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- PDB-3a0n: Crystal structure of D-glucuronic acid-bound alginate lyase vAL-1... -

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Entry
Database: PDB / ID: 3a0n
TitleCrystal structure of D-glucuronic acid-bound alginate lyase vAL-1 from Chlorella virus
ComponentsVAL-1
KeywordsLYASE / alginate lyase / polysaccharide lyase family 14 / chlorella virus
Function / homologyVAL-1
Function and homology information
Specimen sourceChlorella virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO / 1.45 Å resolution
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.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Mar 23, 2009 / Release: Oct 20, 2009
RevisionDateData content typeGroupProviderType
1.0Oct 20, 2009Structure modelrepositoryInitial release
1.1Jul 13, 2011Structure modelNon-polymer description / Version format compliance

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Structure visualization

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Assembly

Deposited unit
A: VAL-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,2372
Polyers28,0431
Non-polymers1941
Water8,647480
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)40.488, 71.046, 99.316
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP 21 21 21

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Components

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


Mass: 28042.572 Da / Num. of mol.: 1 / Fragment: C-terminal domain, residues 106-349 / Source: (gene. exp.) Chlorella virus / Strain: CVK-2 / Gene: vAL-1 / Plasmid name: pET21b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q9DTZ2, mannuronate-specific alginate lyase
#2: Chemical ChemComp-BDP / BETA-D-GLUCOPYRANURONIC ACID / D-GLUCURONIC ACID


Mass: 194.139 Da / Num. of mol.: 1 / Formula: C6H10O7 / Glucuronic acid
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 480 / Formula: H2O / Water

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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: 2.3 / Density percent sol: 51.71 %
Crystal growTemp: 293 K / Method: vapor diffusion / pH: 7
Details: 15% PEG 3350, 0.2M ammonium formate, 0.1M Hepes, pH 7.0, VAPOR DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 100 kelvins
SourceSource: SYNCHROTRON / Type: SPRING-8 BEAMLINE BL38B1 / Synchrotron site: SPring-8 / Beamline: BL38B1 / Wavelength: 1
DetectorType: RIGAKU JUPITER 210 / Detector: CCD / Collection date: Mar 7, 2009
RadiationMonochromator: Si (111) double crystal monochromator / Diffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionD resolution high: 1.4 Å / D resolution low: 50 Å / Number all: 56405 / Number obs: 56405 / Observed criterion sigma F: 0 / Observed criterion sigma I: 0 / Percent possible obs: 100
Reflection shellHighest resolution: 1.4 Å / Lowest resolution: 1.45 Å / Percent possible all: 100

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Processing

Software
NameClassification
SHELXmodel building
SHELXL-97refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefineMethod to determine structure: AB INITIO / R Free selection details: RANDOM / Cross valid method: FREE R / Sigma F: 4 / Stereochemistry target values: ENGH AND HUBER
Least-squares processR factor R free: 0.2227 / R factor all: 0.1853 / R factor obs: 0.1806 / Highest resolution: 1.45 Å / Lowest resolution: 1 Å / Number parameters: 10175 / Number reflection R free: 2239 / Number reflection all: 48310 / Number reflection obs: 46051 / Number restraintsaints: 8960 / Percent reflection R free: 4.8 / Percent reflection obs: 94
Refine analyzeNumber disordered residues: 33 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 2385
Refine hist #LASTHighest resolution: 1.45 Å / Lowest resolution: 1 Å
Number of atoms included #LASTProtein: 1892 / Nucleic acid: 0 / Ligand: 13 / Solvent: 480 / Total: 2385
Refine LS restraints
Refine IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.011
X-RAY DIFFRACTIONs_angle_d0.026
X-RAY DIFFRACTIONs_similar_dist0.000
X-RAY DIFFRACTIONs_from_restr_planes0.0306
X-RAY DIFFRACTIONs_zero_chiral_vol0.053
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.061
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.007
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.000
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.055
X-RAY DIFFRACTIONs_approx_iso_adps0.000

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