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- PDB-3gne: Crystal structure of alginate lyase vAL-1 from Chlorella virus -

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Basic information

Entry
Database: PDB / ID: 3gne
TitleCrystal structure of alginate lyase vAL-1 from Chlorella virus
ComponentsVAL-1
KeywordsLYASE / alginate lyase / polysaccharide lyase family 14 / chlorella virus
Function / homology: / Polysaccharide lyase 14 / Jelly Rolls - #200 / Jelly Rolls / Sandwich / Mainly Beta / CITRATE ANION / VAL-1
Function and homology information
Biological speciesChlorella virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.2 Å
AuthorsOgura, K. / Yamasaki, M. / Hashidume, T. / Yamada, T. / Mikami, B. / Hashimoto, W. / Murata, K.
CitationJournal: J.Biol.Chem. / Year: 2009
Title: Crystal structure of family 14 polysaccharide lyase with pH-dependent modes of action
Authors: Ogura, K. / Yamasaki, M. / Yamada, T. / Mikami, B. / Hashimoto, W. / Murata, K.
History
DepositionMar 17, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 20, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: VAL-1
B: VAL-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,01610
Polymers56,0852
Non-polymers9318
Water14,106783
1
A: VAL-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,5085
Polymers28,0431
Non-polymers4654
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: VAL-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,5085
Polymers28,0431
Non-polymers4654
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)60.699, 72.026, 60.711
Angle α, β, γ (deg.)90.00, 112.35, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein VAL-1 / alginate lyase vAL-1


Mass: 28042.572 Da / Num. of mol.: 2 / Fragment: C-terminal domain, residues 106-349
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chlorella virus / Strain: CVK-2 / Gene: vAL-1 / Plasmid: pET21b (Novagen) / Production host: Escherichia coli (E. coli)
References: UniProt: Q9DTZ2, mannuronate-specific alginate lyase
#2: Chemical ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H5O7
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 783 / 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: 2.19 Å3/Da / Density % sol: 43.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 15% PEG 4000, 15% iso-Propanol, 0.1M sodium citrate, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 0.7 Å
DetectorType: RIGAKU JUPITER 210 / Detector: CCD / Date: Jun 12, 2008
RadiationMonochromator: Si(111) double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.7 Å / Relative weight: 1
ReflectionResolution: 1.2→50 Å / Num. obs: 142201 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Num. measured all: 747443
Reflection shellResolution: 1.2→1.24 Å

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Processing

Software
NameClassification
HKL-2000data collection
SOLVEphasing
SHELXL-97refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 1.2→10 Å / Num. parameters: 43086 / Num. restraintsaints: 53335 / Isotropic thermal model: anisotropic / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
Details: ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) BY ?
RfactorNum. reflection% reflectionSelection details
Rfree0.1794 7082 5.3 %RANDOM
all0.1317 134829 --
obs0.1313 102582 89.7 %-
Refine analyzeNum. disordered residues: 24 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 4638
Refinement stepCycle: LAST / Resolution: 1.2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3793 0 62 783 4638
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.014
X-RAY DIFFRACTIONs_angle_d0.029
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0332
X-RAY DIFFRACTIONs_zero_chiral_vol0.079
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.098
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.018
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.015
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.046
X-RAY DIFFRACTIONs_approx_iso_adps0.105

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