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- PDB-5agd: An inactive (D125N) variant of the catalytic domain, BcGH76, of B... -

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Basic information

Entry
Database: PDB / ID: 5agd
TitleAn inactive (D125N) variant of the catalytic domain, BcGH76, of Bacillus circulans Aman6 in complex with alpha-1,6-mannopentaose
ComponentsALPHA-1,6-MANNANASE
KeywordsHYDROLASE / ALPHA-MANNANASE / MANNANASE / GLYCOSIDE HYDROLASE / GH76 / CAZY / MANNAN / ENZYME-CARBOHYDRATE INTERACTION / GLYCOSIDASE INHIBITION / QUANTUM MECHANICS / TRANSITION STATE
Function / homology
Function and homology information


catalytic activity / carbohydrate binding / carbohydrate metabolic process
Similarity search - Function
: / Glycoside hydrolase, family 76 / Glycosyl hydrolase family 76 / Cellulose binding, type IV / Cellulose Binding Domain Type IV / Carbohydrate binding module (family 6) / CBM6 (carbohydrate binding type-6) domain profile. / Carbohydrate binding module family 6 / Glycosyltransferase - #20 / Six-hairpin glycosidase superfamily ...: / Glycoside hydrolase, family 76 / Glycosyl hydrolase family 76 / Cellulose binding, type IV / Cellulose Binding Domain Type IV / Carbohydrate binding module (family 6) / CBM6 (carbohydrate binding type-6) domain profile. / Carbohydrate binding module family 6 / Glycosyltransferase - #20 / Six-hairpin glycosidase superfamily / Glycosyltransferase / Alpha/alpha barrel / Galactose-binding-like domain superfamily / Mainly Alpha
Similarity search - Domain/homology
alpha-D-mannopyranose / Alpha-1,6-mannanase
Similarity search - Component
Biological speciesBACILLUS CIRCULANS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å
AuthorsThompson, A.J. / Speciale, G. / Iglesias-Fernandez, J. / Hakki, Z. / Belz, T. / Cartmell, A. / Spears, R.J. / Chandler, E. / Temple, M.J. / Stepper, J. ...Thompson, A.J. / Speciale, G. / Iglesias-Fernandez, J. / Hakki, Z. / Belz, T. / Cartmell, A. / Spears, R.J. / Chandler, E. / Temple, M.J. / Stepper, J. / Gilbert, H.J. / Rovira, C. / Williams, S.J. / Davies, G.J.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2015
Title: Evidence for a Boat Conformation at the Transition State of Gh76 Alpha-1,6-Mannanases- Key Enzymes in Bacterial and Fungal Mannoprotein Metabolism
Authors: Thompson, A.J. / Speciale, G. / Iglesias-Fernandez, J. / Hakki, Z. / Belz, T. / Cartmell, A. / Spears, R.J. / Chandler, E. / Temple, M.J. / Stepper, J. / Gilbert, H.J. / Rovira, C. / ...Authors: Thompson, A.J. / Speciale, G. / Iglesias-Fernandez, J. / Hakki, Z. / Belz, T. / Cartmell, A. / Spears, R.J. / Chandler, E. / Temple, M.J. / Stepper, J. / Gilbert, H.J. / Rovira, C. / Williams, S.J. / Davies, G.J.
History
DepositionJan 29, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 25, 2015Provider: repository / Type: Initial release
Revision 1.1Apr 1, 2015Group: Database references
Revision 1.2May 6, 2015Group: Database references
Revision 1.3Jul 12, 2017Group: Derived calculations / Category: struct_conn / Item: _struct_conn.pdbx_leaving_atom_flag
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / 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 / 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_alt_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.pdbx_PDB_ins_code / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_PDB_ins_code / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_alt_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_database_status.status_code_sf / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_PDB_ins_code / _struct_conn.pdbx_ptnr1_label_alt_id / _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_comp_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1May 1, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ALPHA-1,6-MANNANASE
B: ALPHA-1,6-MANNANASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,8786
Polymers81,8602
Non-polymers2,0184
Water18,5911032
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A: ALPHA-1,6-MANNANASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,9393
Polymers40,9301
Non-polymers1,0092
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: ALPHA-1,6-MANNANASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,9393
Polymers40,9301
Non-polymers1,0092
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)83.520, 85.725, 102.613
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein ALPHA-1,6-MANNANASE


Mass: 40929.875 Da / Num. of mol.: 2 / Fragment: CATALYTIC DOMAIN, UNP RESIDUES 35-375 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BACILLUS CIRCULANS (bacteria) / Strain: TN31 / Plasmid: PET28A / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / Variant (production host): TUNER
References: UniProt: Q9Z4P9, mannan endo-1,6-alpha-mannosidase
#2: Polysaccharide alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-6)-alpha-D- ...alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose


Type: oligosaccharide / Mass: 828.719 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-6DManpa1-6DManpa1-6DManpa1-6DManpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,5,4/[a1122h-1b_1-5][a1122h-1a_1-5]/1-2-2-2-2/a6-b1_b6-c1_c6-d1_d6-e1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-Manp]{[(6+1)][a-D-Manp]{[(6+1)][a-D-Manp]{[(6+1)][a-D-Manp]{}}}}LINUCSPDB-CARE
#3: Sugar ChemComp-MAN / alpha-D-mannopyranose / alpha-D-mannose / D-mannose / mannose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DManpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-mannopyranoseCOMMON NAMEGMML 1.0
a-D-ManpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
ManSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1032 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsNATIVE PROTEIN TRUNCATED AT AMINO ACID 39 (SERINE). VECTOR-ADDED PURIFICATION TAG AT N-TERMINUS ...NATIVE PROTEIN TRUNCATED AT AMINO ACID 39 (SERINE). VECTOR-ADDED PURIFICATION TAG AT N-TERMINUS (VISIBLE DENSITY IN MOLECULE B). TWO MUTATIONS OF NATIVE SEQUENCE, R341Q AND D125N

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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: 45.12 % / Description: NONE
Crystal growpH: 6.5 / Details: 0.1 M AMMONIUM NITRATE, PH 6.5, 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 7, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.2→44.02 Å / Num. obs: 228606 / % possible obs: 99.5 % / Observed criterion σ(I): -3.7 / Redundancy: 7.9 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 18.6
Reflection shellResolution: 1.2→1.22 Å / Redundancy: 7.7 % / Rmerge(I) obs: 1 / Mean I/σ(I) obs: 1.9 / % possible all: 94.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
XDSdata reduction
Aimlessdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PREVIOUSLY SOLVED NATIVE APO STRUCTURE

Resolution: 1.2→65.79 Å / Cor.coef. Fo:Fc: 0.985 / Cor.coef. Fo:Fc free: 0.981 / SU B: 1.086 / SU ML: 0.021 / Cross valid method: THROUGHOUT / ESU R: 0.03 / ESU R Free: 0.031 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.14417 11136 4.9 %RANDOM
Rwork0.12054 ---
obs0.12169 217369 99.42 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.036 Å2
Baniso -1Baniso -2Baniso -3
1-0.28 Å20 Å20 Å2
2---0.34 Å20 Å2
3---0.06 Å2
Refinement stepCycle: LAST / Resolution: 1.2→65.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5372 0 136 1032 6540
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0195858
X-RAY DIFFRACTIONr_bond_other_d0.0020.025107
X-RAY DIFFRACTIONr_angle_refined_deg1.4361.9248040
X-RAY DIFFRACTIONr_angle_other_deg1.147311753
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2925730
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.48725.197304
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.03115865
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.3241513
X-RAY DIFFRACTIONr_chiral_restr0.1040.2863
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.026767
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021460
X-RAY DIFFRACTIONr_nbd_refined0.2610.22543
X-RAY DIFFRACTIONr_nbd_other0.1870.24908
X-RAY DIFFRACTIONr_nbtor_refined0.190.22942
X-RAY DIFFRACTIONr_nbtor_other0.0750.22258
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.130.2167
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0490.24
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2810.2104
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2650.2104
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.4650.25
X-RAY DIFFRACTIONr_symmetry_hbond_other0.2830.21
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.7191.9072765
X-RAY DIFFRACTIONr_mcbond_other1.7161.9062764
X-RAY DIFFRACTIONr_mcangle_it2.0052.8693465
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.2642.1143093
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.6223.0974547
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr2.754310965
X-RAY DIFFRACTIONr_sphericity_free39.8955249
X-RAY DIFFRACTIONr_sphericity_bonded13.026511552
LS refinement shellResolution: 1.199→1.23 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.268 795 -
Rwork0.255 15393 -
obs--95.67 %

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