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- PDB-7k4o: Tannin acyl hydrolase from Aspergillus niger -

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Basic information

Entry
Database: PDB / ID: 7k4o
TitleTannin acyl hydrolase from Aspergillus niger
ComponentsCarboxylic ester hydrolaseCarboxylesterase
KeywordsHYDROLASE / esterase / tannin / serine hydrolase
Function / homologyTannase/feruloyl esterase / Tannase and feruloyl esterase / Hydrolases; Acting on ester bonds; Carboxylic-ester hydrolases / carboxylic ester hydrolase activity / Alpha/Beta hydrolase fold / metal ion binding / 2-[2-(2-ethoxyethoxy)ethoxy]ethanol / 3,4,5-trihydroxybenzoic acid / Carboxylic ester hydrolase
Function and homology information
Biological speciesAspergillus niger (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsRen, B.
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2021
Title: Crystal structure of fungal tannase from Aspergillus niger.
Authors: Dong, L. / McKinstry, W.J. / Pan, L. / Newman, J. / Ren, B.
History
DepositionSep 15, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 17, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _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
A: Carboxylic ester hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,16419
Polymers60,8101
Non-polymers5,35418
Water13,962775
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)170.920, 170.920, 111.061
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-605-

ZN

21A-606-

ZN

31A-607-

ZN

41A-740-

HOH

51A-842-

HOH

61A-873-

HOH

71A-945-

HOH

81A-971-

HOH

91A-1304-

HOH

101A-1371-

HOH

111A-1389-

HOH

121A-1421-

HOH

131A-1461-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Carboxylic ester hydrolase / Carboxylesterase


Mass: 60809.836 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus niger (mold) / Production host: Aspergillus niger (mold)
References: UniProt: A2QIR3, Hydrolases; Acting on ester bonds; Carboxylic-ester hydrolases

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Sugars , 4 types, 8 molecules

#2: Polysaccharide alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]alpha-D- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]alpha-D-mannopyranose-(1-6)-[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: 1397.245 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-2DManpa1-6[DManpa1-3]DManpa1-6[DManpa1-3]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,8,7/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3-3-3/a4-b1_b4-c1_c3-d1_c6-e1_e3-f1_e6-g1_g2-h1WURCSPDB2Glycan 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]{[(3+1)][a-D-Rhap]{}[(6+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}}}}}LINUCSPDB-CARE
#3: Polysaccharide alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D- ...alpha-D-mannopyranose-(1-2)-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
DManpa1-2DManpa1-3[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_d2-e1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}[(6+1)][a-D-Manp]{}}}}LINUCSPDB-CARE
#4: 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.: 4
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
#5: 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 / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2 / Source method: obtained synthetically / 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 , 7 types, 785 molecules

#6: Chemical ChemComp-GDE / 3,4,5-trihydroxybenzoic acid / Gallate / Gallic acid


Mass: 170.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H6O5 / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#8: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#9: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#10: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#11: Chemical ChemComp-FWN / 2-[2-(2-ethoxyethoxy)ethoxy]ethanol


Mass: 178.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O4
#12: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 775 / 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: 3.85 Å3/Da / Density % sol: 68.06 %
Crystal growTemperature: 281 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: zinc sulfate, polyethylene glycol monomethyl ether 500 and 0.1 M sodium MES at pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 21, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.65→19.76 Å / Num. obs: 114035 / % possible obs: 99.9 % / Redundancy: 13.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.079 / Rpim(I) all: 0.023 / Net I/σ(I): 20.9
Reflection shellResolution: 1.65→1.71 Å / Rmerge(I) obs: 1.396 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 11292 / CC1/2: 0.689 / Rpim(I) all: 0.384

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3wmt

3wmt


Resolution: 1.65→19.76 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.97 / Cross valid method: FREE R-VALUE / ESU R: 0.064 / ESU R Free: 0.066
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1738 5698 4.997 %
Rwork0.1521 108337 -
all0.153 --
obs-114035 99.897 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 30.724 Å2
Baniso -1Baniso -2Baniso -3
1--0.272 Å2-0.136 Å2-0 Å2
2---0.272 Å20 Å2
3---0.881 Å2
Refinement stepCycle: LAST / Resolution: 1.65→19.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4280 0 337 775 5392
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0134856
X-RAY DIFFRACTIONr_bond_other_d0.0350.0184103
X-RAY DIFFRACTIONr_angle_refined_deg1.881.7456706
X-RAY DIFFRACTIONr_angle_other_deg3.1651.6619653
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2475594
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.10524.035228
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.74515676
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.1331516
X-RAY DIFFRACTIONr_chiral_restr0.0960.2712
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.025368
X-RAY DIFFRACTIONr_gen_planes_other0.0190.02975
X-RAY DIFFRACTIONr_nbd_refined0.2190.2927
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2140.23781
X-RAY DIFFRACTIONr_nbtor_refined0.1780.22478
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.1040.21951
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2320.2570
X-RAY DIFFRACTIONr_metal_ion_refined0.1230.27
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2120.213
X-RAY DIFFRACTIONr_nbd_other0.1870.234
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1460.234
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.1120.22
X-RAY DIFFRACTIONr_mcbond_it2.5622.9542257
X-RAY DIFFRACTIONr_mcbond_other2.5622.9542256
X-RAY DIFFRACTIONr_mcangle_it3.4644.4232830
X-RAY DIFFRACTIONr_mcangle_other3.4644.4232831
X-RAY DIFFRACTIONr_scbond_it3.6833.4892597
X-RAY DIFFRACTIONr_scbond_other3.93.4872598
X-RAY DIFFRACTIONr_scangle_it5.4695.1393855
X-RAY DIFFRACTIONr_scangle_other5.5935.1383856
X-RAY DIFFRACTIONr_lrange_it6.79238.585807
X-RAY DIFFRACTIONr_lrange_other6.48737.3455540
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.65-1.6930.274100.2617951X-RAY DIFFRACTION100
1.693-1.7390.2743830.2417729X-RAY DIFFRACTION100
1.739-1.790.2594010.2287509X-RAY DIFFRACTION100
1.79-1.8450.2213840.2027284X-RAY DIFFRACTION100
1.845-1.9050.2153970.1927073X-RAY DIFFRACTION100
1.905-1.9720.1963780.1776830X-RAY DIFFRACTION100
1.972-2.0470.1933590.1676610X-RAY DIFFRACTION100
2.047-2.130.193310.1626382X-RAY DIFFRACTION99.9405
2.13-2.2250.182960.1486184X-RAY DIFFRACTION100
2.225-2.3330.172870.1435881X-RAY DIFFRACTION100
2.333-2.4590.1593060.1345585X-RAY DIFFRACTION100
2.459-2.6090.152570.1285323X-RAY DIFFRACTION100
2.609-2.7890.1722740.1294993X-RAY DIFFRACTION100
2.789-3.0120.1662860.144633X-RAY DIFFRACTION100
3.012-3.2990.172190.1544322X-RAY DIFFRACTION100
3.299-3.6890.1692300.1513900X-RAY DIFFRACTION100
3.689-4.2590.1371780.1223484X-RAY DIFFRACTION99.8092
4.259-5.2150.1411560.1212975X-RAY DIFFRACTION99.9681
5.215-7.370.156980.1592386X-RAY DIFFRACTION99.9195
7.37-19.760.203680.1791303X-RAY DIFFRACTION92.9492

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