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- PDB-3wh9: The ligand-free structure of ManBK from Aspergillus niger BK01 -

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Basic information

Entry
Database: PDB / ID: 3wh9
TitleThe ligand-free structure of ManBK from Aspergillus niger BK01
ComponentsEndo-beta-1,4-mannanase
KeywordsHYDROLASE / beta-mannanase / rational design / thermophilic / TIM-barrel fold
Function / homology
Function and homology information


mannan catabolic process / mannan endo-1,4-beta-mannosidase / mannan endo-1,4-beta-mannosidase activity / hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate metabolic process / extracellular region
Similarity search - Function
Glycoside hydrolase, family 5 / Cellulase (glycosyl hydrolase family 5) / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Probable mannan endo-1,4-beta-mannosidase A / Endo-beta-1,4-mannanase
Similarity search - Component
Biological speciesAspergillus niger (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.57 Å
AuthorsHuang, J.W. / Chen, C.C. / Huang, C.H. / Huang, T.Y. / Wu, T.H. / Cheng, Y.S. / Ko, T.P. / Lin, C.Y. / Liu, J.R. / Guo, R.T.
CitationJournal: To be Published
Title: Structural Analysis and Rational Design to Improve Specific Activity of beta-Mannanase from Aspergillus Niger BK01
Authors: Huang, J.W. / Chen, C.C. / Huang, C.H. / Huang, T.Y. / Wu, T.H. / Cheng, Y.S. / Ko, T.P. / Lin, C.Y. / Liu, J.R. / Guo, R.T.
History
DepositionAug 22, 2013Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 8, 2014Provider: repository / Type: Initial release
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 / pdbx_struct_special_symmetry / 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 / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_special_symmetry.label_asym_id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _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_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 8, 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

Downloads & links

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Assembly

Deposited unit
A: Endo-beta-1,4-mannanase
B: Endo-beta-1,4-mannanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,9459
Polymers75,3742
Non-polymers1,5717
Water17,943996
1
A: Endo-beta-1,4-mannanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,4905
Polymers37,6871
Non-polymers8034
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Endo-beta-1,4-mannanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,4554
Polymers37,6871
Non-polymers7683
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)93.584, 97.051, 147.838
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-577-

HOH

21A-724-

HOH

31A-883-

HOH

41A-982-

HOH

51B-528-

HOH

61B-633-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Endo-beta-1,4-mannanase / ManBK


Mass: 37687.047 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus niger (mold) / Plasmid: pPICZ A / Production host: Komagataella pastoris (fungus) / Strain (production host): X33 / References: UniProt: B6V876, UniProt: A2QKT4*PLUS

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Sugars , 2 types, 4 molecules

#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#3: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 3 types, 999 molecules

#4: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 996 / 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: 2.23 Å3/Da / Density % sol: 44.76 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.4M magnesium chloride hexahydrate, 0.1M Bis-Tris pH 5.5, 29% (w/v) polyethylene glycol 3350, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13C1 / Wavelength: 0.97622 Å
DetectorType: MX300HE / Detector: CCD / Date: Nov 26, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97622 Å / Relative weight: 1
ReflectionResolution: 1.57→25 Å / Num. obs: 94099 / % possible obs: 99.5 % / Redundancy: 5.5 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 39.8
Reflection shellResolution: 1.57→1.63 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.367 / Mean I/σ(I) obs: 5.2 / Num. unique all: 9231 / % possible all: 98.8

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
CNS1.2refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1QNR

1qnr


Resolution: 1.57→25 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.19 4580 RANDOM
Rwork0.159 --
all-93771 -
obs-91321 -
Refinement stepCycle: LAST / Resolution: 1.57→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5314 0 101 996 6411
LS refinement shellResolution: 1.57→1.63 Å /
RfactorNum. reflection
Rfree0.274 -
Rwork0.221 -
obs-8528

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