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- PDB-5bxx: Crystal structure of the ectoine synthase from the cold-adapted m... -

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Basic information

Entry
Database: PDB / ID: 5bxx
TitleCrystal structure of the ectoine synthase from the cold-adapted marine bacterium Sphingopyxis alaskensis
ComponentsL-ectoine synthase
KeywordsLYASE / Compatible solute / Osmostress protectant / Chemical chaperone / Cupin
Function / homology
Function and homology information


ectoine synthase / ectoine synthase activity / ectoine biosynthetic process
Similarity search - Function
Ectoine synthase / Ectoine synthase / RmlC-like cupin domain superfamily / Jelly Rolls / RmlC-like jelly roll fold / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesSphingopyxis alaskensis RB2256 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2 Å
AuthorsWidderich, N. / Kobus, S. / Hoeppner, A. / Bremer, E. / Smits, S.H.J.
CitationJournal: Plos One / Year: 2016
Title: Biochemistry and Crystal Structure of Ectoine Synthase: A Metal-Containing Member of the Cupin Superfamily.
Authors: Widderich, N. / Kobus, S. / Hoppner, A. / Riclea, R. / Seubert, A. / Dickschat, J.S. / Heider, J. / Smits, S.H. / Bremer, E.
History
DepositionJun 9, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Apr 27, 2016Provider: repository / Type: Initial release
Revision 1.1Jul 20, 2016Group: Database references
Revision 1.2May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: L-ectoine synthase
B: L-ectoine synthase
C: L-ectoine synthase
D: L-ectoine synthase


Theoretical massNumber of molelcules
Total (without water)65,3094
Polymers65,3094
Non-polymers00
Water3,711206
1
A: L-ectoine synthase
B: L-ectoine synthase


Theoretical massNumber of molelcules
Total (without water)32,6552
Polymers32,6552
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2930 Å2
ΔGint-31 kcal/mol
Surface area10430 Å2
MethodPISA
2
C: L-ectoine synthase
D: L-ectoine synthase


Theoretical massNumber of molelcules
Total (without water)32,6552
Polymers32,6552
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2880 Å2
ΔGint-33 kcal/mol
Surface area10260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.520, 43.960, 138.540
Angle α, β, γ (deg.)90.00, 101.50, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
L-ectoine synthase / N-acetyldiaminobutyrate dehydratase


Mass: 16327.341 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sphingopyxis alaskensis RB2256 (bacteria)
Gene: ectC, Sala_2951 / Production host: Escherichia coli (E. coli) / References: UniProt: Q1GNW6, ectoine synthase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 206 / 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: 2.23 Å3/Da / Density % sol: 44.83 %
Crystal growTemperature: 285 K / Method: vapor diffusion / pH: 8
Details: 0.05 M calcium acetate, 0.1 M sodium acetate pH 4.5, 40% (v/v) 1,2-propanediol, hexanediol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97625 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Nov 19, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2→45.3 Å / Num. obs: 38862 / % possible obs: 98.73 % / Redundancy: 5.7 % / Rmerge(I) obs: 0.092 / Net I/σ(I): 11.8
Reflection shellResolution: 2→2.1 Å / Rmerge(I) obs: 0.532

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MIR / Resolution: 2→45.253 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.68 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2574 1730 4.45 %
Rwork0.2042 --
obs0.2065 38862 98.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→45.253 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3568 0 0 206 3774
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0153637
X-RAY DIFFRACTIONf_angle_d1.5734924
X-RAY DIFFRACTIONf_dihedral_angle_d14.1171330
X-RAY DIFFRACTIONf_chiral_restr0.063560
X-RAY DIFFRACTIONf_plane_restr0.007642
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0001-2.0590.32091430.27713056X-RAY DIFFRACTION99
2.059-2.12550.3281410.25783045X-RAY DIFFRACTION98
2.1255-2.20140.29031440.24163093X-RAY DIFFRACTION99
2.2014-2.28960.35191330.30762860X-RAY DIFFRACTION93
2.2896-2.39380.31621440.23513098X-RAY DIFFRACTION99
2.3938-2.520.27551450.23593100X-RAY DIFFRACTION99
2.52-2.67780.31450.24153116X-RAY DIFFRACTION99
2.6778-2.88450.29411440.24073094X-RAY DIFFRACTION100
2.8845-3.17480.30831460.23273140X-RAY DIFFRACTION100
3.1748-3.6340.25761470.20253124X-RAY DIFFRACTION99
3.634-4.57770.22331460.15993154X-RAY DIFFRACTION100
4.5777-45.26430.19171520.16033252X-RAY DIFFRACTION99

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