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- PDB-8tne: Crystal structure of bacterial pectin methylesterase Pme8A from r... -

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Basic information

Entry
Database: PDB / ID: 8tne
TitleCrystal structure of bacterial pectin methylesterase Pme8A from rumen Butyrivibrio
ComponentsPectinesterase
KeywordsSUGAR BINDING PROTEIN / Pectin methylesterase / Butyrivibrio / rumen / pectin / methanol / methane
Function / homology
Function and homology information


pectinesterase / pectinesterase activity / : / cell wall modification / pectin catabolic process
Similarity search - Function
Pectinesterase, Asp active site / Pectinesterase signature 2. / Pectinesterase, catalytic / Pectinesterase / Pectin lyase fold / Pectin lyase fold/virulence factor
Similarity search - Domain/homology
Biological speciesButyrivibrio proteoclasticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsCarbone, V. / Reilly, K. / Sang, C. / Schofield, L. / Ronimus, R. / Kelly, W.J. / Attwood, G.T. / Palevich, N.
Funding support New Zealand, 1items
OrganizationGrant numberCountry
Other governmentIF_AgR_Methanol New Zealand
CitationJournal: Int J Mol Sci / Year: 2023
Title: Crystal Structures of Bacterial Pectin Methylesterases Pme8A and PmeC2 from Rumen Butyrivibrio .
Authors: Carbone, V. / Reilly, K. / Sang, C. / Schofield, L.R. / Ronimus, R.S. / Kelly, W.J. / Attwood, G.T. / Palevich, N.
History
DepositionAug 1, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 16, 2023Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Oct 11, 2023Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Pectinesterase
B: Pectinesterase
C: Pectinesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,4077
Polymers122,1593
Non-polymers2484
Water1,74797
1
A: Pectinesterase
hetero molecules


  • defined by author
  • 40.8 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)40,8443
Polymers40,7201
Non-polymers1242
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Pectinesterase
hetero molecules


  • defined by author
  • 40.8 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)40,8443
Polymers40,7201
Non-polymers1242
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Pectinesterase


  • defined by author
  • 40.7 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)40,7201
Polymers40,7201
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)228.797, 49.272, 100.588
Angle α, β, γ (deg.)90.00, 101.03, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Pectinesterase


Mass: 40719.695 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Butyrivibrio proteoclasticus (bacteria)
Gene: pme8A / Production host: Escherichia coli (E. coli) / References: UniProt: E0S1Z9
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 97 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.48 Å3/Da / Density % sol: 50 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.1 M Sodium HEPES 7.5, 20 % w/v PEG 10,000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95374 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 7, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95374 Å / Relative weight: 1
ReflectionResolution: 2.3→48.76 Å / Num. obs: 48330 / % possible obs: 97.3 % / Redundancy: 6.8 % / CC1/2: 0.997 / Rmerge(I) obs: 0.105 / Rpim(I) all: 0.044 / Rrim(I) all: 0.114 / Χ2: 1 / Net I/σ(I): 8.8 / Num. measured all: 327785
Reflection shellResolution: 2.3→2.37 Å / % possible obs: 71 % / Redundancy: 6 % / Rmerge(I) obs: 1.283 / Num. measured all: 19428 / Num. unique obs: 3213 / CC1/2: 0.693 / Rpim(I) all: 0.552 / Rrim(I) all: 1.401 / Χ2: 0.96 / Net I/σ(I) obs: 1.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0411refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→48.17 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.945 / SU B: 26.539 / SU ML: 0.266 / Cross valid method: THROUGHOUT / ESU R: 0.359 / ESU R Free: 0.246 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2495 2389 4.9 %RANDOM
Rwork0.2001 ---
obs0.20245 45937 97.27 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 68.198 Å2
Baniso -1Baniso -2Baniso -3
1-0.14 Å20 Å2-1.71 Å2
2--6.91 Å2-0 Å2
3----5.93 Å2
Refinement stepCycle: 1 / Resolution: 2.3→48.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7872 0 16 97 7985
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0128068
X-RAY DIFFRACTIONr_bond_other_d0.0010.0167469
X-RAY DIFFRACTIONr_angle_refined_deg1.3921.64910870
X-RAY DIFFRACTIONr_angle_other_deg0.4551.57817197
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.58351005
X-RAY DIFFRACTIONr_dihedral_angle_2_deg12.133557
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.536101383
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0620.21156
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.029663
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021953
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.1382.6294011
X-RAY DIFFRACTIONr_mcbond_other2.1372.6294011
X-RAY DIFFRACTIONr_mcangle_it3.3944.7145010
X-RAY DIFFRACTIONr_mcangle_other3.3944.7155011
X-RAY DIFFRACTIONr_scbond_it2.5172.9194057
X-RAY DIFFRACTIONr_scbond_other2.5162.9184056
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.0655.2395858
X-RAY DIFFRACTIONr_long_range_B_refined6.09824.948596
X-RAY DIFFRACTIONr_long_range_B_other6.09824.918588
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.358 Å
RfactorNum. reflection% reflection
Rfree0.364 106 -
Rwork0.396 2218 -
obs--63.81 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.97550.26550.8261.0127-0.24784.2674-0.0610.29160.1649-0.10480.04390.0967-0.1-0.04570.01710.02010.0320.01090.41490.0080.3497-69.8807-25.869611.5915
22.210.03111.27461.5252-0.36074.15690.1287-0.157-0.07990.2693-0.0978-0.18750.26990.4915-0.03090.0768-0.0067-0.03310.4763-0.00510.3824-44.6783-30.027348.5586
32.3965-0.2097-1.47460.6879-0.02547.27130.0044-0.3890.02350.16130.0215-0.00480.2858-0.1767-0.02590.1335-0.08790.01160.6199-0.02920.5545-10.1301-14.06620.0698
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 402
2X-RAY DIFFRACTION2B5 - 402
3X-RAY DIFFRACTION3C4 - 341

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