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- PDB-5xd9: Crystal structure analysis of 3,6-anhydro-L-galactonate cycloisomerase -

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Basic information

Entry
Database: PDB / ID: 5xd9
TitleCrystal structure analysis of 3,6-anhydro-L-galactonate cycloisomerase
Components3,6-anhydro-alpha-L-galactonate cycloisomerase
KeywordsISOMERASE / Enolase superfamily / 3 / 6-anhydro-L-galactonate cycloisomerase / lyase / barrel domain / capping domain
Function / homology
Function and homology information


3,6-anhydro-L-galactonate cycloisomerase / galactose catabolic process / hydro-lyase activity / isomerase activity / magnesium ion binding
Similarity search - Function
3,6-anhydro-alpha-L-galactonate cycloisomerase / : / Mandelate racemase/muconate lactonizing enzyme, N-terminal domain / Mandelate racemase / muconate lactonizing enzyme, N-terminal domain / Mandelate racemase/muconate lactonizing enzyme, C-terminal / Mandelate racemase / muconate lactonizing enzyme, C-terminal domain / Enolase C-terminal domain-like / Enolase C-terminal domain-like / Enolase-like C-terminal domain / Enolase-like, N-terminal domain ...3,6-anhydro-alpha-L-galactonate cycloisomerase / : / Mandelate racemase/muconate lactonizing enzyme, N-terminal domain / Mandelate racemase / muconate lactonizing enzyme, N-terminal domain / Mandelate racemase/muconate lactonizing enzyme, C-terminal / Mandelate racemase / muconate lactonizing enzyme, C-terminal domain / Enolase C-terminal domain-like / Enolase C-terminal domain-like / Enolase-like C-terminal domain / Enolase-like, N-terminal domain / Enolase-like, N-terminal / Enolase-like, C-terminal domain superfamily / Enolase-like; domain 1 / TIM Barrel / Alpha-Beta Barrel / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
3,6-anhydro-alpha-L-galactonate cycloisomerase
Similarity search - Component
Biological speciesVibrio sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsLee, S. / Choi, I.-G. / Kim, H.-Y.
CitationJournal: Biochem. Biophys. Res. Commun. / Year: 2017
Title: Crystal structure analysis of 3,6-anhydro-l-galactonate cycloisomerase suggests emergence of novel substrate specificity in the enolase superfamily
Authors: Lee, S. / Kim, K.H. / Kim, H.-Y. / Choi, I.-G.
History
DepositionMar 27, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 27, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 22, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 3,6-anhydro-alpha-L-galactonate cycloisomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,3453
Polymers41,2971
Non-polymers492
Water1,00956
1
A: 3,6-anhydro-alpha-L-galactonate cycloisomerase
hetero molecules

A: 3,6-anhydro-alpha-L-galactonate cycloisomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,6916
Polymers82,5932
Non-polymers974
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_557y,x,-z+21
Buried area4150 Å2
ΔGint-54 kcal/mol
Surface area25120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.821, 89.821, 142.467
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-521-

HOH

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Components

#1: Protein 3,6-anhydro-alpha-L-galactonate cycloisomerase / AHGA cycloisomerase


Mass: 41296.691 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio sp. (strain EJY3) (bacteria) / Strain: EJY3 / Gene: Vejaci, VEJY3_09370 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: H2IFX0, 3,6-anhydro-L-galactonate cycloisomerase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 56 / 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: 3.48 Å3/Da / Density % sol: 64.65 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.2M magnesium acetate tetrahydrate, 0.1M sodium cacodylate (pH 6.5), 20% (w/v) polyethylene glycol 8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9796 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 11, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 119413 / % possible obs: 95.2 % / Redundancy: 6.1 % / Net I/σ(I): 13.5

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIX1.9_1692phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5XD7

5xd7


Resolution: 2.6→47.406 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.46 / Phase error: 21.48
RfactorNum. reflection% reflection
Rfree0.2334 1769 10 %
Rwork0.1687 --
obs0.1752 17687 95.04 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.6→47.406 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2844 0 2 56 2902
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092909
X-RAY DIFFRACTIONf_angle_d1.1083941
X-RAY DIFFRACTIONf_dihedral_angle_d14.1791057
X-RAY DIFFRACTIONf_chiral_restr0.042431
X-RAY DIFFRACTIONf_plane_restr0.004507
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5996-2.66980.35351250.27221126X-RAY DIFFRACTION90
2.6698-2.74840.34781330.26811194X-RAY DIFFRACTION95
2.7484-2.83710.32851350.24921210X-RAY DIFFRACTION96
2.8371-2.93850.31531340.22451214X-RAY DIFFRACTION96
2.9385-3.05610.26491350.19721213X-RAY DIFFRACTION95
3.0561-3.19520.27931350.17441213X-RAY DIFFRACTION96
3.1952-3.36360.21911350.15271219X-RAY DIFFRACTION96
3.3636-3.57420.2231380.14761237X-RAY DIFFRACTION96
3.5742-3.85010.20611350.13631224X-RAY DIFFRACTION95
3.8501-4.23730.19351380.12161235X-RAY DIFFRACTION96
4.2373-4.850.18711370.12661240X-RAY DIFFRACTION96
4.85-6.10840.18851410.15681267X-RAY DIFFRACTION95
6.1084-47.41380.20711480.16941326X-RAY DIFFRACTION93

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