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- PDB-5ylk: Complex structure of GH 113 family beta-1,4-mannanase with mannobiose -

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Basic information

Entry
Database: PDB / ID: 5ylk
TitleComplex structure of GH 113 family beta-1,4-mannanase with mannobiose
Componentsbeta-1,4-mannanase
KeywordsHYDROLASE / Complex
Function / homology
Function and homology information


: / Glycoside Hydrolase Family 113 / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
4beta-beta-mannobiose / beta-D-mannopyranose / 1,4-beta-xylanase
Similarity search - Component
Biological speciesAmphibacillus xylanus NBRC 15112 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.09 Å
AuthorsJiang, Z.Q. / You, X. / Yang, S.Q. / Huang, P. / Ma, J.W.
CitationJournal: J. Biol. Chem. / Year: 2018
Title: Structural insights into the catalytic mechanism of a novel glycoside hydrolase family 113 beta-1,4-mannanase fromn Amphibacillus xylanus
Authors: You, X. / Qin, Z. / Yan, Q. / Yang, S. / Li, Y. / Jiang, Z.
History
DepositionOct 17, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 20, 2018Provider: repository / Type: Initial release
Revision 1.1Aug 8, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
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 / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / 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_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_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_value_order / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 22, 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
B: beta-1,4-mannanase
A: beta-1,4-mannanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,9967
Polymers72,4472
Non-polymers1,5495
Water8,989499
1
B: beta-1,4-mannanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,9083
Polymers36,2231
Non-polymers6852
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: beta-1,4-mannanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,0884
Polymers36,2231
Non-polymers8653
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2030 Å2
ΔGint-10 kcal/mol
Surface area22890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.985, 72.177, 177.160
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-1,4-mannanase


Mass: 36223.473 Da / Num. of mol.: 2 / Mutation: E223A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Amphibacillus xylanus NBRC 15112 (bacteria)
Strain: NBRC 15112 / Gene: AXY_22370 / Production host: Escherichia coli (E. coli) / References: UniProt: K0J0N5
#2: Polysaccharide
beta-D-mannopyranose-(1-4)-beta-D-mannopyranose / 4beta-beta-mannobiose


Type: oligosaccharide, Oligosaccharide / Class: Metabolism / Mass: 342.297 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Details: oligosaccharide / References: 4beta-beta-mannobiose
DescriptorTypeProgram
DManpb1-4DManpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a1122h-1b_1-5]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][b-D-Manp]{[(4+1)][b-D-Manp]{}}LINUCSPDB-CARE
#3: Sugar ChemComp-BMA / beta-D-mannopyranose / beta-D-mannose / D-mannose / mannose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C6H12O6
IdentifierTypeProgram
DManpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-mannopyranoseCOMMON NAMEGMML 1.0
b-D-ManpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
ManSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 499 / 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: 2.16 Å3/Da / Density % sol: 43.09 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: PEG 4000, HEPES Na, 2-Propylalcohol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.979 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Jun 12, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.09→40.53 Å / Num. obs: 36641 / % possible obs: 92 % / Redundancy: 4.5 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 16
Reflection shellResolution: 2.09→2.17 Å / Rmerge(I) obs: 0.09 / Mean I/σ(I) obs: 7.3 / Rsym value: 0.086 / % possible all: 91.99

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Processing

Software
NameVersionClassification
PHENIXV.1.12refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXV.1.12phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3CIV

3civ


Resolution: 2.09→40.53 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.1947 1900 5.43 %
Rwork0.154 --
obs0.1564 35003 92 %
Refinement stepCycle: LAST / Resolution: 2.09→40.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5080 0 104 499 5683
LS refinement shellHighest resolution: 2.09 Å

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