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- PDB-1qaz: CRYSTAL STRUCTURE OF ALGINATE LYASE A1-III FROM SPHINGOMONAS SPEC... -

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Entry
Database: PDB / ID: 1qaz
TitleCRYSTAL STRUCTURE OF ALGINATE LYASE A1-III FROM SPHINGOMONAS SPECIES A1 AT 1.78A RESOLUTION
ComponentsPROTEIN (ALGINATE LYASE A1-III)
KeywordsLYASE / ALGINATE LYASE / CRYSTALS
Function / homology
Function and homology information


periplasmic space / lyase activity
Similarity search - Function
Alginate lyase domain / Alginate lyase / Alginate lyase 2 / Alginate lyase / Chondroitin AC/alginate lyase / Chondroitin AC/alginate lyase / Glycosyltransferase / Alpha/alpha barrel / Concanavalin A-like lectin/glucanase domain superfamily / Mainly Alpha
Similarity search - Domain/homology
Biological speciesSphingomonas sp. (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 1.78 Å
AuthorsYoon, H.-J.
CitationJournal: J.Mol.Biol. / Year: 1999
Title: Crystal structure of alginate lyase A1-III from Sphingomonas species A1 at 1.78 A resolution.
Authors: Yoon, H.J. / Mikami, B. / Hashimoto, W. / Murata, K.
History
DepositionApr 8, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 19, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: PROTEIN (ALGINATE LYASE A1-III)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,8423
Polymers39,6501
Non-polymers1922
Water5,368298
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.9, 92.4, 81.6
Angle α, β, γ (deg.)90.0, 104.0, 90.0
Int Tables number5
Cell settingmonoclinic
Space group name H-MC121

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Components

#1: Protein PROTEIN (ALGINATE LYASE A1-III) / E.C.3.5.1.45


Mass: 39649.594 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sphingomonas sp. (bacteria) / Plasmid: PISA412 / Production host: Bacillus subtilis (bacteria) / References: UniProt: Q9KWU1, EC: 3.5.1.45
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 298 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.25 Å3/Da / Density % sol: 45.44 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 49% (NH4)2SO4, 0.1M HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Components of the solutions
IDNameCrystal-IDSol-ID
1(NH4)2SO411
2HEPES11
3(NH4)2SO412
Crystal
*PLUS
Density % sol: 46 %
Crystal grow
*PLUS
Temperature: 20 ℃
Details: drop consists of equal volume of protein and reservoir solutions
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
117.2 mg/mlprotein1drop
20.1 M1drop
347-49 %satammonium sulfate1reservoir
40.1 MHEPES1reservoir

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: MACSCIENCE / Wavelength: 1.5418
DetectorType: SIEMENS HI-STAR / Detector: AREA DETECTOR / Date: Oct 23, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.79→26.31 Å / Num. obs: 30410 / % possible obs: 88.4 % / Observed criterion σ(F): 1 / Redundancy: 2.12 % / Rsym value: 0.032 / Net I/σ(I): 7.9
Reflection shellResolution: 1.78→1.84 Å / % possible all: 49.9
Reflection
*PLUS
Num. obs: 34661 / % possible obs: 90.2 % / Num. measured all: 127587 / Rmerge(I) obs: 0.05
Reflection shell
*PLUS

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Processing

Software
NameVersionClassification
FRAMBOdata collection
SADIEdata reduction
SAINTdata reduction
PHASESphasing
X-PLOR3.1refinement
SADIEdata scaling
SAINTdata scaling
RefinementResolution: 1.78→10 Å / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.233 2993 10 %RANDOM
Rwork0.18 ---
all-29746 --
obs-26753 89.9 %-
Refinement stepCycle: LAST / Resolution: 1.78→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2793 0 10 298 3101
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.012
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d2.67
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Num. reflection obs: 26746
Solvent computation
*PLUS
Displacement parameters
*PLUS

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