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- PDB-5c1c: Crystal Structure of the Pectin Methylesterase from Aspergillus n... -

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Basic information

Entry
Database: PDB / ID: 5c1c
TitleCrystal Structure of the Pectin Methylesterase from Aspergillus niger in Deglycosylated Form
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: 1.8 Å
Model detailsAsn84 N-linked glycan removed with PNGaseF
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 1.4Sep 27, 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: Pectinesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,64411
Polymers31,7931
Non-polymers85110
Water5,621312
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)75.249, 113.843, 88.741
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-

ACT

21A-410-

ACT

DetailsMonomer according to Gel filtration

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Pectinesterase


Mass: 31793.271 Da / Num. of mol.: 1 / Fragment: N-terminal truncated exported protein / Mutation: N84D
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

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Non-polymers , 5 types, 322 molecules

#2: Chemical
ChemComp-SO4 / SULFATE ION


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


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


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-ACT / ACETATE ION


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


Mass: 18.015 Da / Num. of mol.: 312 / 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: 2.99 Å3/Da / Density % sol: 58.85 % / Description: Flattened needle 0.3x0.015x0.010 mm
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 4.1
Details: Protein (6.5 mg/mL) in 50-100 mM acetate buffer mixed 1:1 with 1.8 M ammonium sulfate, 100 mM sodium acetate, pH 4.1

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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: Oct 23, 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: 1.8→36.23 Å / Num. all: 34221 / Num. obs: 34221 / % possible obs: 95.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.79 % / Rmerge(I) obs: 0.075 / Net I/av σ(I): 9.8 / Net I/σ(I): 5.2
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 3.75 % / Rmerge(I) obs: 0.313 / Mean I/σ(I) obs: 3.7 / % possible all: 91.4

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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: 1.8→36.23 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.944 / WRfactor Rfree: 0.1975 / WRfactor Rwork: 0.1652 / FOM work R set: 0.8823 / SU B: 4.473 / SU ML: 0.071 / SU R Cruickshank DPI: 0.1097 / SU Rfree: 0.1075 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.11 / ESU R Free: 0.108 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2033 1709 5 %RANDOM
Rwork0.1704 ---
obs0.172 32510 95.67 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 63.83 Å2 / Biso mean: 19.485 Å2 / Biso min: 11.05 Å2
Baniso -1Baniso -2Baniso -3
1-0.26 Å2-0 Å20 Å2
2--0.42 Å20 Å2
3----0.68 Å2
Refinement stepCycle: final / Resolution: 1.8→36.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2235 0 48 312 2595
Biso mean--36.14 30.4 -
Num. residues----299
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.022371
X-RAY DIFFRACTIONr_bond_other_d0.0010.022041
X-RAY DIFFRACTIONr_angle_refined_deg1.2581.953246
X-RAY DIFFRACTIONr_angle_other_deg0.73734716
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.515313
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.92225.192104
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.17415339
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.67158
X-RAY DIFFRACTIONr_chiral_restr0.0730.2368
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022782
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02532
X-RAY DIFFRACTIONr_mcbond_it0.7291.6541221
X-RAY DIFFRACTIONr_mcbond_other0.7271.651219
X-RAY DIFFRACTIONr_mcangle_it1.1812.4731530
LS refinement shellResolution: 1.798→1.845 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.314 116 -
Rwork0.272 2245 -
all-2361 -
obs--90.63 %
Refinement TLS params.Method: refined / Origin x: -19.4005 Å / Origin y: 25.794 Å / Origin z: 12.2271 Å
111213212223313233
T0.0026 Å2-0.0019 Å2-0.0006 Å2-0.0015 Å20.0006 Å2--0.016 Å2
L0.0778 °2-0.1252 °2-0.1633 °2-0.2089 °20.2268 °2--0.6738 °2
S-0 Å °-0.0025 Å °0.0094 Å °-0.0016 Å °0.0072 Å °-0.0094 Å °0.0279 Å °-0.011 Å °-0.0072 Å °

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