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- PDB-3uw0: Pectin methylesterase from Yersinia enterocolitica -

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Basic information

Entry
Database: PDB / ID: 3uw0
TitlePectin methylesterase from Yersinia enterocolitica
Componentspectinesterase
KeywordsHYDROLASE / right-handed beta-helix / carbohydrate esterase
Function / homology
Function and homology information


pectinesterase activity / cell wall modification / cell outer membrane
Similarity search - Function
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
Biological speciesYersinia enterocolitica subsp. enterocolitica (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å
AuthorsAbbott, D.W. / Boraston, A.B.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2012
Title: Structure of a pectin methylesterase from Yersinia enterocolitica.
Authors: Boraston, A.B. / Abbott, D.W.
History
DepositionNov 30, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 8, 2012Provider: repository / Type: Initial release
Revision 1.1Mar 28, 2012Group: Database references
Revision 1.2Sep 13, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.3Nov 20, 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


Theoretical massNumber of molelcules
Total (without water)39,7841
Polymers39,7841
Non-polymers00
Water23413
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)170.640, 170.640, 170.640
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number212
Space group name H-MP4332

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Components

#1: Protein pectinesterase / YeCE8 / pectin methylesterase


Mass: 39784.465 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yersinia enterocolitica subsp. enterocolitica (bacteria)
Strain: 8081 / Gene: YE0549 / Production host: Escherichia coli (E. coli) / References: UniProt: A1JJ76, pectinesterase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 13 / Source method: isolated from a natural source / Formula: H2O
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: 5.26 Å3/Da / Density % sol: 76.61 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 4.0 M sodium formate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 4r / Detector: CCD / Date: Aug 14, 2007
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 3.5→39.147 Å / Num. obs: 10653 / % possible obs: 99.9 % / Redundancy: 24.7 % / Rmerge(I) obs: 0.17 / Net I/σ(I): 21.2
Reflection shellResolution: 3.5→3.69 Å / Redundancy: 21.1 % / Rmerge(I) obs: 0.6 / Mean I/σ(I) obs: 5.9 / % possible all: 99.9

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC6.2refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1QJV

1qjv


Resolution: 3.5→39.147 Å / Cor.coef. Fo:Fc: 0.903 / Cor.coef. Fo:Fc free: 0.865 / SU B: 38.309 / SU ML: 0.273 / Cross valid method: THROUGHOUT / ESU R Free: 0.416 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.245 530 4.7 %RANDOM
Rwork0.19527 ---
obs0.19762 10653 99.65 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 57.949 Å2
Refinement stepCycle: LAST / Resolution: 3.5→39.147 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2412 0 0 13 2425
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.022475
X-RAY DIFFRACTIONr_angle_refined_deg0.9241.9383378
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8455319
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.72224.196112
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.54915349
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.4341513
X-RAY DIFFRACTIONr_chiral_restr0.0610.2370
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0211951
X-RAY DIFFRACTIONr_rigid_bond_restr1.16232475
X-RAY DIFFRACTIONr_sphericity_free42.195513
X-RAY DIFFRACTIONr_sphericity_bonded20.70652412
LS refinement shellResolution: 3.5→3.592 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.264 25 -
Rwork0.183 669 -
obs--99.57 %

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