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- PDB-1p9r: Crystal Structure of Vibrio cholerae putative NTPase EpsE -

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Basic information

Entry
Database: PDB / ID: 1p9r
TitleCrystal Structure of Vibrio cholerae putative NTPase EpsE
ComponentsGeneral secretion pathway protein E
KeywordsPROTEIN TRANSPORT / Bacterial Type II secretion system cytoplasmic protein - GSPE / putative ATPase/ ATP binding protein / Metalloprotein (Metal-Cys4 site)
Function / homology
Function and homology information


protein-exporting ATPase activity / protein-secreting ATPase / protein secretion by the type II secretion system / type II protein secretion system complex / ATP hydrolysis activity / ATP binding / metal ion binding / plasma membrane
Similarity search - Function
Type II secretion system protein GspE / Beta-Lactamase - #90 / Type II secretion system protein GspE, N-terminal superfamily / Bacterial type II secretion system protein E signature. / Type II/IV secretion system protein / Type II/IV secretion system protein / Beta-Lactamase / P-loop containing nucleotide triphosphate hydrolases / ATPases associated with a variety of cellular activities / AAA+ ATPase domain ...Type II secretion system protein GspE / Beta-Lactamase - #90 / Type II secretion system protein GspE, N-terminal superfamily / Bacterial type II secretion system protein E signature. / Type II/IV secretion system protein / Type II/IV secretion system protein / Beta-Lactamase / P-loop containing nucleotide triphosphate hydrolases / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Type II secretion system ATPase E
Similarity search - Component
Biological speciesVibrio cholerae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.5 Å
AuthorsRobien, M.A. / Krumm, B.E. / Sandkvist, M. / Hol, W.G.J.
CitationJournal: J.Mol.Biol. / Year: 2003
Title: Crystal structure of the extracellular protein secretion NTPase EpsE of Vibrio cholerae
Authors: Robien, M.A. / Krumm, B.E. / Sandkvist, M. / Hol, W.G.J.
History
DepositionMay 12, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 14, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: General secretion pathway protein E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,2203
Polymers47,1191
Non-polymers1012
Water2,000111
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)103.611, 103.611, 166.261
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein General secretion pathway protein E / Type II traffic warden ATPase / Cholera toxin secretion protein epsE


Mass: 47118.906 Da / Num. of mol.: 1 / Fragment: N-terminal truncation of residues 1-90
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae (bacteria) / Gene: EPSE OR VC2732 / Plasmid: pQE70 / Production host: Escherichia coli (E. coli) / Strain (production host): M15 / References: UniProt: P37093
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 111 / 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: 2.73 Å3/Da / Density % sol: 54.99 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.2
Details: PEG 200,3-morpholinopropanesulfonate, ammonium acetate, AMP-PNP, pH 7.2, VAPOR DIFFUSION, SITTING DROP, temperature 293.0K
Crystal grow
*PLUS
pH: 6.3 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
15 mg/mlprotein1drop
20.1 MTEA1drop
30.5 M1dropNaCl
410 %glycerol1drop
51 mMTCEP1drop
61 mMEDTA1drop
712-18 %(v/v)PEG5000 MME1reservoir
80.15-0.20 Mammonium sulfate1reservoir
90.1 MMES1reservoirpH6.3

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 0.9748 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Aug 27, 2002 / Details: KOHZU: Double crystal: Si(111)
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9748 Å / Relative weight: 1
ReflectionResolution: 2.5→60 Å / Num. obs: 18982 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 12.7 % / Biso Wilson estimate: 48.8 Å2 / Rsym value: 0.102 / Net I/σ(I): 18.6
Reflection shellResolution: 2.5→2.54 Å / Redundancy: 13.2 % / Mean I/σ(I) obs: 4.3 / Num. unique all: 930 / Rsym value: 0.653 / % possible all: 100
Reflection
*PLUS
Highest resolution: 2.5 Å / Redundancy: 12.71 % / Num. measured all: 241296 / Rmerge(I) obs: 0.102
Reflection shell
*PLUS
% possible obs: 65.3 %

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
MOSFLMdata reduction
ELVESdata reduction
CCP4(SCALA)data scaling
SOLVEV. 2.02phasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 2.5→50 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc free: 0.89 / SU B: 5.11 / SU ML: 0.123 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.571 / ESU R Free: 0.318 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.26508 808 5 %RANDOM
Rwork0.21397 ---
obs0.21653 15262 84.9 %-
all-18927 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 39.879 Å2
Baniso -1Baniso -2Baniso -3
1-0.76 Å20.38 Å20 Å2
2--0.76 Å20 Å2
3----1.14 Å2
Refinement stepCycle: LAST / Resolution: 2.5→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2932 0 2 111 3045
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0212972
X-RAY DIFFRACTIONr_angle_refined_deg1.3741.9784005
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1555374
X-RAY DIFFRACTIONr_chiral_restr0.090.2475
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022171
X-RAY DIFFRACTIONr_nbd_refined0.2210.21276
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1640.2194
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2310.268
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1680.215
X-RAY DIFFRACTIONr_mcbond_it1.6572.51874
X-RAY DIFFRACTIONr_mcangle_it3.12563029
X-RAY DIFFRACTIONr_scbond_it4.22351098
X-RAY DIFFRACTIONr_scangle_it6.1278976
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.285 47
Rwork0.215 804
Refinement
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 50 Å / Rfactor Rfree: 0.265 / Rfactor Rwork: 0.214
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.011
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.374

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