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- PDB-4bq1: Crystal structure of of LamAcat from Zobellia galactanivorans -

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Basic information

Entry
Database: PDB / ID: 4bq1
TitleCrystal structure of of LamAcat from Zobellia galactanivorans
ComponentsENDO-1,3-BETA-GLUCANASE, FAMILY GH16
KeywordsHYDROLASE / MARINE LAMINARINASE
Function / homology
Function and homology information


glucan endo-1,3-beta-D-glucosidase / glucan endo-1,3-beta-D-glucosidase activity / carbohydrate metabolic process / metal ion binding
Similarity search - Function
Glycosyl hydrolases family 16 / Glycoside hydrolase family 16 / Glycosyl hydrolases family 16 (GH16) domain profile. / PKD domain superfamily / 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
Endo-1,3-beta-glucanase, family GH16
Similarity search - Component
Biological speciesZOBELLIA GALACTANIVORANS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsLabourel, A. / Jam, M. / Jeudy, A. / Michel, G. / Czjzek, M.
CitationJournal: J.Biol.Chem. / Year: 2014
Title: The Beta Glucanase Zglama from Zobellia Galactanivorans Evolved a Bent Active Site Adapted for Efficient Degradation of Algal Laminarin
Authors: Labourel, A. / Jam, M. / Jeudy, A. / Hehemann, J.H. / Czjzek, M. / Michel, G.
History
DepositionMay 29, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 18, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 25, 2013Group: Database references
Revision 1.2Feb 5, 2014Group: Database references
Revision 1.3Apr 3, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval
Revision 1.4May 8, 2019Group: Data collection / Experimental preparation
Category: database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow
Item: _exptl_crystal_grow.method
Revision 1.5Dec 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.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.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.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_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: ENDO-1,3-BETA-GLUCANASE, FAMILY GH16
B: ENDO-1,3-BETA-GLUCANASE, FAMILY GH16
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,7886
Polymers58,5242
Non-polymers2644
Water9,476526
1
A: ENDO-1,3-BETA-GLUCANASE, FAMILY GH16
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,3943
Polymers29,2621
Non-polymers1322
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: ENDO-1,3-BETA-GLUCANASE, FAMILY GH16
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,3943
Polymers29,2621
Non-polymers1322
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)44.559, 76.564, 142.119
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: LEU / Beg label comp-ID: LEU / End auth comp-ID: ARG / End label comp-ID: ARG / Refine code: 5 / Auth seq-ID: 140 - 380 / Label seq-ID: 13 - 253

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

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(0.749431, -0.29566, -0.5924), (-0.27028, -0.953423, 0.133918), (-0.604401, 0.059752, -0.794436)16.71359, 56.94989, 21.1462

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Components

#1: Protein ENDO-1,3-BETA-GLUCANASE, FAMILY GH16


Mass: 29261.910 Da / Num. of mol.: 2 / Fragment: CATALYTIC DOMAIN, RESIDUES 136-383
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ZOBELLIA GALACTANIVORANS (bacteria) / Strain: DSIJT
Description: GERMAN COLLECTION OF MICROORGANISMS (DSM) AND INHOUSE AT ROSCOFF COLLECTION.
Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: G0L5X4, glucan endo-1,3-beta-D-glucosidase
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 526 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE CONSTRUCTION CONTAINS THE CATALYTIC MODULE ONLY. THE N- TERMINAL PKD-MODULE HAS NOT BEEN CLONED.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.08 Å3/Da / Density % sol: 40.8 % / Description: NONE
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.2
Details: MONO-CRYSTALS WERE GROWN AT 4 DEGREE CELSIUS IN HANGING DROPS COMPOSED OF 2 MICROL OF ENZYME AT 10 MG.ML-1 AND 2 MICROL OF RESERVOIR SOLUTION CONTAINING 24% PEG 3350 AND 100 MM NA CITRATE PH 5.2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97915
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 17, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 1.45→47.37 Å / Num. obs: 86903 / % possible obs: 99.7 % / Observed criterion σ(I): 0 / Redundancy: 6.3 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 11
Reflection shellResolution: 1.45→1.53 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 3.5 / % possible all: 99.7

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3ILN

3iln


Resolution: 1.5→71.06 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.965 / SU B: 2.163 / SU ML: 0.037 / Cross valid method: THROUGHOUT / ESU R: 0.079 / ESU R Free: 0.064 / 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
Rfree0.1664 3929 5 %RANDOM
Rwork0.13752 ---
obs0.139 74179 99.14 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 18.139 Å2
Baniso -1Baniso -2Baniso -3
1-1.36 Å20 Å20 Å2
2---0.4 Å20 Å2
3----0.96 Å2
Refinement stepCycle: LAST / Resolution: 1.5→71.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4050 0 14 526 4590
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0280.024235
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.291.925776
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5345518
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.54125.242227
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.70515651
X-RAY DIFFRACTIONr_dihedral_angle_4_deg27.511510
X-RAY DIFFRACTIONr_chiral_restr0.2420.2587
X-RAY DIFFRACTIONr_gen_planes_refined0.0160.0213380
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_restr9.74934235
X-RAY DIFFRACTIONr_sphericity_free19.2555137
X-RAY DIFFRACTIONr_sphericity_bonded11.6654495
Refine LS restraints NCS

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

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A955medium positional0.20.5
2B955medium positional0.20.5
1A953loose positional0.485
2B953loose positional0.485
1A955medium thermal5.782
2B955medium thermal5.782
1A953loose thermal6.4410
2B953loose thermal6.4410
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.233 273 -
Rwork0.187 5145 -
obs--100 %
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)
10.0092-0.00220.00390.0116-0.00080.0094-0.00010.0001-0.00030.00080.0006-0.0006-0.00170.0007-0.00050.0005-0.0003-0.00010.00310.00020.00143.482720.382230.0626
20.0167-0.0011-0.00650.0013-0.00510.03070.00210.0008-0.00020.0011-0.00120.0002-0.0070.0004-0.00090.0025-0.0005-0.00020.0019-0.00010.0009-5.406839.3161-4.1401
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A133 - 383
2X-RAY DIFFRACTION2B133 - 383

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