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Basic information

Entry
Database: PDB / ID: 4crq
TitleCrystal structure of the catalytic domain of the modular laminarinase ZgLamC mutant E142S
ComponentsENDO-1,3-BETA-GLUCANASE, FAMILY GH16
KeywordsHYDROLASE / GLYCOSIDE HYDROLASE FAMILLY GH16 / MARINE BACTERIAL ENZYME
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 / Jelly Rolls - #200 / Galactose-binding-like domain superfamily / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
ACETATE ION / 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. / Legentil, L. / Sylla, B. / Ficko-Blean, E. / Hehemann, J.H. / Ferrieres, V. / Czjzek, M. / Michel, G.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2015
Title: Structural and Biochemical Characterization of the Laminarina Zglamc[Gh16] from Zobellia Galactanivorans Suggests Preferred Recognition of Branched Laminarin
Authors: Labourel, A. / Jam, M. / Legentil, L. / Sylla, B. / Hehemann, J.H. / Ferrieres, V. / Czjzek, M. / Michel, G.
History
DepositionFeb 28, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 14, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 11, 2015Group: Database references
Revision 1.2Feb 25, 2015Group: Database references
Revision 1.3Sep 13, 2017Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.type
Revision 1.4Dec 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)53,15217
Polymers52,4692
Non-polymers68215
Water7,674426
1
A: ENDO-1,3-BETA-GLUCANASE, FAMILY GH16
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,5778
Polymers26,2351
Non-polymers3427
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)26,5759
Polymers26,2351
Non-polymers3408
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)67.108, 68.061, 143.282
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: _ / Ens-ID: 1 / Beg auth comp-ID: ASP / Beg label comp-ID: ASP / End auth comp-ID: LYS / End label comp-ID: LYS / Refine code: _ / Auth seq-ID: 24 - 254 / Label seq-ID: 2 - 232

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

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 26234.705 Da / Num. of mol.: 2 / Fragment: CATALYTIC MODULE, RESIDUES 23-255 / Mutation: YES
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: G0L2L9, glucan endo-1,3-beta-D-glucosidase

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Non-polymers , 7 types, 441 molecules

#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical ChemComp-NA / SODIUM ION


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


Mass: 18.015 Da / Num. of mol.: 426 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsTHE CRYSTAL STRUCTURE CONTAINS A CONSTRUCTION CONSISTING OF THE N-TERMINAL CATALYTIC DOMAIN ONLY ...THE CRYSTAL STRUCTURE CONTAINS A CONSTRUCTION CONSISTING OF THE N-TERMINAL CATALYTIC DOMAIN ONLY AND THE ENZYME WAS INACTIVATED BY POINT MUTATION E142S

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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: 2.72 Å3/Da / Density % sol: 54.9 % / Description: NONE
Crystal growpH: 5
Details: 14% PEG 6000, 100 MM NA ACETATE PH 5.0, 220 MM MGCL2 AND 10% GLYCEROL.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.98
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 11, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.5→49.34 Å / Num. obs: 105701 / % possible obs: 99.8 % / Observed criterion σ(I): 0.1 / Redundancy: 6.6 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 17.9
Reflection shellResolution: 1.5→1.58 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.69 / Mean I/σ(I) obs: 2.6 / % possible all: 98.5

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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→48.98 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.965 / SU B: 2.562 / SU ML: 0.041 / Cross valid method: THROUGHOUT / ESU R: 0.058 / ESU R Free: 0.058 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES WITH TLS ADDED. HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.18576 5273 5 %RANDOM
Rwork0.14802 ---
obs0.14987 100295 99.9 %-
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: 27.847 Å2
Baniso -1Baniso -2Baniso -3
1-0.08 Å20 Å20 Å2
2---0.05 Å20 Å2
3----0.03 Å2
Refinement stepCycle: LAST / Resolution: 1.5→48.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3682 0 36 426 4144
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.023846
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6861.9015223
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7285469
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.41425.253217
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.22215573
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.431514
X-RAY DIFFRACTIONr_chiral_restr0.0880.2510
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0213112
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_restr3.6533846
X-RAY DIFFRACTIONr_sphericity_free26.5185172
X-RAY DIFFRACTIONr_sphericity_bonded15.47253995
Refine LS restraints NCS

Ens-ID: 1 / Number: 293 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.13 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.304 390 -
Rwork0.273 6839 -
obs--98.57 %
Refinement TLS params.

S33: -0.0004 Å ° / T12: -0.0003 Å2 / 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 °)T11 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.0123-0.013-0.0050.02720.00970.01390.00070.0033-0.0016-0.0048-0.00030.00110.0008-0.00430.00290.00080.0087-0.00010.008348.7523.26745.439
20.005-0.0027-0.00830.02340.00710.01560.00040.001-0.00010.00020-0.00080.0003-0.00090.00070.00020.00810.00010.00959.821-7.04159.233
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-10 - 9999
2X-RAY DIFFRACTION2B-10 - 9999

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