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- PDB-3oxp: Structure of phosphotransferase enzyme II, A component from Yersi... -

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Basic information

Entry
Database: PDB / ID: 3oxp
TitleStructure of phosphotransferase enzyme II, A component from Yersinia pestis CO92 at 1.2 A resolution
ComponentsPhosphotransferase enzyme II, A component
KeywordsTRANSFERASE / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / Phosphotransferase enzyme II / A component / Yersinia pestis CO92 / Amino acid biosynthesis
Function / homology
Function and homology information


carbohydrate transport / transferase activity
Similarity search - Function
PTS EIIA type-2 domain / Phosphoenolpyruvate-dependent sugar phosphotransferase system, EIIA 2 / PTS_EIIA type-2 domain profile. / Mannitol-specific EII; Chain A / Mannitol-specific EII; Chain A / Phosphotransferase/anion transporter / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PTS mannitol transporter subunit IIA / Phosphotransferase enzyme II, A component
Similarity search - Component
Biological speciesYersinia pestis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.2 Å
AuthorsFilippova, E.V. / Wawrzak, Z. / Kudritska, M. / Edwards, A. / Savchenko, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To be Published
Title: Structure of phosphotransferase enzyme II, A component from Yersinia pestis CO92 at 1.2 A resolution
Authors: Filippova, E.V. / Wawrzak, Z. / Kudritska, M. / Edwards, A. / Savchenko, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionSep 21, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 13, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Phosphotransferase enzyme II, A component
B: Phosphotransferase enzyme II, A component
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,7285
Polymers32,4442
Non-polymers2843
Water7,386410
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2170 Å2
ΔGint-33 kcal/mol
Surface area12440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.906, 57.946, 78.742
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1116A0 - 147
2116B0 - 147

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Components

#1: Protein Phosphotransferase enzyme II, A component / Putative phosphotransferase system IIA component


Mass: 16222.048 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yersinia pestis (bacteria) / Strain: CO92 / Gene: ptsN1, YPO2569, YP_2380, y1618 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIPL / References: UniProt: Q7CJ97, UniProt: A0A3N4AZU4*PLUS
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#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.: 410 / 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 Å3/Da / Density % sol: 38.52 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 2.5 M NH4 Sulphate, 0.1M Bis-Tris propane, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.96107 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 31, 2010 / Details: MIRROR
RadiationMonochromator: SI-111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96107 Å / Relative weight: 1
ReflectionResolution: 1.2→30 Å / Num. all: 81918 / Num. obs: 81918 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 5.9 % / Biso Wilson estimate: 16.1 Å2 / Rmerge(I) obs: 0.059 / Net I/σ(I): 23.12
Reflection shellResolution: 1.2→1.22 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.66 / Mean I/σ(I) obs: 2.2 / % possible all: 100

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Processing

Software
NameVersionClassification
Blu-IceMaxdata collection
PHENIXmodel building
CCP4model building
MrBUMPphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
CCP4phasing
RefinementMethod to determine structure: SAD / Resolution: 1.2→46.67 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.965 / SU B: 1.207 / SU ML: 0.025 / Isotropic thermal model: ANISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.041 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17861 4096 5 %RANDOM
Rwork0.14679 ---
obs0.14843 77534 99.59 %-
all-77534 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 10.718 Å2
Baniso -1Baniso -2Baniso -3
1-0.15 Å20 Å20 Å2
2--0.02 Å20 Å2
3----0.17 Å2
Refine analyzeLuzzati coordinate error obs: 0.15 Å
Refinement stepCycle: LAST / Resolution: 1.2→46.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2240 0 16 410 2666
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0222361
X-RAY DIFFRACTIONr_bond_other_d0.0030.021494
X-RAY DIFFRACTIONr_angle_refined_deg1.7181.9743238
X-RAY DIFFRACTIONr_angle_other_deg1.05433697
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9295310
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.22125.25897
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.35215379
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.7711512
X-RAY DIFFRACTIONr_chiral_restr0.1050.2392
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0212668
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02426
X-RAY DIFFRACTIONr_mcbond_it1.9021.51528
X-RAY DIFFRACTIONr_mcbond_other0.6731.5606
X-RAY DIFFRACTIONr_mcangle_it2.80522486
X-RAY DIFFRACTIONr_scbond_it4.1983833
X-RAY DIFFRACTIONr_scangle_it6.144.5752
X-RAY DIFFRACTIONr_rigid_bond_restr1.63533855
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 1748 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
loose positional0.515
loose thermal2.4910
LS refinement shellResolution: 1.2→1.22 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.269 262 -
Rwork0.232 5637 -
obs--100 %

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