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- PDB-2cdp: Structure of a CBM6 in complex with neoagarohexaose -

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Basic information

Entry
Database: PDB / ID: 2cdp
TitleStructure of a CBM6 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 / MOLECULAR REPLACEMENT / Resolution: 1.59 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 26, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 8, 2006Provider: repository / Type: Initial release
Revision 1.1Jun 2, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 28, 2017Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
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.occupancy / _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 2.1Dec 13, 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
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)72,28831
Polymers67,5284
Non-polymers4,75927
Water10,305572
1
A: BETA-AGARASE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,0688
Polymers16,8821
Non-polymers1,1857
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: BETA-AGARASE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,0688
Polymers16,8821
Non-polymers1,1857
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
C: BETA-AGARASE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,0327
Polymers16,8821
Non-polymers1,1506
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
4
D: BETA-AGARASE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,1218
Polymers16,8821
Non-polymers1,2397
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)53.720, 54.996, 195.908
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(-0.172, -0.985, -0.029), (0.049, -0.037, 0.998), (-0.984, 0.17, 0.055)59.44933, -37.24403, 46.19801
2given(0.033, 0.01, -0.999), (0.065, 0.998, 0.012), (0.997, -0.065, 0.033)47.72117, 10.58282, -4.40216
3given(-0.068, -0.998, -0.016), (-0.997, 0.067, 0.042), (-0.041, 0.019, -0.999)68.18204, 63.42153, 50.58269

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Components

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Protein / Sugars , 2 types, 8 molecules ABCD

#1: Protein
BETA-AGARASE 1


Mass: 16882.111 Da / Num. of mol.: 4 / Fragment: CARBOHYDRATE-BINDING MODULE, RESIDUES 456-593
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROPHAGUS DEGRADANS (bacteria) / Strain: 2-40 / Description: FROM THE LABORATORY OF RON WEINER / 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, 595 molecules

#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 572 / Source method: isolated from a natural source / Formula: H2O

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Details

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 % / Description: STRUCTURE ISOMORPHOUS WITH STARTING MODEL
Crystal growpH: 7.5
Details: 2M NACL, 16-20% PEG 4000 BUFFERED TO PH 7.5 WITH TRIS/HCL

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Data collection

DiffractionMean temperature: 113 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54178
DetectorType: RIGAKU RAXIS-4 / Detector: IMAGE PLATE / Details: MULTIWIRE OPTICS
RadiationMonochromator: MULTIWIRE OPTICS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.59→19.62 Å / Num. obs: 79215 / % possible obs: 98.5 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 13.1
Reflection shellRedundancy: 3 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 2.9 / % possible all: 96.1

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
CrystalCleardata reduction
d*TREKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2CDO

2cdo


Resolution: 1.59→19.62 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.939 / SU B: 2.272 / SU ML: 0.08 / Cross valid method: THROUGHOUT / ESU R: 0.102 / ESU R Free: 0.106 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES 18 TO 25 OF CHAINS B AND C AND RESIDUES 20 TO 25 OF CHAIN D ARE DISORDERED RESIDUES 19 AND 26 OF CHAIN D HAVE BEEN MODELLED WITH HALF OCCUPANCY
RfactorNum. reflection% reflectionSelection details
Rfree0.253 3909 5 %RANDOM
Rwork0.21 ---
obs0.212 73859 98.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.77 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.59→19.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3905 0 297 572 4774
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0214430
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8721.9656136
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.5685566
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.2726.268209
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.28915542
X-RAY DIFFRACTIONr_dihedral_angle_4_deg4.217154
X-RAY DIFFRACTIONr_chiral_restr0.1420.2745
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023318
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2140.22016
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3140.23019
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1510.2486
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1930.2118
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2780.247
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1051.52668
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.61624213
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.36532015
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.1934.51898
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: 1.59→1.63 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.439 249
Rwork0.351 5147

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