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- PDB-1txk: Crystal structure of Escherichia coli OpgG -

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Basic information

Entry
Database: PDB / ID: 1txk
TitleCrystal structure of Escherichia coli OpgG
ComponentsGlucans biosynthesis protein G
KeywordsBIOSYNTHETIC PROTEIN / beta-sandwich
Function / homology
Function and homology information


beta-glucan biosynthetic process / catalytic activity / outer membrane-bounded periplasmic space / carbohydrate binding
Similarity search - Function
Glucan biosynthesis protein G / Glucan biosynthesis, periplasmic, MdoG C-terminal / Glucan biosynthesis protein MdoG/MdoD / Periplasmic glucan biosynthesis protein, MdoG / Beta-galactosidase; Chain A, domain 5 - #10 / Glycoside hydrolase-type carbohydrate-binding / Beta-galactosidase; Chain A, domain 5 / Galactose mutarotase-like domain superfamily / Distorted Sandwich / Immunoglobulin E-set ...Glucan biosynthesis protein G / Glucan biosynthesis, periplasmic, MdoG C-terminal / Glucan biosynthesis protein MdoG/MdoD / Periplasmic glucan biosynthesis protein, MdoG / Beta-galactosidase; Chain A, domain 5 - #10 / Glycoside hydrolase-type carbohydrate-binding / Beta-galactosidase; Chain A, domain 5 / Galactose mutarotase-like domain superfamily / Distorted Sandwich / Immunoglobulin E-set / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Glucans biosynthesis protein G
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.5 Å
AuthorsHanoulle, X. / Rollet, E. / Clantin, B. / Landrieu, I. / Odberg-Ferragut, C. / Lippens, G. / Bohin, J.P. / Villeret, V.
CitationJournal: J.Mol.Biol. / Year: 2004
Title: Structural Analysis of Escherichia coli OpgG, a Protein Required for the Biosynthesis of Osmoregulated Periplasmic Glucans.
Authors: Hanoulle, X. / Rollet, E. / Clantin, B. / Landrieu, I. / Odberg-Ferragut, C. / Lippens, G. / Bohin, J.P. / Villeret, V.
History
DepositionJul 5, 2004Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 7, 2004Provider: 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: Glucans biosynthesis protein G
B: Glucans biosynthesis protein G
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,2043
Polymers114,1812
Non-polymers231
Water8,593477
1
A: Glucans biosynthesis protein G
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,1132
Polymers57,0901
Non-polymers231
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Glucans biosynthesis protein G


Theoretical massNumber of molelcules
Total (without water)57,0901
Polymers57,0901
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3770 Å2
ΔGint-12 kcal/mol
Surface area41100 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)63.860, 88.120, 215.650
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Glucans biosynthesis protein G / OpgG


Mass: 57090.438 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: opgG / Plasmid: pET29a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)star / References: UniProt: P33136
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 477 / 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: 2.7 Å3/Da / Density % sol: 54 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG 200, sodium acetate, MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.9793, 0.9795, 0.9739
DetectorType: MARRESEARCH / Detector: CCD / Date: Jul 4, 2003 / Details: mirrors
RadiationMonochromator: Si crystals / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97931
20.97951
30.97391
ReflectionResolution: 2.5→20 Å / Num. obs: 80513 / % possible obs: 99 % / Biso Wilson estimate: 34.4 Å2
Reflection shellResolution: 2.5→2.6 Å / Num. unique all: 8507

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Processing

Software
NameVersionClassification
CNS1.1refinement
XNEMOdata reduction
XDSdata scaling
SHELXDphasing
RefinementMethod to determine structure: MAD / Resolution: 2.5→19.99 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 3445747.35 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.229 7856 9.8 %RANDOM
Rwork0.192 ---
obs0.192 80513 99 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 42.3278 Å2 / ksol: 0.346719 e/Å3
Displacement parametersBiso mean: 36.1 Å2
Baniso -1Baniso -2Baniso -3
1-5.35 Å20 Å20 Å2
2--4.28 Å20 Å2
3----9.63 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.33 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.32 Å0.2 Å
Refinement stepCycle: LAST / Resolution: 2.5→19.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7813 0 1 477 8291
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d26.1
X-RAY DIFFRACTIONc_improper_angle_d0.89
LS refinement shellResolution: 2.5→2.66 Å / Rfactor Rfree error: 0.008 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.273 1188 9.2 %
Rwork0.219 11756 -
obs-11756 95.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP

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