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Basic information

Entry
Database: PDB / ID: 2cdo
Titlestructure of agarase carbohydrate binding module in complex with neoagarohexaose
ComponentsBETA-AGARASE 1
KeywordsHYDROLASE / CARBOHYDRATE-BINDING MODULE
Function / homology
Function and homology information


beta-agarase activity / carbohydrate binding / carbohydrate metabolic process / metal ion binding
Similarity search - Function
Beta-agarase / Cellulose binding, type IV / Cellulose Binding Domain Type IV / 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 ...Beta-agarase / Cellulose binding, type IV / Cellulose Binding Domain Type IV / 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
Biological speciesSACCHAROPHAGUS DEGRADANS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.64 Å
AuthorsHenshaw, J. / Horne, A. / Van Bueren, A.L. / Money, V.A. / Bolam, D.N. / Czjzek, M. / Weiner, R.M. / Hutcheson, S.W. / Davies, G.J. / Boraston, A.B. / Gilbert, H.J.
CitationJournal: J.Biol.Chem. / Year: 2006
Title: Family 6 Carbohydrate Binding Modules in Beta-Agarases Display Exquisite Selectivity for the Non- Reducing Termini of Agarose Chains.
Authors: Henshaw, J. / Horne, A. / Van Bueren, A.L. / Money, V.A. / Bolam, D.N. / Czjzek, M. / Ekborg, N.A. / Weiner, R.M. / Hutcheson, S.W. / Davies, G.J. / Boraston, A.B. / Gilbert, H.J.
History
DepositionJan 25, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 16, 2006Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / 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 / struct_asym / struct_conn / 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.type_symbol / _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_seq_id / _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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 23, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: BETA-AGARASE 1
B: BETA-AGARASE 1
C: BETA-AGARASE 1
D: BETA-AGARASE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,28033
Polymers68,4234
Non-polymers4,85729
Water10,791599
1
A: BETA-AGARASE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,2297
Polymers17,1061
Non-polymers1,1236
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: BETA-AGARASE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,3809
Polymers17,1061
Non-polymers1,2748
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
C: BETA-AGARASE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,41510
Polymers17,1061
Non-polymers1,3109
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
4
D: BETA-AGARASE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,2567
Polymers17,1061
Non-polymers1,1506
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)54.036, 54.979, 196.820
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.163, -0.986, -0.027), (0.059, -0.037, 0.998), (-0.985, 0.161, 0.064)59.48732, -37.77884, 46.2617
2given(0.022, 0.019, -1), (0.081, 0.996, 0.021), (0.996, -0.082, 0.021)48.13741, 9.58189, -3.41072
3given(-0.051, -0.999, -0.015), (-0.998, 0.05, 0.041), (-0.04, 0.017, -0.999)68.11546, 64.29702, 50.83907

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Components

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Protein / Sugars , 2 types, 8 molecules ABCD

#1: Protein
BETA-AGARASE 1


Mass: 17105.768 Da / Num. of mol.: 4 / Fragment: CARBOHYDRATE-BINDING MODULE, RESIDUES 456-593 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROPHAGUS DEGRADANS (bacteria) / Plasmid: PET28A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q6DN99
#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


Type: oligosaccharide / Mass: 936.815 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
WURCS=2.0/2,6,5/[a2112h-1b_1-5][a1221h-1a_1-5_3-6]/1-2-1-2-1-2/a3-b1_b4-c1_c3-d1_d4-e1_e3-f1WURCSPDB2Glycan 1.1.0

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Non-polymers , 4 types, 624 molecules

#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Cl
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 599 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsENGINEERED RESIDUE IN CHAIN A, ILE 460 TO MET ENGINEERED RESIDUE IN CHAIN A, LEU 532 TO MET ...ENGINEERED RESIDUE IN CHAIN A, ILE 460 TO MET ENGINEERED RESIDUE IN CHAIN A, LEU 532 TO MET ENGINEERED RESIDUE IN CHAIN B, ILE 460 TO MET ENGINEERED RESIDUE IN CHAIN B, LEU 532 TO MET ENGINEERED RESIDUE IN CHAIN C, ILE 460 TO MET ENGINEERED RESIDUE IN CHAIN C, LEU 532 TO MET ENGINEERED RESIDUE IN CHAIN D, ILE 460 TO MET ENGINEERED RESIDUE IN CHAIN D, LEU 532 TO MET
Has protein modificationY
Sequence detailsRESIDUE 23 (NUMBERED 1 IN THE PDB FILE) IN THE GIVEN SEQUENCE CORRESPONDS TO RESIDUE 456 IN THE ...RESIDUE 23 (NUMBERED 1 IN THE PDB FILE) IN THE GIVEN SEQUENCE CORRESPONDS TO RESIDUE 456 IN THE DATABASE ENTRY, RESIDUES BEFORE THIS DERIVE FROM THE VECTOR AND AFFINITY TAG.

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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: 2.49 Å3/Da / Density % sol: 51 %
Crystal growpH: 7.5
Details: 2 M NACL, 16-20 % PEG 4000, BUFFERED TO PH 7.5 WITH 100 MM TRIS/HCL.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97910,0.97565,0.97950
DetectorType: ADSC CCD / Detector: CCD / Date: May 8, 2005 / Details: MIRRORS
RadiationMonochromator: SILICON (1 1 1) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97911
20.975651
30.97951
ReflectionResolution: 1.6→96.12 Å / Num. obs: 35218 / % possible obs: 69.5 % / Redundancy: 6.3 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 16.9
Reflection shellResolution: 1.6→1.7 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.14 / Mean I/σ(I) obs: 3.7 / % possible all: 11.3

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
SHELXphasing
RefinementMethod to determine structure: MAD / Resolution: 1.64→98.53 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.908 / SU B: 1.99 / SU ML: 0.069 / Cross valid method: THROUGHOUT / ESU R: 0.143 / ESU R Free: 0.149 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.241 2565 5.1 %RANDOM
Rwork0.176 ---
obs0.179 47616 69.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.41 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20 Å20 Å2
2--0.86 Å20 Å2
3----0.89 Å2
Refinement stepCycle: LAST / Resolution: 1.64→98.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4083 0 302 599 4984
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0214584
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8751.9656321
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.4775576
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.12426.313217
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.62415576
X-RAY DIFFRACTIONr_dihedral_angle_4_deg7.035154
X-RAY DIFFRACTIONr_chiral_restr0.1480.2750
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023448
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.210.22003
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3170.23115
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1420.2486
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2140.2111
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1770.246
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1791.52782
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.66324359
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.56632072
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.474.51947
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.65→1.69 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.435 17
Rwork0.268 325

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