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- PDB-2qsw: Crystal structure of C-terminal domain of ABC transporter / ATP-b... -

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Basic information

Entry
Database: PDB / ID: 2qsw
TitleCrystal structure of C-terminal domain of ABC transporter / ATP-binding protein from Enterococcus faecalis
ComponentsMethionine import ATP-binding protein metN 2
KeywordsHYDROLASE / ABC transporter / ATP-binding protein / structural genomics / APC87322.1 / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG / Amino-acid transport / Membrane / Nucleotide-binding
Function / homology
Function and homology information


ABC-type methionine transporter / ABC-type amino acid transporter activity / ATP hydrolysis activity / ATP binding / plasma membrane
Similarity search - Function
: / NIL domain / NIL domain / Methionine import ATP-binding protein metN family profile. / NIL / Methionine import ATP-binding protein MetN, ATP-binding domain / ACT domain / ABC transporter-like, conserved site / ABC transporters family signature. / ABC transporter ...: / NIL domain / NIL domain / Methionine import ATP-binding protein metN family profile. / NIL / Methionine import ATP-binding protein MetN, ATP-binding domain / ACT domain / ABC transporter-like, conserved site / ABC transporters family signature. / ABC transporter / ABC transporter-like, ATP-binding domain / ATP-binding cassette, ABC transporter-type domain profile. / Alpha-Beta Plaits / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Methionine import ATP-binding protein MetN 2
Similarity search - Component
Biological speciesEnterococcus faecalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.5 Å
AuthorsOsipiuk, J. / Bigelow, L. / Clancy, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: X-ray structure of C-terminal domain of ABC transporter / ATP-binding protein from Enterococcus faecalis.
Authors: Osipiuk, J. / Bigelow, L. / Clancy, S. / Joachimiak, A.
History
DepositionJul 31, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 21, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Remark 300 BIOMOLECULE: 1 SEE REMARK 350 FOR THE PROGRAM GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN ... BIOMOLECULE: 1 SEE REMARK 350 FOR THE PROGRAM GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN THIS ENTRY. AUTHORS STATE THAT THE BIOLOGICAL UNIT OF THIS POLYPEPTIDE IS UNKNOWN.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Methionine import ATP-binding protein metN 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,5705
Polymers11,2821
Non-polymers2884
Water1,838102
1
A: Methionine import ATP-binding protein metN 2
hetero molecules

A: Methionine import ATP-binding protein metN 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,14010
Polymers22,5632
Non-polymers5778
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_755-x+2,y,-z1
Buried area2530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.896, 38.896, 111.938
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number95
Space group name H-MP4322
Components on special symmetry positions
IDModelComponents
11A-57-

HOH

21A-80-

HOH

31A-91-

HOH

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Components

#1: Protein Methionine import ATP-binding protein metN 2


Mass: 11281.647 Da / Num. of mol.: 1 / Fragment: C-terminal domain: Residues 249-345
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterococcus faecalis (bacteria) / Strain: V583 / Gene: metN2, EF_2498 / Plasmid: pMCSG7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q831K6, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to catalyse transmembrane movement of substances
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 102 / 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: 1.88 Å3/Da / Density % sol: 34.72 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.9
Details: 0.01 M Zinc sulfate, 0.1 M MES buffer pH 6.9, 25% PEG 550 MME, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9792 Å
DetectorType: SBC-3 / Detector: CCD / Date: Jul 30, 2007
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.5→26.8 Å / Num. all: 14492 / Num. obs: 14492 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11.2 % / Biso Wilson estimate: 25.1 Å2 / Rmerge(I) obs: 0.067 / Net I/σ(I): 45.5
Reflection shellResolution: 1.5→1.53 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.438 / Mean I/σ(I) obs: 2.48 / Num. unique all: 879 / % possible all: 94.2

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
SHELXDphasing
MLPHAREphasing
DMphasing
SOLVEphasing
RESOLVEphasing
HKL-3000phasing
RefinementMethod to determine structure: SAD / Resolution: 1.5→26.8 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.966 / SU B: 2.643 / SU ML: 0.045 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.092 / ESU R Free: 0.073 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1842 728 5 %RANDOM
Rwork0.1471 ---
all0.149 13709 --
obs0.149 13709 99.41 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.295 Å2
Baniso -1Baniso -2Baniso -3
1-0.23 Å20 Å20 Å2
2--0.23 Å20 Å2
3----0.45 Å2
Refinement stepCycle: LAST / Resolution: 1.5→26.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms712 0 9 102 823
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.022830
X-RAY DIFFRACTIONr_bond_other_d0.0020.02562
X-RAY DIFFRACTIONr_angle_refined_deg1.7041.9821144
X-RAY DIFFRACTIONr_angle_other_deg1.47131412
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6665117
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.78626.73946
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.21515169
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.781154
X-RAY DIFFRACTIONr_chiral_restr0.1950.2134
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02945
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02143
X-RAY DIFFRACTIONr_nbd_refined0.2380.2162
X-RAY DIFFRACTIONr_nbd_other0.2120.2646
X-RAY DIFFRACTIONr_nbtor_refined0.1730.2385
X-RAY DIFFRACTIONr_nbtor_other0.0870.2452
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1820.270
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.1470.26
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2720.223
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2620.273
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3120.217
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.0870.22
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.7431.5599
X-RAY DIFFRACTIONr_mcbond_other0.5841.5200
X-RAY DIFFRACTIONr_mcangle_it2.1072812
X-RAY DIFFRACTIONr_scbond_it3.183364
X-RAY DIFFRACTIONr_scangle_it4.5974.5317
X-RAY DIFFRACTIONr_rigid_bond_restr1.98131579
X-RAY DIFFRACTIONr_sphericity_free6.3923106
X-RAY DIFFRACTIONr_sphericity_bonded2.74531370
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.219 52 -
Rwork0.176 931 -
obs-983 94.61 %

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