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- PDB-3im0: Crystal structure of Chlorella virus vAL-1 soaked in 200mM D-gluc... -

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Entry
Database: PDB / ID: 3im0
TitleCrystal structure of Chlorella virus vAL-1 soaked in 200mM D-glucuronic acid, 10% PEG-3350, and 200mM glycine-NaOH (pH 10.0)
ComponentsVAL-1
KeywordsLYASE / alginate lyase / polysaccharide lyase family 14 / chlorella virus
Function / homology: / Polysaccharide lyase 14 / Jelly Rolls - #200 / Jelly Rolls / Sandwich / Mainly Beta / beta-D-glucopyranuronic acid / VAL-1
Function and homology information
Biological speciesChlorella virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO / Resolution: 1.66 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
DepositionAug 8, 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 1.2Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _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: VAL-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,2372
Polymers28,0431
Non-polymers1941
Water8,161453
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)40.402, 71.121, 100.705
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 VAL-1 / alginate lyase vAL-1


Mass: 28042.572 Da / Num. of mol.: 1 / Fragment: C-terminal domain, UNP residues 106-349
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chlorella virus / Strain: CVK-2 / Gene: vAL-1 / Plasmid: pET21b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q9DTZ2, mannuronate-specific alginate lyase
#2: Sugar ChemComp-BDP / beta-D-glucopyranuronic acid / beta-D-glucuronic acid / D-glucuronic acid / glucuronic acid


Type: D-saccharide, beta linking / Mass: 194.139 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H10O7
IdentifierTypeProgram
DGlcpAbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-glucopyranuronic acidCOMMON NAMEGMML 1.0
b-D-GlcpAIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcASNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 453 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsSINCE O1 OF BDP IS MISSING IN THIS ENTRY, ALTERNATIVELY IT MAY BE GCU(ALPHA-D-GLUCOPYRANURONIC ACID).

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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: 2.58 Å3/Da / Density % sol: 52.32 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 12% PEG 3350, 0.2M ammonium formate, 0.1M hepes-NaOH pH7.0, 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: 1 Å
DetectorType: RIGAKU JUPITER 210 / Detector: CCD / Date: Jun 29, 2009
RadiationMonochromator: Fixed exit Si 111 double crystal monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.66→26.32 Å / Num. all: 34464 / Num. obs: 34464 / % possible obs: 97.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.4 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 74.6
Reflection shellResolution: 1.66→1.72 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.144 / Mean I/σ(I) obs: 16.5 / Num. unique all: 3330 / % possible all: 97.5

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Processing

Software
NameClassification
HKL-2000data collection
CNSrefinement
SHELXL-97refinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: AB INITIO
Starting model: PDB ENTRY 3GNE

3gne


Resolution: 1.66→10 Å / Num. parameters: 9879 / Num. restraintsaints: 8643 / Isotropic thermal model: Isotropic / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.2163 1711 -RANDOM
Rwork0.1606 ---
all0.1634 32576 --
obs0.1634 32576 93 %-
Refine analyzeNum. disordered residues: 14 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 2363.52
Refinement stepCycle: LAST / Resolution: 1.66→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1901 0 12 453 2366
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.009
X-RAY DIFFRACTIONs_angle_d0.025
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0302
X-RAY DIFFRACTIONs_zero_chiral_vol0.05
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.061
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.009
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.059
X-RAY DIFFRACTIONs_approx_iso_adps0

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