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- PDB-2d27: Structure of the N-terminal domain of XpsE (crystal form I4122) -

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Basic information

Entry
Database: PDB / ID: 2d27
TitleStructure of the N-terminal domain of XpsE (crystal form I4122)
Componentstype II secretion ATPase XpsEType II secretion system
KeywordsPROTEIN TRANSPORT / alpha-beta sandwich
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 / identical protein binding / plasma membrane
Similarity search - Function
Ribonucleotide Reductase Protein R1; domain 1 - #70 / Type II secretion system, protein E, N-terminal domain / Type II secretion system protein GspE / Type II secretion system protein GspE, N-terminal / MshEN domain / 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 / Ribonucleotide Reductase Protein R1; domain 1 ...Ribonucleotide Reductase Protein R1; domain 1 - #70 / Type II secretion system, protein E, N-terminal domain / Type II secretion system protein GspE / Type II secretion system protein GspE, N-terminal / MshEN domain / 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 / Ribonucleotide Reductase Protein R1; domain 1 / GMP Synthetase; Chain A, domain 3 / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Type II secretion system protein E
Similarity search - Component
Biological speciesXanthomonas campestris (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.21 Å
AuthorsChen, Y. / Shiue, S.-J. / Huang, C.-W. / Chang, J.-L. / Chien, Y.-L. / Hu, N.-T. / Chan, N.-L.
CitationJournal: J.Biol.Chem. / Year: 2005
Title: Structure and Function of the XpsE N-Terminal Domain, an Essential Component of the Xanthomonas campestris Type II Secretion System
Authors: Chen, Y. / Shiue, S.-J. / Huang, C.-W. / Chang, J.-L. / Chien, Y.-L. / Hu, N.-T. / Chan, N.-L.
History
DepositionSep 3, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 20, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: type II secretion ATPase XpsE


Theoretical massNumber of molelcules
Total (without water)16,9581
Polymers16,9581
Non-polymers00
Water3,927218
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: type II secretion ATPase XpsE

A: type II secretion ATPase XpsE

A: type II secretion ATPase XpsE

A: type II secretion ATPase XpsE


Theoretical massNumber of molelcules
Total (without water)67,8324
Polymers67,8324
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z1
crystal symmetry operation10_555-x,-y,z1
crystal symmetry operation15_555y,x,-z1
Buried area12490 Å2
ΔGint-58 kcal/mol
Surface area27540 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)92.479, 92.479, 123.763
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122

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Components

#1: Protein type II secretion ATPase XpsE / Type II secretion system / XpsE


Mass: 16957.996 Da / Num. of mol.: 1 / Fragment: N-terminal domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xanthomonas campestris (bacteria) / Gene: xpsE / Plasmid: pET21C / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P31742
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 218 / 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: 3.15 Å3/Da / Density % sol: 60.9 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: ammonium sulfate, MgCl2, MES pH 5.6, PEG8000, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL12B2 / Wavelength: 0.9537, 0.9801, 0.9796
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 4, 2004
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.95371
20.98011
30.97961
ReflectionResolution: 2.21→28 Å / Num. obs: 13800 / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 2.21→2.29 Å / % possible all: 99.2

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Processing

Software
NameVersionClassificationNB
REFMACrefinement
PDB_EXTRACT1.7data extraction
HKL-2000data reduction
SCALEPACKdata scaling
SHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 2.21→28 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.925 / SU B: 4.49 / SU ML: 0.114 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.19 / ESU R Free: 0.175 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.236 677 5 %RANDOM
Rwork0.193 ---
all0.195 13800 --
obs0.195 13571 98.4 %-
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: 33.889 Å2
Baniso -1Baniso -2Baniso -3
1--0.67 Å20 Å20 Å2
2---0.67 Å20 Å2
3---1.34 Å2
Refinement stepCycle: LAST / Resolution: 2.21→28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1165 0 0 218 1383
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0211183
X-RAY DIFFRACTIONr_bond_other_d0.0020.021151
X-RAY DIFFRACTIONr_angle_refined_deg2.0552.0011602
X-RAY DIFFRACTIONr_angle_other_deg1.03532647
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.7855147
X-RAY DIFFRACTIONr_chiral_restr0.1590.2184
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021312
X-RAY DIFFRACTIONr_gen_planes_other0.010.02242
X-RAY DIFFRACTIONr_nbd_refined0.2480.2274
X-RAY DIFFRACTIONr_nbd_other0.2460.21332
X-RAY DIFFRACTIONr_nbtor_other0.0990.2804
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2480.2179
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1470.219
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3450.2101
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3120.227
X-RAY DIFFRACTIONr_mcbond_it1.281.5735
X-RAY DIFFRACTIONr_mcangle_it2.32521171
X-RAY DIFFRACTIONr_scbond_it3.5693448
X-RAY DIFFRACTIONr_scangle_it5.944.5431
LS refinement shellResolution: 2.21→2.267 Å / Total num. of bins used: 20
RfactorNum. reflection
Rfree0.395 77
Rwork0.296 911
all-988

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