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- PDB-5fui: Crystal structure of the C-terminal CBM6 of LamC a marine laminar... -

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Basic information

Entry
Database: PDB / ID: 5fui
TitleCrystal structure of the C-terminal CBM6 of LamC a marine laminarianse from Zobellia galactanivorans
ComponentsENDO-1,3-BETA-GLUCANASE, FAMILY GH16
KeywordsHYDROLASE / CARBOHYDRATE BINDING MODULE / CBM6 / POLYSACCHARIDE FIXATION / MARINE BACTERIAL LAMINARINASE / ZOBELLIA GALACTANIVORANS
Function / homology
Function and homology information


glucan endo-1,3-beta-D-glucosidase / glucan endo-1,3-beta-D-glucosidase activity / carbohydrate binding / carbohydrate metabolic process / metal ion binding
Similarity search - Function
Secretion system C-terminal sorting domain / Secretion system C-terminal sorting domain / : / Cellulose binding, type IV / Cellulose Binding Domain Type IV / Glycosyl hydrolases family 16 / Carbohydrate binding module (family 6) / Glycoside hydrolase family 16 / Glycosyl hydrolases family 16 (GH16) domain profile. / CBM6 (carbohydrate binding type-6) domain profile. ...Secretion system C-terminal sorting domain / Secretion system C-terminal sorting domain / : / Cellulose binding, type IV / Cellulose Binding Domain Type IV / Glycosyl hydrolases family 16 / Carbohydrate binding module (family 6) / Glycoside hydrolase family 16 / Glycosyl hydrolases family 16 (GH16) domain profile. / CBM6 (carbohydrate binding type-6) domain profile. / Carbohydrate binding module family 6 / Galactose-binding domain-like / Galactose-binding-like domain superfamily / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
2-AMINOMETHYL-PYRIDINE / Endo-1,3-beta-glucanase, family GH16 / Endo-1,3-beta-glucanase, family GH16
Similarity search - Component
Biological speciesZOBELLIA GALACTANIVORANS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsLabourel, A. / Jam, M. / Legentil, L. / Sylla, B. / Hehemann, J.H. / Ficko-Blean, E. / Ferrieres, V. / Czjzek, M. / Michel, G.
CitationJournal: FEBS J. / Year: 2016
Title: Unraveling the Multivalent Binding of a Marine Family 6 Carbohydrate-Binding Module with its Native Laminarin Ligand.
Authors: Jam, M. / Ficko-Blean, E. / Labourel, A. / Larocque, R. / Czjzek, M. / Michel, G.
History
DepositionJan 27, 2016Deposition site: PDBE / Processing site: PDBE
SupersessionMar 2, 2016ID: 4CRR
Revision 1.0Mar 2, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 23, 2016Group: Database references
Revision 1.2Jun 8, 2016Group: Database references
Revision 1.3Jan 10, 2024Group: 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_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_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: ENDO-1,3-BETA-GLUCANASE, FAMILY GH16
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,8455
Polymers14,5131
Non-polymers3334
Water2,576143
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)78.056, 29.523, 51.872
Angle α, β, γ (deg.)90.00, 115.79, 90.00
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 14512.704 Da / Num. of mol.: 1 / Fragment: CARBOHYDRATE BINDING MODULE, RESIDUES 262-385
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ZOBELLIA GALACTANIVORANS (bacteria) / Description: GERMAN COLLECTION OF MICROORGANISMS (DSM) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: GOL2L9, UniProt: G0L2L9*PLUS
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-APY / 2-AMINOMETHYL-PYRIDINE


Mass: 108.141 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H8N2
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 143 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE CRYSTAL STRUCTURE CONTAINS THE CENTRAL CBM6 MODULE 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: 2.24 Å3/Da / Density % sol: 45.13 % / Description: NONE
Crystal growpH: 7.2
Details: 100 MM HEPES PH 7.2, 10 MM MGCL2 AND 27 % POLYACRYLIC ACID. MICROSEEDING WAS ESSENTIAL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.98
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 8, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.4→46.7 Å / Num. obs: 19499 / % possible obs: 93 % / Observed criterion σ(I): 0.1 / Redundancy: 2.8 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 10.5
Reflection shellResolution: 1.4→1.43 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 2 / % possible all: 65.3

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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 1UXZ

1uxz


Resolution: 1.4→46.71 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.968 / SU B: 2.346 / SU ML: 0.041 / Cross valid method: THROUGHOUT / ESU R: 0.067 / ESU R Free: 0.061 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.12704 1014 5.1 %RANDOM
Rwork0.1255 ---
obs0.12787 18751 92.6 %-
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: 16.104 Å2
Baniso -1Baniso -2Baniso -3
1--0.24 Å20 Å20.16 Å2
2---0.3 Å20.23 Å2
3---0.69 Å2
Refinement stepCycle: LAST / Resolution: 1.4→46.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms956 0 23 143 1122
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.021022
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.0641.9391394
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6735131
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.21125.31947
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.91215151
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.694153
X-RAY DIFFRACTIONr_chiral_restr0.1630.2147
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.021800
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_restr9.52531022
X-RAY DIFFRACTIONr_sphericity_free20.128534
X-RAY DIFFRACTIONr_sphericity_bonded8.90751107
LS refinement shellResolution: 1.398→1.434 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.314 54 -
Rwork0.213 862 -
obs--58.83 %

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