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- PDB-4be3: crystal structure of the exolytic PL7 alginate lyase AlyA5 from Z... -

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Basic information

Entry
Database: PDB / ID: 4be3
Titlecrystal structure of the exolytic PL7 alginate lyase AlyA5 from Zobellia galactanivorans
ComponentsALGINATE LYASE, FAMILY PL7
KeywordsLYASE / FLAVOBACTERIUM
Function / homology
Function and homology information


mannuronate-specific alginate lyase / poly(beta-D-mannuronate) lyase activity / hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate metabolic process
Similarity search - Function
Alginate lyase 2 / Alginate lyase / Jelly Rolls - #200 / Prokaryotic membrane lipoprotein lipid attachment site profile. / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
S,R MESO-TARTARIC ACID / D(-)-TARTARIC ACID / L(+)-TARTARIC ACID / Alginate lyase, family PL7
Similarity search - Component
Biological speciesZOBELLIA GALACTANIVORANS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsThomas, F. / Jeudy, A. / Michel, G. / Czjzek, M.
CitationJournal: J.Biol.Chem. / Year: 2013
Title: Comparative Characterization of Two Marine Alginate Lyases from Zobellia Galactanivorans Reveals Distinct Modes of Action and Exquisite Adaptation to Their Natural Substrate.
Authors: Thomas, F. / Lundqvist, L.C.E. / Jam, M. / Jeudy, A. / Barbeyron, T. / Sandstrom, C. / Michel, G. / Czjzek, M.
History
DepositionMar 5, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 26, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 3, 2013Group: Database references
Revision 1.2Aug 28, 2013Group: Database references
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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

Downloads & links

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Assembly

Deposited unit
A: ALGINATE LYASE, FAMILY PL7
B: ALGINATE LYASE, FAMILY PL7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,0256
Polymers70,5522
Non-polymers4734
Water10,431579
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1780 Å2
ΔGint-16.6 kcal/mol
Surface area24830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.420, 93.910, 130.150
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein ALGINATE LYASE, FAMILY PL7


Mass: 35275.758 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ZOBELLIA GALACTANIVORANS (bacteria)
Description: ROSCOFF INHOUSE CULTURE AND ISOLATE AND GERMAN COLLECTION OF MICROORGANISMS (DSM)
Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21
References: UniProt: G0L2Y1, guluronate-specific alginate lyase, mannuronate-specific alginate lyase

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Non-polymers , 5 types, 583 molecules

#2: Chemical ChemComp-SRT / S,R MESO-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O6
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-TAR / D(-)-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O6
#5: Chemical ChemComp-TLA / L(+)-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O6
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 579 / 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: 3.63 Å3/Da / Density % sol: 66 % / Description: NONE
Crystal growpH: 7
Details: 22% PEG 3350 AND 0.2 M SODIUM/POTASSIUM TARTRATE, pH 7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.98
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 13, 2011 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.75→41.95 Å / Num. obs: 114168 / % possible obs: 99.4 % / Observed criterion σ(I): 0.1 / Redundancy: 8.47 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 16.53
Reflection shellResolution: 1.75→1.8 Å / Redundancy: 8.4 % / Rmerge(I) obs: 0.84 / Mean I/σ(I) obs: 2.3 / % possible all: 93.3

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2Z42

2z42


Resolution: 1.75→41.95 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.967 / SU B: 2.985 / SU ML: 0.05 / Cross valid method: THROUGHOUT / ESU R: 0.072 / ESU R Free: 0.073 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT. U VALUES WITH TLS ADDED. DISORDERED REGIONS WERE MODELED USING LOWERED OCCUPATION FACTORS ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT. U VALUES WITH TLS ADDED. DISORDERED REGIONS WERE MODELED USING LOWERED OCCUPATION FACTORS FOR SIDE CHAINS OF NOT WELL DEFINED RESIDUES
RfactorNum. reflection% reflectionSelection details
Rfree0.17802 5709 5 %RANDOM
Rwork0.15634 ---
obs0.15744 108458 99.44 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.959 Å2
Baniso -1Baniso -2Baniso -3
1-0.32 Å20 Å20 Å2
2--0.98 Å20 Å2
3----1.3 Å2
Refinement stepCycle: LAST / Resolution: 1.75→41.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4960 0 31 579 5570
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0330.025211
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.8961.9397092
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1095654
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.77925.294255
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.94615864
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.161513
X-RAY DIFFRACTIONr_chiral_restr0.3820.2743
X-RAY DIFFRACTIONr_gen_planes_refined0.0170.0214057
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.755→1.801 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.273 372 -
Rwork0.249 7119 -
obs--92.99 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.42790.06-0.07761.3321-0.53090.6669-0.0302-0.02750.0472-0.14330.10490.12020.07480.0341-0.07470.0396-0.0135-0.01610.05440.02660.03424.38391.56132.359
20.7144-0.1641-0.37730.58510.26370.76930.0358-0.04540.0531-0.0286-0.02930.03340.02630.0183-0.00660.0471-0.01010.0240.0213-0.00760.022125.292114.1940.54
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A40 - 350
2X-RAY DIFFRACTION2B40 - 350

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