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

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Basic information

Entry
Database: PDB / ID: 2ckr
TitleX-RAY CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF THERMOBIFIDA FUSCA ENDOGLUCANASE CEL5A (E5) E355Q IN COMPLEX WITH CELLOTETRAOSE
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
beta-cellopentaose / BENZAMIDINE / Endoglucanase E-5
Similarity search - Component
Biological speciesTHERMOBIFIDA FUSCA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 1.77 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_unobs_or_zero_occ_atoms / struct_conn
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 / Derived calculations / Experimental preparation
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / struct_conn
Item: _exptl_crystal_grow.method / _struct_conn.pdbx_leaving_atom_flag
Revision 3.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / 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_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / 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_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.type_symbol / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _pdbx_database_status.status_code_sf / _pdbx_struct_assembly_gen.asym_id_list / _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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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 / _struct_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
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)69,96512
Polymers68,3522
Non-polymers1,61310
Water9,620534
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A: ENDOGLUCANASE E-5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,6215
Polymers34,1761
Non-polymers4454
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: ENDOGLUCANASE E-5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,3447
Polymers34,1761
Non-polymers1,1686
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)49.365, 70.850, 76.278
Angle α, β, γ (deg.)90.00, 93.86, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein / Sugars , 2 types, 3 molecules AB

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


Mass: 34175.980 Da / Num. of mol.: 2 / Fragment: CATALYTIC DOMAIN, RESIDUES 161-466 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: MUTATION GLU 355 GLN IN COORDINATES / Source: (gene. exp.) THERMOBIFIDA FUSCA (bacteria) / Plasmid: PBS42 / Production host: BACILLUS SUBTILIS (bacteria) / References: UniProt: Q01786, cellulase
#2: Polysaccharide beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D- ...beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose / beta-cellopentaose


Type: oligosaccharide, Oligosaccharide / Class: Metabolism / Mass: 828.719 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: beta-cellopentaose
DescriptorTypeProgram
DGlcpb1-4DGlcpb1-4DGlcpb1-4DGlcpb1-4DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,5,4/[a2122h-1b_1-5]/1-1-1-1-1/a4-b1_b4-c1_c4-d1_d4-e1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{}}}}}LINUCSPDB-CARE

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Non-polymers , 5 types, 543 molecules

#3: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#4: Chemical ChemComp-BEN / BENZAMIDINE / Benzamidine


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


Mass: 65.409 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Zn
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 534 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsENDOHYDROLYSIS OF 1,4-BETA-D-GLUCOSIDIC LINKAGES IN CELLULOSE, LICHENIN AND CEREAL BETA-D-GLUCANS ...ENDOHYDROLYSIS OF 1,4-BETA-D-GLUCOSIDIC LINKAGES IN CELLULOSE, LICHENIN AND CEREAL BETA-D-GLUCANS ENGINEERED RESIDUE IN CHAIN A, GLU 391 TO GLN ENGINEERED RESIDUE IN CHAIN B, GLU 391 TO GLN

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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: 31.1 %
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 29, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.77→32.1 Å / Num. obs: 50412 / % possible obs: 98.8 % / Redundancy: 2.3 % / Biso Wilson estimate: 13.4 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 11.7
Reflection shellResolution: 1.77→1.82 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 2.9 / % possible all: 99.7

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Processing

Software
NameVersionClassification
REFMAC5refinement
MOSFLMdata reduction
SCALAdata scaling
REFMACphasing
RefinementMethod to determine structure: OTHER / Resolution: 1.77→32.11 Å / Cross valid method: THROUGHOUT / ESU R: 0.136 / ESU R Free: 0.12
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. CHAIN A AND B HAVE BEEN REFINED INDEPENDENTLY. NO NCS SYMMETRY HAS BEEN APPLIED. THE FOLLOWING RESIDUES HAVE BEEN MODELLED IN MULTIPLE ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. CHAIN A AND B HAVE BEEN REFINED INDEPENDENTLY. NO NCS SYMMETRY HAS BEEN APPLIED. THE FOLLOWING RESIDUES HAVE BEEN MODELLED IN MULTIPLE CONFORMATIONS A136, A169, A206, A248, A271, A274, A290, A305, A323, A337, A343, A378, A388, A416, A425, A1432, B131, B169, B206, B248, B249, B252, B271, B274, B297, B305, B321, B343, B422, B1436, Y60, Y109, Y173, Y180, Z104, Z122, Z217, Z228, Z230, Z235, Z250, Z262. 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
Rfree0.19303 2582 5.1 %RANDOM
Rwork0.15841 ---
obs0.1602 47827 99.8 %-
Displacement parametersBiso mean: 12.118 Å2
Baniso -1Baniso -2Baniso -3
1-0.61 Å20 Å20.1 Å2
2---0.56 Å20 Å2
3----0.04 Å2
Refinement stepCycle: LAST / Resolution: 1.77→32.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4803 0 93 534 5430

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