chiral_restr0.0650.2600
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.022953
X-RAY DIFFRACTIONr_nbd_refined0.1850.21769
X-RAY DIFFRACTIONr_nbtor_refined0.2950.22694
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1080.2116
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1570.284
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1130.27
LS refinement shellResolution: 2.91→2.985 Å / Rfactor Rfree error: 0.053 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.388 53 -
Rwork0.345 1183 -
obs-1183 93.71 %

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