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- PDB-1vav: Crystal structure of alginate lyase PA1167 from Pseudomonas aerug... -

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Basic information

Entry
Database: PDB / ID: 1vav
TitleCrystal structure of alginate lyase PA1167 from Pseudomonas aeruginosa at 2.0 A resolution
ComponentsAlginate lyase PA1167
KeywordsLYASE / beta-sandwich / STRUCTURAL GENOMICS
Function / homologyAlginate lyase 2 / Alginate lyase / Jelly Rolls - #200 / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Mainly Beta / : / Alginate lyase 2 domain-containing protein
Function and homology information
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2 Å
AuthorsYamasaki, M. / Moriwaki, S. / Miyake, O. / Hashimoto, W. / Murata, K. / Mikami, B.
CitationJournal: J.Biol.Chem. / Year: 2004
Title: Structure and function of a hypothetical Pseudomonas aeruginosa protein PA1167 classified into family PL-7: a novel alginate lyase with a beta-sandwich fold.
Authors: Yamasaki, M. / Moriwaki, S. / Miyake, O. / Hashimoto, W. / Murata, K. / Mikami, B.
History
DepositionFeb 19, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 25, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Dec 27, 2023Group: 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

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Assembly

Deposited unit
A: Alginate lyase PA1167
B: Alginate lyase PA1167


Theoretical massNumber of molelcules
Total (without water)50,0362
Polymers50,0362
Non-polymers00
Water5,368298
1
A: Alginate lyase PA1167


Theoretical massNumber of molelcules
Total (without water)25,0181
Polymers25,0181
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Alginate lyase PA1167


Theoretical massNumber of molelcules
Total (without water)25,0181
Polymers25,0181
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.359, 70.219, 67.299
Angle α, β, γ (deg.)90.00, 94.77, 90.00
Int Tables number4
Space group name H-MP1211
Detailsbiological unit is monomer.

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Components

#1: Protein Alginate lyase PA1167


Mass: 25017.846 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: PAO1 / Plasmid: pET3a-PA1167 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: GenBank: 15596364, UniProt: Q9I4H0*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 298 / 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: 1.85 Å3/Da / Density % sol: 33.04 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: NaCl, Potassium sodium phosphate, MES-sodium phosphate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.9 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Mar 14, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. all: 34620 / Num. obs: 30777 / % possible obs: 88.9 % / Redundancy: 4 % / Biso Wilson estimate: 10.3 Å2 / Rmerge(I) obs: 0.106
Reflection shellResolution: 1.85→1.92 Å / Redundancy: 2 % / Rmerge(I) obs: 0.516 / Num. unique all: 1515 / % possible all: 43.8

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Processing

Software
NameVersionClassification
CNS1refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASESphasing
RefinementMethod to determine structure: MIR / Resolution: 2→37.78 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 827983.26 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.24 2472 10 %RANDOM
Rwork0.187 ---
obs0.187 24766 90.6 %-
all-27238 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 48.8885 Å2 / ksol: 0.382748 e/Å3
Displacement parametersBiso mean: 26.6 Å2
Baniso -1Baniso -2Baniso -3
1--0.97 Å20 Å20.5 Å2
2--8.13 Å20 Å2
3----7.16 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.27 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.22 Å0.13 Å
Refinement stepCycle: LAST / Resolution: 2→37.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3534 0 0 298 3832
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d26.2
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.8
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.279 379 10.3 %
Rwork0.203 3316 -
obs--81.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP

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