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- PDB-2cks: X-RAY CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF THERMOBIFIDA F... -

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Basic information

Entry
Database: PDB / ID: 2cks
TitleX-RAY CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF THERMOBIFIDA FUSCA ENDOGLUCANASE CEL5A (E5)
ComponentsENDOGLUCANASE E-5
KeywordsHYDROLASE / CARBOHYDRATE METABOLISM / POLYSACCHARIDE DEGRADATION / GLYCOSIDE HYDROLASE FAMILY 5 / GLYCOSIDASE / ENDOGLUCANASE / THERMOBIFIDA FUSCA E5 / CELLULOSE DEGRADATION
Function / homology
Function and homology information


cellulase / polysaccharide binding / cellulase activity / cellulose catabolic process
Similarity search - Function
Cellulose binding domain / Carbohydrate-binding type-2 domain / CBM2 (Carbohydrate-binding type-2) domain profile. / CBD_II / CBM2, carbohydrate-binding domain superfamily / Glycoside hydrolase, family 5, conserved site / Glycosyl hydrolases family 5 signature. / CBM2/CBM3, carbohydrate-binding domain superfamily / Glycoside hydrolase, family 5 / Cellulase (glycosyl hydrolase family 5) ...Cellulose binding domain / Carbohydrate-binding type-2 domain / CBM2 (Carbohydrate-binding type-2) domain profile. / CBD_II / CBM2, carbohydrate-binding domain superfamily / Glycoside hydrolase, family 5, conserved site / Glycosyl hydrolases family 5 signature. / CBM2/CBM3, carbohydrate-binding domain superfamily / Glycoside hydrolase, family 5 / Cellulase (glycosyl hydrolase family 5) / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
BENZAMIDINE / Endoglucanase E-5
Similarity search - Component
Biological speciesTHERMOBIFIDA FUSCA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsBerglund, G.I. / Gualfetti, P.J. / Requadt, C. / Gross, L.S. / Bergfors, T. / Shaw, A. / Saldajeno, M. / Mitchinson, C. / Sandgren, M.
CitationJournal: To be Published
Title: The Crystal Structure of the Catalytic Domain of Thermobifida Fusca Endoglucanase Cel5A in Complex with Cellotetraose
Authors: Berglund, G.I. / Gualfetti, P.J. / Requadt, C. / Gross, L.S. / Bergfors, T. / Shaw, A. / Saldajeno, M. / Mitchinson, C. / Sandgren, M.
History
DepositionApr 21, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 29, 2007Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Dec 19, 2018Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations
Category: atom_site / pdbx_struct_conn_angle ...atom_site / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_conn_type
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
Revision 2.1May 8, 2019Group: Data collection / Experimental preparation
Category: database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow
Item: _exptl_crystal_grow.method
Revision 2.2May 1, 2024Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / struct_conn
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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_alt_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_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_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _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.ptnr2_symmetry
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "BB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ENDOGLUCANASE E-5
B: ENDOGLUCANASE E-5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,20916
Polymers68,3542
Non-polymers85614
Water11,530640
1
A: ENDOGLUCANASE E-5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,6058
Polymers34,1771
Non-polymers4287
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: ENDOGLUCANASE E-5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,6058
Polymers34,1771
Non-polymers4287
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)48.888, 70.970, 75.624
Angle α, β, γ (deg.)90.00, 94.05, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein ENDOGLUCANASE E-5 / ENDOGLUCANASE CEL5A / ENDO-1 / 4-BETA-GLUCANASE E-4 / CELLULASE E-5 / CELLULASE E5


Mass: 34176.965 Da / Num. of mol.: 2 / Fragment: CATALYTIC DOMAIN, RESIDUES 161-466
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) THERMOBIFIDA FUSCA (bacteria) / Plasmid: PBS42 / Production host: BACILLUS SUBTILIS (bacteria) / References: UniProt: Q01786, cellulase
#2: Chemical ChemComp-BEN / BENZAMIDINE / Benzamidine


Mass: 120.152 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H8N2
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#4: Chemical
ChemComp-NA / SODIUM ION


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


Mass: 18.015 Da / Num. of mol.: 640 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENDOHYDROLYSIS OF 1,4-BETA-D-GLUCOSIDIC LINKAGES IN CELLULOSE, LICHENIN AND CEREAL BETA-D-GLUCANS

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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: 1.8 Å3/Da / Density % sol: 30.3 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 5.2
Details: PROTEIN WAS CRYSTALLISED USING THE HANGING DROP VAPOUR DIFFUSION METHOD BY MIXING 2 MICROLITER OF WELL SOLUTION CONTAINING 10 % PEG 8000, 0.1 M HEPES PH 7.0, 0.1 M NA ACETATE, 5MM ZN ACETATE ...Details: PROTEIN WAS CRYSTALLISED USING THE HANGING DROP VAPOUR DIFFUSION METHOD BY MIXING 2 MICROLITER OF WELL SOLUTION CONTAINING 10 % PEG 8000, 0.1 M HEPES PH 7.0, 0.1 M NA ACETATE, 5MM ZN ACETATE WITH 2 MICROLITER 1MG/ML PROTEIN SOLUTION AND 0.5 MICROLITER OF 20 % BENZAMIDINE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: ADSC CCD / Detector: CCD / Date: Sep 28, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.6→42.3 Å / Num. obs: 67888 / % possible obs: 99.8 % / Redundancy: 4 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 15.1
Reflection shellResolution: 1.6→1.64 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.27 / Mean I/σ(I) obs: 4.1 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: THEORETICAL MODEL PRODUCED BY SWISS-MODEL

Resolution: 1.6→42.26 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.955 / Cross valid method: THROUGHOUT / ESU R: 0.087 / ESU R Free: 0.083 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE FOLLOWING RESIDUES HAVE BEEN MODELLED IN MULTIPLE CONFORMATIONS A136, A138, A143, A166, A169, A206, A207, A248, A263, A271, A274, A289, ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE FOLLOWING RESIDUES HAVE BEEN MODELLED IN MULTIPLE CONFORMATIONS A136, A138, A143, A166, A169, A206, A207, A248, A263, A271, A274, A289, A290, A305, A323, A337, A343, A378, A388, A416, A425, A1431, B131, B138, B143, B166, B169, B206, B225, B248, B249, B252, B263, B271, B274, B289, B290, B297, B321, B343, B422, B1431, Y46, Y69, Y71, Y82, Y128, Y172, Y215, Y221, Y260, Y267, Z137, Z187, Z246, Z256, Z273, Z277, Z279, Z284, Z289. ATOMS WITH MISSING ELECTRON DENSITY ARE ASSIGNED ZERO OCCUPANCY. ATOMS ARE ASSIGNED REDUCED OCCUPANCIES WHEN ELECTRON DENSITY IS WEAK OR ATOMS HAVE PARTIAL OCCUPANCY. NO NCS CONSTRAINTS OR RESTRAINTS HAVE BEEN USED IN REFINEMENT OF THE TWO PROTEIN CHAINS IN THE ASYMMETRIC UNIT.
RfactorNum. reflection% reflectionSelection details
Rfree0.169 3442 5.1 %RANDOM
Rwork0.142 ---
obs0.142 64443 99.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL PLUS MASK
Displacement parametersBiso mean: 8.97 Å2
Baniso -1Baniso -2Baniso -3
1-0.18 Å20 Å2-0.16 Å2
2---0.2 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.6→42.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4810 0 30 640 5480
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0215340
X-RAY DIFFRACTIONr_bond_other_d00.024532
X-RAY DIFFRACTIONr_angle_refined_deg1.1341.9227308
X-RAY DIFFRACTIONr_angle_other_deg4.483310558
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7885689
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0710.2743
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.026321
X-RAY DIFFRACTIONr_gen_planes_other0.0060.021183
X-RAY DIFFRACTIONr_nbd_refined0.2240.21233
X-RAY DIFFRACTIONr_nbd_other0.2740.25320
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.1220.22519
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1160.2487
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2340.253
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2830.2110
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1940.266
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5021.53283
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.95325309
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.51832057
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.4614.51999
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: 1.6→1.64 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.214 234
Rwork0.169 4634

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