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- PDB-4tn5: Crystal Structure of Predicted Fructose Specific IIB from Escheri... -

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Basic information

Entry
Database: PDB / ID: 4tn5
TitleCrystal Structure of Predicted Fructose Specific IIB from Escherichia Coli
ComponentsFructose-like phosphotransferase enzyme IIB component 3
KeywordsTRANSFERASE / IIB / EIIB(fruc) / alpha/beta / phosphoryl group transferase / EIIA / EIIC
Function / homology
Function and homology information


protein-phosphocysteine-D-fructose-phosphotransferase system transporter activity / protein-Npi-phosphohistidine-D-fructose phosphotransferase / protein-N(PI)-phosphohistidine-fructose phosphotransferase system transporter activity / protein-phosphocysteine-sugar phosphotransferase activity / phosphoenolpyruvate-dependent sugar phosphotransferase system / kinase activity / plasma membrane / cytoplasm
Similarity search - Function
Phosphotransferase system, fructose-specific IIB subunit / Phosphotransferase system, EIIB component, type 2 / PTS_EIIB type-2 domain profile. / Phosphotransferase system, EIIB component, type 2/3 / PTS system IIB component-like superfamily / PTS system, Lactose/Cellobiose specific IIB subunit / Response regulator / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NICKEL (II) ION / PTS system fructose-like EIIB component 3
Similarity search - Component
Biological speciesEscherichia coli K12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.285 Å
AuthorsKim, M.S. / Shin, D.H.
Funding support Korea, Republic Of, 5items
OrganizationGrant numberCountry
NRF by MEST (NCRC)2012-0000952 Korea, Republic Of
NRF by MEST (CRC)2010K000266 Korea, Republic Of
NRF by MEST2008-331-C0023 Korea, Republic Of
NRF by MEST2010-0003907 Korea, Republic Of
NRF by MEST2013R1A1A1A05008769 Korea, Republic Of
CitationJournal: To Be Published
Title: High-accuracy protein modeling and its application to molecular replacement of crystallographic phasing
Authors: Kim, M.S. / Shin, D.H. / Lee, J. / Joo, K. / Park, J. / Lee, D. / Berry, E.A. / Jhon, G.-J.
History
DepositionJun 3, 2014Deposition site: RCSB / Processing site: PDBJ
SupersessionJun 10, 2015ID: 4JXD
Revision 1.0Jun 10, 2015Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Fructose-like phosphotransferase enzyme IIB component 3
B: Fructose-like phosphotransferase enzyme IIB component 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,6433
Polymers25,5852
Non-polymers591
Water30617
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area970 Å2
ΔGint-11 kcal/mol
Surface area11890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)33.110, 33.110, 154.281
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

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Components

#1: Protein Fructose-like phosphotransferase enzyme IIB component 3 / PTS system fructose-like EIIB component 3


Mass: 12792.314 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K12 (bacteria) / Gene: frwD, yijN, b3953, JW3925 / Production host: Escherichia coli (E. coli)
References: UniProt: P32676, protein-Npi-phosphohistidine-sugar phosphotransferase
#2: Chemical ChemComp-NI / NICKEL (II) ION / Nickel


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 17 / 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: 1.93 Å3/Da / Density % sol: 36.3 %
Description: 0.1M BIS-TRIS, 10MM NICKEL (II) HLORIDE, 10MM CESIUM CHLORIDE, 20% PEG MME 2000, PH 8.5,
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1M BIS-TRIS, 10MM NICKEL (II) CHLORIDE, 10MM CESIUM CHLORIDE, 20% PEG MME 2000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1.4869 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 14, 2005
RadiationMonochromator: SILICON DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.4869 Å / Relative weight: 1
ReflectionResolution: 2.28→51.43 Å / Num. obs: 7223 / % possible obs: 83.6 % / Redundancy: 5.8 % / Net I/σ(I): 11.6

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: dev_1420) / Classification: refinement
RefinementResolution: 2.285→51.427 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 41.63 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.299 717 10.01 %
Rwork0.2226 --
obs0.2302 7166 83.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.285→51.427 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1768 0 1 17 1786
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051792
X-RAY DIFFRACTIONf_angle_d1.2742426
X-RAY DIFFRACTIONf_dihedral_angle_d16.498664
X-RAY DIFFRACTIONf_chiral_restr0.087288
X-RAY DIFFRACTIONf_plane_restr0.005310
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2849-2.46130.4393490.2844468X-RAY DIFFRACTION30
2.4613-2.7090.37761420.29521393X-RAY DIFFRACTION89
2.709-3.1010.37251720.26691518X-RAY DIFFRACTION100
3.101-3.90670.31491770.23151539X-RAY DIFFRACTION100
3.9067-51.440.24621770.18951531X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 24.5925 Å / Origin y: -4.6085 Å / Origin z: 0.1919 Å
111213212223313233
T0.1726 Å2-0.0033 Å2-0.0307 Å2-0.1407 Å2-0.0127 Å2--0.2107 Å2
L0.8872 °20.61 °22.1633 °2-0.6521 °21.5285 °2--5.2794 °2
S0.0307 Å °-0.0014 Å °-0.1211 Å °-0.0261 Å °-0.0109 Å °-0.0807 Å °-0.1675 Å °-0.1231 Å °0.1894 Å °
Refinement TLS groupSelection details: all

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