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- PDB-5yli: Complex structure of GH113 beta-1,4-mannanase -

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Basic information

Entry
Database: PDB / ID: 5yli
TitleComplex structure of GH113 beta-1,4-mannanase
Componentsbeta-1,4-mannanas
KeywordsHYDROLASE / Complex
Function / homologyGlycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta / 1,4-beta-xylanase
Function and homology information
Biological speciesAmphibacillus xylanus NBRC 15112 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.37 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 from 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.page_last
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / 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_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_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _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-mannanas
A: beta-1,4-mannanas
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,7804
Polymers72,4472
Non-polymers1,3332
Water3,891216
1
B: beta-1,4-mannanas
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,8902
Polymers36,2231
Non-polymers6671
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1130 Å2
ΔGint14 kcal/mol
Surface area12500 Å2
MethodPISA
2
A: beta-1,4-mannanas
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,8902
Polymers36,2231
Non-polymers6671
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1160 Å2
ΔGint14 kcal/mol
Surface area12450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.142, 69.612, 188.752
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-mannanas


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-(1-4)-beta-D-mannopyranose-(1-4)-beta-D-mannopyranose


Type: oligosaccharide / Mass: 666.578 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DManpb1-4DManpb1-4DManpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,4,3/[a1122h-1b_1-5]/1-1-1-1/a4-b1_b4-c1_c4-d1WURCSPDB2Glycan 1.1.0
[][b-D-Manp]{[(4+1)][b-D-Manp]{[(4+1)][b-D-Manp]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 216 / 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: 2.5 Å3/Da / Density % sol: 50.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: PEG4000, 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 MX225-HS / Detector: CCD / Date: Apr 29, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.37→35.85 Å / Num. obs: 29759 / % possible obs: 98 % / Redundancy: 5.7 % / Rmerge(I) obs: 0.088 / Net I/σ(I): 26.1
Reflection shellResolution: 2.37→2.46 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.088 / Mean I/σ(I) obs: 9.1 / Rsym value: 0.087 / % possible all: 98.19

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Processing

Software
NameVersionClassification
PHENIXV1.12refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXV1.12phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5YLH

5ylh


Resolution: 2.37→35.85 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.234 2000 6.72 %
Rwork0.1804 --
obs0.1831 29753 98 %
Refinement stepCycle: LAST / Resolution: 2.37→35.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5112 0 90 216 5418
LS refinement shellHighest resolution: 2.37 Å

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