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- PDB-1u0a: Crystal structure of the engineered beta-1,3-1,4-endoglucanase H(... -

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Basic information

Entry
Database: PDB / ID: 1u0a
TitleCrystal structure of the engineered beta-1,3-1,4-endoglucanase H(A16-M) in complex with beta-glucan tetrasaccharide
ComponentsBeta-glucanase
KeywordsHYDROLASE / 1 / 3-1 / 4-beta-glucanase / protein-carbohydrate interaction / active-site variant / jellyroll architecture
Function / homology
Function and homology information


licheninase activity / licheninase / carbohydrate metabolic process
Similarity search - Function
Beta-glucanase/XTH / Beta-glucanase / Glycoside hydrolase, family 16, active site / Glycosyl hydrolases family 16 active sites. / Glycosyl hydrolases family 16 / Glycoside hydrolase family 16 / Glycosyl hydrolases family 16 (GH16) domain profile. / Jelly Rolls - #200 / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls ...Beta-glucanase/XTH / Beta-glucanase / Glycoside hydrolase, family 16, active site / Glycosyl hydrolases family 16 active sites. / Glycosyl hydrolases family 16 / Glycoside hydrolase family 16 / Glycosyl hydrolases family 16 (GH16) domain profile. / Jelly Rolls - #200 / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesPaenibacillus macerans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.64 Å
AuthorsGaiser, O.J. / Piotukh, K. / Ponnuswamy, M.N. / Planas, A. / Borriss, R. / Heinemann, U.
CitationJournal: J.Mol.Biol. / Year: 2006
Title: Structural Basis for the Substrate Specificity of a Bacillus 1,3-1,4-beta-Glucanase
Authors: Gaiser, O.J. / Piotukh, K. / Ponnuswamy, M.N. / Planas, A. / Borriss, R. / Heinemann, U.
History
DepositionJul 13, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 6, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / diffrn_source / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_remark / 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 / pdbx_validate_close_contact / 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 / _diffrn_source.pdbx_synchrotron_site / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_database_remark.text / _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_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_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 / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _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 / _struct_conn.ptnr2_symmetry
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 27, 2021Group: Database references / Structure summary / Category: chem_comp / database_2 / struct_ref_seq_dif
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 2.2Aug 23, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Remark 999SEQUENCE The 16 N-terminal residues of the sequence are derived from Bacillus amyloliquefaciens.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Beta-glucanase
B: Beta-glucanase
C: Beta-glucanase
D: Beta-glucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,75615
Polymers95,7334
Non-polymers3,02311
Water28,7521596
1
A: Beta-glucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,7715
Polymers23,9331
Non-polymers8374
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: Beta-glucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,7054
Polymers23,9331
Non-polymers7723
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
C: Beta-glucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,6403
Polymers23,9331
Non-polymers7072
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
4
D: Beta-glucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,6403
Polymers23,9331
Non-polymers7072
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
5


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4680 Å2
ΔGint-146 kcal/mol
Surface area35950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.769, 88.758, 154.795
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
Beta-glucanase / endo-1 / 3-1 / 4-beta-D-glucan 4-glucanohydrolase / beta-1 / 3-1 / 4-endoglucanase / Endo-beta-1 / ...endo-1 / 3-1 / 4-beta-D-glucan 4-glucanohydrolase / beta-1 / 3-1 / 4-endoglucanase / Endo-beta-1 / 3-1 / 4 glucanase / Lichenase


Mass: 23933.260 Da / Num. of mol.: 4 / Mutation: E105Q, E109Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Paenibacillus macerans (bacteria) / Plasmid: pTZ19R / Production host: Escherichia coli (E. coli) / Strain (production host): DH5a / References: UniProt: P23904, licheninase
#2: Polysaccharide
beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-3)-beta-D-glucopyranose


Type: oligosaccharide / Mass: 666.578 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpb1-4DGlcpb1-4DGlcpb1-3DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,4,3/[a2122h-1b_1-5]/1-1-1-1/a3-b1_b4-c1_c4-d1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(3+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{}}}}LINUCSPDB-CARE
#3: Chemical
ChemComp-CA / CALCIUM ION


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


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1596 / Source method: isolated from a natural source / Formula: H2O

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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: 2.72 Å3/Da / Density % sol: 54.44 %
Crystal growTemperature: 293 K / pH: 6.5
Details: 25% (v/v) PEG Monomethyl Ether 550, 0.01 M Zinc Sulfate heptahydrate, 0.1 M MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K, pH 6.50

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.8337
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 15, 2000 / Details: MIRRORS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8337 Å / Relative weight: 1
ReflectionResolution: 1.64→34.46 Å / Num. obs: 118568 / % possible obs: 92.5 % / Observed criterion σ(I): 1 / Rsym value: 0.057
Reflection shellResolution: 1.64→1.65 Å / % possible all: 84

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Processing

Software
NameVersionClassification
DENZOdata reduction
TRUNCATEdata reduction
AMoREphasing
REFMACrefinement
CCP4(TRUNCATE)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2YAH

2yah


Resolution: 1.64→34.46 Å / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.16 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.197 8310 7 %RANDOM
Rwork0.161 ---
obs0.164 118568 92.5 %-
all-118568 --
Displacement parametersBiso mean: 15.88 Å2
Baniso -1Baniso -2Baniso -3
1--0.36 Å20 Å20 Å2
2---0.08 Å20 Å2
3---0.44 Å2
Refinement stepCycle: LAST / Resolution: 1.64→34.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6788 0 187 1596 8571
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0120.021
X-RAY DIFFRACTIONp_angle_d1.6591.933
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.0882
X-RAY DIFFRACTIONp_mcangle_it1.6853
X-RAY DIFFRACTIONp_scbond_it1.2522
X-RAY DIFFRACTIONp_scangle_it1.9013
X-RAY DIFFRACTIONp_plane_restr0.0060.02
X-RAY DIFFRACTIONp_chiral_restr0.1530.2
X-RAY DIFFRACTIONp_singtor_nbd5.1153
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor

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