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- PDB-3our: Crystal structure of complex between EIIA and a novel pyruvate de... -

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Basic information

Entry
Database: PDB / ID: 3our
TitleCrystal structure of complex between EIIA and a novel pyruvate decarboxylase
Components
  • Phosphotransferase system IIA component
  • UPF0255 protein VV1_0328
KeywordsLYASE/TRANSFERASE / exhibit no hydrolase activity1 / LYASE-TRANSFERASE complex
Function / homology
Function and homology information


protein-Npi-phosphohistidine-sugar phosphotransferase / protein-N(pi)-phosphohistidine--N-acetyl-D-glucosamine phosphotransferase activity / protein-N(PI)-phosphohistidine-sugar phosphotransferase activity / carboxylesterase / carboxylesterase activity / phosphoenolpyruvate-dependent sugar phosphotransferase system / kinase activity
Similarity search - Function
Esterase FrsA / PTS EIIA domains phosphorylation site signature 1. / Phosphotransferase system, sugar-specific permease EIIA type 1 / phosphoenolpyruvate-dependent sugar phosphotransferase system, EIIA 1 / PTS_EIIA type-1 domain profile. / Esterase FrsA-like / Esterase FrsA-like / Glucose Permease (Domain IIA) / Glucose Permease (Domain IIA) / Duplicated hybrid motif ...Esterase FrsA / PTS EIIA domains phosphorylation site signature 1. / Phosphotransferase system, sugar-specific permease EIIA type 1 / phosphoenolpyruvate-dependent sugar phosphotransferase system, EIIA 1 / PTS_EIIA type-1 domain profile. / Esterase FrsA-like / Esterase FrsA-like / Glucose Permease (Domain IIA) / Glucose Permease (Domain IIA) / Duplicated hybrid motif / Distorted Sandwich / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
PTS system, glucose-specific IIA component / Esterase FrsA / PTS system, glucose-specific IIA component
Similarity search - Component
Biological speciesVibrio vulnificus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsJeong, C.S. / An, Y.J. / Cha, S.S.
CitationJournal: Nat.Chem.Biol. / Year: 2011
Title: FrsA functions as a cofactor-independent decarboxylase to control metabolic flux
Authors: Lee, K.J. / Jeong, C.S. / An, Y.J. / Lee, H.J. / Park, S.J. / Seok, Y.J. / Kim, P. / Lee, J.H. / Lee, K.H. / Cha, S.S.
History
DepositionSep 15, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 1, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 9, 2013Group: Database references
Revision 1.3Nov 1, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: UPF0255 protein VV1_0328
B: Phosphotransferase system IIA component
C: UPF0255 protein VV1_0328
D: Phosphotransferase system IIA component
E: UPF0255 protein VV1_0328
F: Phosphotransferase system IIA component
G: UPF0255 protein VV1_0328
H: Phosphotransferase system IIA component


Theoretical massNumber of molelcules
Total (without water)275,4388
Polymers275,4388
Non-polymers00
Water16,700927
1
A: UPF0255 protein VV1_0328
B: Phosphotransferase system IIA component


Theoretical massNumber of molelcules
Total (without water)68,8592
Polymers68,8592
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1740 Å2
ΔGint-10 kcal/mol
Surface area20920 Å2
MethodPISA
2
C: UPF0255 protein VV1_0328
D: Phosphotransferase system IIA component


Theoretical massNumber of molelcules
Total (without water)68,8592
Polymers68,8592
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1750 Å2
ΔGint-14 kcal/mol
Surface area21290 Å2
MethodPISA
3
E: UPF0255 protein VV1_0328
F: Phosphotransferase system IIA component


Theoretical massNumber of molelcules
Total (without water)68,8592
Polymers68,8592
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1680 Å2
ΔGint-11 kcal/mol
Surface area21210 Å2
MethodPISA
4
G: UPF0255 protein VV1_0328
H: Phosphotransferase system IIA component


Theoretical massNumber of molelcules
Total (without water)68,8592
Polymers68,8592
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1730 Å2
ΔGint-10 kcal/mol
Surface area20930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)322.866, 62.067, 126.362
Angle α, β, γ (deg.)90.00, 110.80, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
UPF0255 protein VV1_0328 / FERMENTATION/RESPIRATION SWITCH PROTEIN


Mass: 49265.230 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio vulnificus (bacteria) / Strain: CMCP6 / Gene: VV1_0328 / Plasmid: pQE / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: Q8DF91
#2: Protein
Phosphotransferase system IIA component / EIIA


Mass: 19594.232 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio vulnificus (bacteria) / Strain: CMCP6 / Gene: VV1_0212 / Plasmid: pQE / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: Q8DFJ9, UniProt: A0A3Q0L1G8*PLUS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 927 / 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: 2.15 Å3/Da / Density % sol: 42.75 %
Crystal growTemperature: 295 K / Method: microbatch / pH: 6.5
Details: 20% PEG MME 550, 0.1M MES pH 6.5, 0.01M Zn-Acetate, microbatch, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Feb 23, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.19→50 Å / Num. obs: 119307 / % possible obs: 98.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 13.7 Å2
Reflection shellResolution: 2.19→2.23 Å / % possible all: 95.1

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
CCP4model building
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
CCP4phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3MVE, 1O2F

3mve

1o2f


Resolution: 2.2→49.37 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 44259.56 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 1.1
RfactorNum. reflection% reflectionSelection details
Rfree0.248 5459 5 %RANDOM
Rwork0.201 ---
obs0.201 108181 90.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 43.3292 Å2 / ksol: 0.323852 e/Å3
Displacement parametersBiso mean: 36.9 Å2
Baniso -1Baniso -2Baniso -3
1--3.04 Å20 Å21.44 Å2
2--3.22 Å20 Å2
3----0.18 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.33 Å0.26 Å
Luzzati d res low-5 Å
Luzzati sigma a0.35 Å0.32 Å
Refinement stepCycle: LAST / Resolution: 2.2→49.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16723 0 0 927 17650
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d23.8
X-RAY DIFFRACTIONc_improper_angle_d0.91
LS refinement shellResolution: 2.2→2.34 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.312 757 5.1 %
Rwork0.287 14187 -
obs--75.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2ion.paramion.top
X-RAY DIFFRACTION3water_rep.paramwater_rep.top

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