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Basic information

Entry
Database: PDB / ID: 4atf
TitleCrystal structure of inactivated mutant beta-agarase B in complex with agaro-octaose
ComponentsBETA-AGARASE B
KeywordsHYDROLASE / POLYSACCHARIDASE / AGAROLYTIC ENZYME
Function / homology
Function and homology information


beta-agarase / beta-agarase activity / cell outer membrane / carbohydrate metabolic process / protein homodimerization activity
Similarity search - Function
Beta-agarase / Glycosyl hydrolases family 16 / Glycoside hydrolase family 16 / Glycosyl hydrolases family 16 (GH16) domain profile. / 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
Biological speciesZOBELLIA GALACTANIVORANS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsBernard, T. / Hehemann, J.H. / Correc, G. / Jam, M. / Michel, G. / Czjzek, M.
Citation
Journal: J.Biol.Chem. / Year: 2012
Title: Biochemical and Structural Characterization of the Complex Agarolytic Enzyme System from the Marine Bacterium Zobellia Galactanivorans.
Authors: Hehemann, J.H. / Correc, G. / Thomas, F. / Bernard, T. / Barbeyron, T. / Jam, M. / Helbert, W. / Michel, G. / Czjzek, M.
#1: Journal: Nature / Year: 2010
Title: Transfer of Carbohydrate-Active Enzymes from Marine Bacteria to Japanese Gut Microbiota.
Authors: Hehemann, J. / Correc, G. / Barbeyron, T. / Helbert, W. / Czjzek, M. / Michel, G.
History
DepositionMay 6, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 25, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 12, 2012Group: Database references / Structure summary
Revision 1.2Aug 9, 2017Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.type
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / database_PDB_caveat / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_validate_chiral / pdbx_validate_close_contact / struct_asym / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.occupancy / _atom_site.type_symbol / _atom_site_anisotrop.pdbx_label_asym_id / _chem_comp.name / _chem_comp.type / _pdbx_database_status.status_code_sf / _pdbx_struct_assembly_gen.asym_id_list / _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.ptnr2_label_asym_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 / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_comp_id / _pdbx_validate_chiral.auth_seq_id / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: BETA-AGARASE B
B: BETA-AGARASE B
C: BETA-AGARASE B
D: BETA-AGARASE B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)148,04112
Polymers142,9774
Non-polymers5,0648
Water17,024945
1
A: BETA-AGARASE B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,0103
Polymers35,7441
Non-polymers1,2662
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: BETA-AGARASE B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,0103
Polymers35,7441
Non-polymers1,2662
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: BETA-AGARASE B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,0103
Polymers35,7441
Non-polymers1,2662
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: BETA-AGARASE B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,0103
Polymers35,7441
Non-polymers1,2662
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)73.187, 106.234, 96.983
Angle α, β, γ (deg.)90.00, 93.22, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ASP / Beg label comp-ID: ASP / End auth comp-ID: PHE / End label comp-ID: PHE / Refine code: 5 / Auth seq-ID: 68 - 340 / Label seq-ID: 22 - 294

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC
4DD

NCS oper:
IDCodeMatrixVector
1given(-0.23661, -0.88939, -0.39116), (0.88443, -0.36383, 0.29225), (-0.40224, -0.2768, 0.87269)56.32158, 30.0444, -39.64339
2given(0.99958, -0.01041, 0.0269), (0.0088, 0.9982, 0.05926), (-0.02747, -0.059, 0.99788)72.66839, 51.32857, 0.28564

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Components

#1: Protein
BETA-AGARASE B / BETA-AGARASE B\ / FAMILY GH16


Mass: 35744.266 Da / Num. of mol.: 4 / Fragment: CATALYTIC DOMAIN, RESIDUES 53-353 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ZOBELLIA GALACTANIVORANS (bacteria)
Description: IDENTIFIED AND ISOLATED FROM THE RED ALGAE DELESSERIA SANGUINEA AND FROM THE GERMAN COLLECTION OF MICROORGANISMS (DSM)
Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9RGX8, beta-agarase
#2: Polysaccharide
3,6-anhydro-alpha-L-galactopyranose-(1-3)-beta-D-galactopyranose-(1-4)-3,6-anhydro-alpha-L- ...3,6-anhydro-alpha-L-galactopyranose-(1-3)-beta-D-galactopyranose-(1-4)-3,6-anhydro-alpha-L-galactopyranose-(1-3)-beta-D-galactopyranose-(1-4)-3,6-anhydro-alpha-L-galactopyranose-(1-3)-beta-D-galactopyranose-(1-4)-3,6-anhydro-alpha-L-galactopyranose-(1-3)-beta-D-galactopyranose


Type: oligosaccharide / Mass: 1243.082 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
WURCS=2.0/2,8,7/[a2112h-1b_1-5][a1221h-1a_1-5_3-6]/1-2-1-2-1-2-1-2/a3-b1_b4-c1_c3-d1_d4-e1_e3-f1_f4-g1_g3-h1WURCSPDB2Glycan 1.1.0
[][<C36O27>]{[(1+1)][b-D-Galp]{[(3+1)]{}}}LINUCSPDB-CARE
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 945 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, GLU 189 TO ASP ENGINEERED RESIDUE IN CHAIN B, GLU 189 TO ASP ...ENGINEERED RESIDUE IN CHAIN A, GLU 189 TO ASP ENGINEERED RESIDUE IN CHAIN B, GLU 189 TO ASP ENGINEERED RESIDUE IN CHAIN C, GLU 189 TO ASP ENGINEERED RESIDUE IN CHAIN D, GLU 189 TO ASP

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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: 2.81 Å3/Da / Density % sol: 56.3 % / Description: NONE
Crystal growpH: 7.5
Details: 58% METHYL-PENTANE-DIOL, 20 MM CALCIUM CHLORIDE AND 100 MM HEPES PH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Dec 6, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.8→39.4 Å / Num. obs: 357984 / % possible obs: 96.4 % / Observed criterion σ(I): 0 / Redundancy: 2.7 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 9.8
Reflection shellResolution: 1.8→1.87 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 2.2 / % possible all: 87.8

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1OYZ

1oyz


Resolution: 1.9→65.35 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.948 / SU B: 5.248 / SU ML: 0.072 / Cross valid method: THROUGHOUT / ESU R: 0.289 / ESU R Free: 0.119 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE AGAROSE UNITS IN THE POSITIVE BINDING SITES WERE MODELED BUT NOT REFINED
RfactorNum. reflection% reflectionSelection details
Rfree0.18967 5657 5 %RANDOM
Rwork0.13406 ---
obs0.13683 107508 97.29 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 18.045 Å2
Baniso -1Baniso -2Baniso -3
1--0.08 Å20 Å2-0.07 Å2
2--0.03 Å20 Å2
3---0.04 Å2
Refinement stepCycle: LAST / Resolution: 1.9→65.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9687 0 344 945 10976
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0260.02110542
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.1191.9614429
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.51251219
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.12524.646536
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.82151618
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.9441548
X-RAY DIFFRACTIONr_chiral_restr0.1840.21546
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0218074
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_it1.8191.56081
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.68429895
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.8434461
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.1494.54534
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr2.532310156
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

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

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A1048medium positional0.150.5
2B1048medium positional0.190.5
3C1048medium positional0.190.5
4D1048medium positional0.140.5
1A1090loose positional0.315
2B1090loose positional0.365
3C1090loose positional0.365
4D1090loose positional0.345
1A1048medium thermal1.82
2B1048medium thermal1.932
3C1048medium thermal1.942
4D1048medium thermal1.892
1A1090loose thermal1.8610
2B1090loose thermal1.9610
3C1090loose thermal1.9710
4D1090loose thermal1.9910
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.226 413 -
Rwork0.148 7783 -
obs--97.46 %
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)
10.04140.09430.00510.40880.21850.23860.00970.0166-0.0166-0.00290.0223-0.0453-0.023-0.0203-0.0320.0207-0.0077-0.00180.0224-0.0040.037531.234-0.0111.484
20.3947-0.2134-0.02150.3171-0.08340.11880.01150.0412-0.03530.02750.00260.0369-0.0350.0099-0.01410.02830.0095-0.00450.0231-0.00470.018875.6451.97737.182
30.3281-0.06330.12220.25530.09010.1465-0.0073-0.05330.0062-0.03290.0317-0.0495-0.0035-0.0393-0.02440.0162-0.00410.00090.0397-0.01210.019672.72622.5951.997
40.2298-0.02410.15540.28630.01850.2596-0.0052-0.03980.0096-0.00650.0281-0.0374-0.0344-0.0366-0.02290.02930.00520.00630.0139-0.00980.023533.59622.12851.068
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A58 - 353
2X-RAY DIFFRACTION2B58 - 353
3X-RAY DIFFRACTION3C58 - 354
4X-RAY DIFFRACTION4D58 - 354

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