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- PDB-5c1e: Crystal Structure of the Pectin Methylesterase from Aspergillus n... -

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Basic information

Entry
Database: PDB / ID: 5c1e
TitleCrystal Structure of the Pectin Methylesterase from Aspergillus niger in Penultimately Deglycosylated Form (N-acetylglucosamine Stub at Asn84)
ComponentsPectinesterase
KeywordsHYDROLASE / parallel beta helix / pectin methylesterase
Function / homology
Function and homology information


pectinesterase / pectinesterase activity / cell wall modification / pectin catabolic process / extracellular region
Similarity search - Function
Pectinesterase, Asp active site / Pectinesterase signature 2. / Pectinesterase, catalytic / Pectinesterase / Single-stranded right-handed beta-helix, Pectin lyase-like / Pectate Lyase C-like / Pectin lyase fold / Pectin lyase fold/virulence factor / 3 Solenoid / Mainly Beta
Similarity search - Domain/homology
ACETATE ION / Pectinesterase
Similarity search - Component
Biological speciesAspergillus niger (mold)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.75 Å
Model detailsProtein deglycosylated with EndoHf to leave an Asn84 N-linked N-acetylglycosamine stub
AuthorsJameson, G.B. / Williams, M.A.K. / Loo, T.S. / Kent, L.M. / Melton, L.D. / Mercadante, D.
Citation
Journal: J.Biol.Chem. / Year: 2016
Title: Structure and Properties of a Non-processive, Salt-requiring, and Acidophilic Pectin Methylesterase from Aspergillus niger Provide Insights into the Key Determinants of Processivity Control.
Authors: Kent, L.M. / Loo, T.S. / Melton, L.D. / Mercadante, D. / Williams, M.A. / Jameson, G.B.
#1: Journal: PLoS ONE / Year: 2014
Title: Processive pectin methylesterases: the role of electrostatic potential, breathing motions and bond cleavage in the rectification of Brownian motions
Authors: Mercadante, D. / Melton, L.D. / Jameson, G.B. / Williams, M.A.K.
#2: Journal: Biophys J / Year: 2013
Title: Substrate Dynamics in Enzyme Action: Rotations of Monosaccharide Subunits in the Binding Groove are Essential for Pectin Methylesterase Processivity
Authors: Mercadante, D. / Melton, L.D. / Jameson, G.B. / Williams, M.A.K. / De Simone, A.
History
DepositionJun 13, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 1, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 2, 2015Group: Database references
Revision 1.2Feb 3, 2016Group: Database references
Revision 1.3Nov 1, 2017Group: Author supporting evidence / Database references ...Author supporting evidence / Database references / Derived calculations / Refinement description
Category: citation / pdbx_struct_assembly_auth_evidence ...citation / pdbx_struct_assembly_auth_evidence / pdbx_struct_oper_list / software
Item: _citation.journal_id_CSD / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5Sep 27, 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
Revision 1.6Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Pectinesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,04914
Polymers31,7921
Non-polymers1,25613
Water5,819323
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)74.614, 113.543, 88.765
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-410-

GOL

21A-412-

ACT

31A-412-

ACT

41A-507-

HOH

DetailsMonomer according to Gel filtration

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Components

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Protein / Sugars , 2 types, 2 molecules A

#1: Protein Pectinesterase


Mass: 31792.287 Da / Num. of mol.: 1 / Fragment: N-terminal truncated exported protein
Source method: isolated from a genetically manipulated source
Details: After purification, protein was deglycosylated with PNGaseF
Source: (gene. exp.) Aspergillus niger (strain ATCC 1015 / CBS 113.46 / FGSC A1144 / LSHB Ac4 / NCTC 3858a / NRRL 328 / USDA 3528.7) (mold)
Strain: van Tieghem, anamorph / Gene: ASPNIDRAFT_214857 / Plasmid: pYES2 / Production host: Saccharomyces cerevisiae (brewer's yeast) / Strain (production host): INVSc1 / References: UniProt: G3YAL0, pectinesterase
#2: 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.: 1
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 , 5 types, 335 molecules

#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 323 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 2.96 Å3/Da / Density % sol: 58.4 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 3.6
Details: Protein (6.5 mg/mL) in 50-100 mM acetate buffer mixed 1:1 with 1.9 M ammonium sulfate, 100 mM sodium acetate, pH 3.6

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Data collection

DiffractionMean temperature: 123 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Nov 4, 2013 / Details: AXCo PX70 QUARTZ GLASS CAPILLARY OPTIC
RadiationMonochromator: AXCo PX70 QUARTZ GLASS CAPILLARY OPTIC / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.75→36.16 Å / Num. all: 36656 / Num. obs: 36656 / % possible obs: 95.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.94 % / Biso Wilson estimate: 19 Å2 / Rmerge(I) obs: 0.084 / Net I/av σ(I): 8.3 / Net I/σ(I): 4.5
Reflection shellResolution: 1.75→1.8 Å / Redundancy: 3.71 % / Rmerge(I) obs: 0.366 / Mean I/σ(I) obs: 3.1 / % possible all: 89.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
d*TREKdata scaling
REFMAC5.8.0073refinement
PDB_EXTRACT3.15data extraction
CrystalCleardata reduction
MrBUMPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1xg2

1xg2


Resolution: 1.75→36.16 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.948 / WRfactor Rfree: 0.1975 / WRfactor Rwork: 0.1688 / FOM work R set: 0.8722 / SU B: 4.407 / SU ML: 0.071 / SU R Cruickshank DPI: 0.1049 / SU Rfree: 0.1022 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.105 / ESU R Free: 0.102 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2015 1835 5 %RANDOM
Rwork0.171 ---
obs0.1725 34821 95.58 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 61.96 Å2 / Biso mean: 20.727 Å2 / Biso min: 12.39 Å2
Baniso -1Baniso -2Baniso -3
1-0.9 Å2-0 Å20 Å2
2---0.23 Å20 Å2
3----0.67 Å2
Refinement stepCycle: final / Resolution: 1.75→36.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2235 0 88 323 2646
Biso mean--46.16 31.31 -
Num. residues----299
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.022466
X-RAY DIFFRACTIONr_bond_other_d0.0010.022108
X-RAY DIFFRACTIONr_angle_refined_deg1.3051.9643376
X-RAY DIFFRACTIONr_angle_other_deg0.74634866
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3665323
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.97425.189106
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.80515345
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.627158
X-RAY DIFFRACTIONr_chiral_restr0.0750.2385
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022883
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02551
X-RAY DIFFRACTIONr_mcbond_it0.8321.7371254
X-RAY DIFFRACTIONr_mcbond_other0.8311.7321251
X-RAY DIFFRACTIONr_mcangle_it1.3172.5971577
LS refinement shellResolution: 1.75→1.795 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.302 122 -
Rwork0.3 2353 -
all-2475 -
obs--88.46 %
Refinement TLS params.Method: refined / Origin x: -19.2157 Å / Origin y: 25.7632 Å / Origin z: 12.2763 Å
111213212223313233
T0.0031 Å2-0.0038 Å20.0008 Å2-0.0075 Å2-0.0024 Å2--0.0122 Å2
L0.0394 °2-0.0818 °2-0.0987 °2-0.1742 °20.2029 °2--0.5202 °2
S-0.0002 Å °-0.0092 Å °0.0006 Å °0.0002 Å °0.0145 Å °0.0045 Å °0.0106 Å °0.0245 Å °-0.0144 Å °

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