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- PDB-8iwf: Aspergillus niger Rha-2 and pNPR -

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Basic information

Entry
Database: PDB / ID: 8iwf
TitleAspergillus niger Rha-2 and pNPR
ComponentsAlpha-L-rhamnosidase
KeywordsHYDROLASE / Alpha-L-rhamnosidase / Pichia pastoris / Aspergillus niger / p-Nitrophenyl-alpha-L-rhamnoside
Function / homologyalpha-L-rhamnosidase / alpha-L-rhamnosidase activity / Alpha-L-rhamnosidase, six-hairpin glycosidase domain / Bacterial alpha-L-rhamnosidase 6 hairpin glycosidase domain / Six-hairpin glycosidase-like superfamily / Six-hairpin glycosidase superfamily / carbohydrate metabolic process / : / alpha-L-rhamnosidase
Function and homology information
Biological speciesAspergillus niger (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.86 Å
AuthorsLi, L.J. / Li, L. / Wang, M.H. / Jiang, Z.D. / Zhu, Y.B. / Jin, T.C. / Ni, H.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32170056 China
National Natural Science Foundation of China (NSFC)U1805235 China
CitationJournal: To Be Published
Title: Crystal structure and catalytic function of alpha-L-rhamnosidase from Aspergillus niger
Authors: Li, L.J. / Li, L. / Wang, M.H. / Jiang, Z.D. / Zhu, Y.B. / Jin, T.C. / Ni, H.
History
DepositionMar 29, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 3, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Alpha-L-rhamnosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,55521
Polymers68,3251
Non-polymers7,23020
Water99155
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7780 Å2
ΔGint94 kcal/mol
Surface area24650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.388, 104.388, 145.334
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Space group name HallP312"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
#4: x-y,-y,-z+2/3
#5: -x,-x+y,-z+1/3
#6: y,x,-z

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Alpha-L-rhamnosidase


Mass: 68325.477 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus niger (mold) / Production host: Komagataella pastoris (fungus) / References: UniProt: R9W5L0

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Sugars , 6 types, 11 molecules

#2: Polysaccharide alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 748.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-6DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3/a4-b1_b4-c1_c6-d1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(6+1)][a-D-Manp]{}}}}LINUCSPDB-CARE
#3: Polysaccharide
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}LINUCSPDB-CARE
#4: Polysaccharide alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 748.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3/a4-b1_b4-c1_c3-d1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}}}}LINUCSPDB-CARE
#5: Polysaccharide alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D- ...alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1072.964 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-6DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,6,5/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3/a4-b1_b4-c1_c3-d1_c6-f1_d6-e1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(6+1)][a-D-Manp]{}}[(6+1)][a-D-Manp]{}}}}LINUCSPDB-CARE
#6: 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-ROHGlycam 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
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#8: 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: obtained synthetically / Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
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, 64 molecules

#7: Chemical ChemComp-RY3 / (2S,3R,4R,5R,6S)-2-methyl-6-[4-[oxidanyl(oxidanylidene)-$l^4-azanyl]phenoxy]oxane-3,4,5-triol


Mass: 285.250 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C12H15NO7 / Feature type: SUBJECT OF INVESTIGATION
#9: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 55 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 3.35 Å3/Da / Density % sol: 63.23 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / Details: 31% PEG1500,0.1M Tris pH 8.4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL10U2 / Wavelength: 0.979021 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 25, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979021 Å / Relative weight: 1
ReflectionResolution: 2.86→90.4 Å / Num. obs: 21144 / % possible obs: 96.9 % / Redundancy: 10.3 % / Biso Wilson estimate: 67.01 Å2 / CC1/2: 0.998 / Net I/σ(I): 15.1
Reflection shellResolution: 2.86→3.01 Å / Num. unique obs: 3146 / CC1/2: 0.895

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PHENIX1.20.1_4487phasing
autoPROCdata reduction
autoPROCdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.86→56.64 Å / SU ML: 0.3313 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 29.8179
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2499 1044 4.96 %
Rwork0.2022 19995 -
obs0.2045 21039 96.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 75.78 Å2
Refinement stepCycle: LAST / Resolution: 2.86→56.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4749 0 480 55 5284
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00465339
X-RAY DIFFRACTIONf_angle_d0.72977284
X-RAY DIFFRACTIONf_chiral_restr0.0512911
X-RAY DIFFRACTIONf_plane_restr0.0049879
X-RAY DIFFRACTIONf_dihedral_angle_d6.7414940
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.86-3.010.34371230.32562921X-RAY DIFFRACTION99.25
3.01-3.20.33531400.27912901X-RAY DIFFRACTION99.61
3.2-3.440.30481960.2412864X-RAY DIFFRACTION99.29
3.44-3.790.29061490.21612573X-RAY DIFFRACTION88.81
3.79-4.340.22781140.1762674X-RAY DIFFRACTION89.19
4.34-5.460.2081720.16612943X-RAY DIFFRACTION99.9
5.47-56.640.21941500.1853119X-RAY DIFFRACTION99.76
Refinement TLS params.Method: refined / Origin x: -44.1311104251 Å / Origin y: 25.6267631753 Å / Origin z: -34.6179765523 Å
111213212223313233
T0.506064355537 Å2-0.140277170769 Å20.000213908027053 Å2-0.590744113118 Å20.0105420061408 Å2--0.330716853305 Å2
L1.05012265964 °2-0.677318529667 °20.247830534422 °2-1.53305290422 °2-0.369238804449 °2--1.61384602765 °2
S-0.0534646459687 Å °0.0461920656862 Å °0.0828495408456 Å °-0.167685629542 Å °0.0177748596548 Å °-0.0864835987268 Å °-0.0982716658627 Å °0.147919700611 Å °0.0260386007421 Å °
Refinement TLS groupSelection details: all

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