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- PDB-3zpy: Crystal structure of the marine PL7 alginate lyase AlyA1 from Zob... -

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Basic information

Entry
Database: PDB / ID: 3zpy
TitleCrystal structure of the marine PL7 alginate lyase AlyA1 from Zobellia galactanivorans
ComponentsALGINATE LYASE, FAMILY PL7
KeywordsLYASE / POLYSACCHARIDASES / MARINE BACTERIAL ENZYME
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 / Coagulation factors 5/8 type C domain (FA58C) profile. / F5/8 type C domain / Coagulation factor 5/8 C-terminal domain / Jelly Rolls - #200 / Galactose-binding-like domain superfamily / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Alginate lyase, family PL7
Similarity search - Component
Biological speciesZOBELLIA GALACTANIVORANS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.43 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 4, 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_ncs_dom_lim / 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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.ptnr1_symmetry / _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_conn.ptnr2_symmetry / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_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)54,2114
Polymers54,1652
Non-polymers462
Water11,385632
1
A: ALGINATE LYASE, FAMILY PL7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,1052
Polymers27,0821
Non-polymers231
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: ALGINATE LYASE, FAMILY PL7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,1052
Polymers27,0821
Non-polymers231
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)43.860, 50.390, 55.520
Angle α, β, γ (deg.)69.14, 90.02, 84.92
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: ASN / End label comp-ID: ASN / Refine code: 5 / Auth seq-ID: 210 - 440 / Label seq-ID: 12 - 242

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.999991, -0.004242, 0.000898), (0.003756, -0.743863, 0.668322), (-0.002167, 0.668319, 0.743872)79.25528, 61.61369, -13.06502

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Components

#1: Protein ALGINATE LYASE, FAMILY PL7


Mass: 27082.391 Da / Num. of mol.: 2 / Fragment: CATALYTIC DOMAIN, RESIDUES 199-446
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ZOBELLIA GALACTANIVORANS (bacteria)
Description: INHOUSE ISOLATE OF ROSCOFF MARINE INSTITUTE AND DSM
Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21
References: UniProt: G0LAE1, mannuronate-specific alginate lyase, guluronate-specific alginate lyase
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 632 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE CRYSTAL STRUCTURE CONTAINS THE C-TERMINAL CATALYTIC DOMAIN ONLY

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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: 2.09 Å3/Da / Density % sol: 41 % / Description: NONE
Crystal growpH: 7 / Details: 0.2 M KSCN AND 28% PEG-MME 2000, pH 7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9334
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 13, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9334 Å / Relative weight: 1
ReflectionResolution: 1.43→43.48 Å / Num. obs: 78881 / % possible obs: 96.1 % / Observed criterion σ(I): 0.1 / Redundancy: 4.5 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 14.2
Reflection shellResolution: 1.43→1.47 Å / Redundancy: 4 % / Rmerge(I) obs: 0.22 / Mean I/σ(I) obs: 7.8 / % possible all: 94.2

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1UAI

1uai


Resolution: 1.43→43.66 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.933 / SU B: 2.005 / SU ML: 0.042 / Cross valid method: THROUGHOUT / ESU R: 0.081 / ESU R Free: 0.074 / 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
RfactorNum. reflection% reflectionSelection details
Rfree0.20451 3944 5 %RANDOM
Rwork0.1596 ---
obs0.16186 74936 96.25 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 10.76 Å2
Baniso -1Baniso -2Baniso -3
1--0.68 Å2-0.2 Å2-0.2 Å2
2--0.75 Å2-0.04 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.43→43.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3810 0 2 632 4444
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.023926
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.1021.9325335
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.695506
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.51725.337193
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.05115615
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.4461512
X-RAY DIFFRACTIONr_chiral_restr0.1860.2565
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.023082
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_restr8.84833926
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded8.25453839
Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A919medium positional0.080.5
2B919medium positional0.080.5
1A853loose positional0.275
2B853loose positional0.275
1A919medium thermal1.982
2B919medium thermal1.982
1A853loose thermal2.7410
2B853loose thermal2.7410
LS refinement shellResolution: 1.429→1.466 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.214 287 -
Rwork0.137 5455 -
obs--94.33 %
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)
10.14560.0871-0.02340.1690.06350.1855-0.00530.00080.0117-0.01930.00650.0099-0.0274-0.014-0.00110.01510.0046-0.00070.00370.00130.009829.326.20418.752
20.12140.0676-0.04790.0808-0.00770.2784-0.00580.0046-0.0160.010.0053-0.0230.0265-0.00480.00050.01380.00360.00060.00210.00150.013849.71547.7970.001
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A200 - 440
2X-RAY DIFFRACTION2B200 - 440

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