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- PDB-8tms: Crystal structure of bacterial pectin methylesterase PmeC2 from r... -

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Basic information

Entry
Database: PDB / ID: 8tms
TitleCrystal structure of bacterial pectin methylesterase PmeC2 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 fibrisolvens (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
DepositionJul 30, 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
D: Pectinesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)138,80123
Polymers137,6754
Non-polymers1,12619
Water6,017334
1
A: Pectinesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,7657
Polymers34,4191
Non-polymers3466
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Pectinesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,6405
Polymers34,4191
Non-polymers2224
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Pectinesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,8538
Polymers34,4191
Non-polymers4347
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Pectinesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,5433
Polymers34,4191
Non-polymers1242
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)48.638, 76.282, 96.779
Angle α, β, γ (deg.)98.36, 104.16, 90.05
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Pectinesterase


Mass: 34418.730 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Butyrivibrio fibrisolvens (bacteria) / Gene: SAMN02745229_01989 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1M5Z711
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 17 / Source method: isolated from a natural source / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 334 / 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: 2.57 Å3/Da / Density % sol: 51.7 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2 M Magnesium chloride hexahydrate, 0.1 M Tris pH 8.5, 20 % w/v PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.95372 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Mar 31, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95372 Å / Relative weight: 1
ReflectionResolution: 2.3→47.2 Å / Num. obs: 56000 / % possible obs: 95.1 % / Redundancy: 3.7 % / CC1/2: 0.994 / Rmerge(I) obs: 0.148 / Rpim(I) all: 0.089 / Rrim(I) all: 0.173 / Χ2: 0.49 / Net I/σ(I): 5.4
Reflection shellResolution: 2.3→2.37 Å / % possible obs: 92.3 % / Redundancy: 3.6 % / Rmerge(I) obs: 1.404 / Num. measured all: 16208 / Num. unique obs: 4465 / CC1/2: 0.349 / Rpim(I) all: 0.842 / Rrim(I) all: 1.639 / Χ2: 0.47 / Net I/σ(I) obs: 0.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0411refinement
Aimlessdata scaling
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→47.17 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.928 / SU B: 24.799 / SU ML: 0.26 / Cross valid method: THROUGHOUT / ESU R: 0.391 / ESU R Free: 0.243 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24013 2790 5 %RANDOM
Rwork0.20448 ---
obs0.20625 53208 95.11 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 42.514 Å2
Baniso -1Baniso -2Baniso -3
1--2.12 Å2-0.31 Å2-0.54 Å2
2--1.18 Å2-0.28 Å2
3---1.11 Å2
Refinement stepCycle: 1 / Resolution: 2.3→47.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9128 0 70 334 9532
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0129454
X-RAY DIFFRACTIONr_bond_other_d0.0010.0168692
X-RAY DIFFRACTIONr_angle_refined_deg1.2981.65812753
X-RAY DIFFRACTIONr_angle_other_deg0.4541.57820085
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.62351162
X-RAY DIFFRACTIONr_dihedral_angle_2_deg6.79563
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.824101584
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.060.21343
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211117
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022239
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_it1.5612.14621
X-RAY DIFFRACTIONr_mcbond_other1.562.14621
X-RAY DIFFRACTIONr_mcangle_it2.6033.7695774
X-RAY DIFFRACTIONr_mcangle_other2.6023.7695775
X-RAY DIFFRACTIONr_scbond_it1.6522.2674833
X-RAY DIFFRACTIONr_scbond_other1.6522.2674834
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.7634.0986974
X-RAY DIFFRACTIONr_long_range_B_refined5.04320.2810109
X-RAY DIFFRACTIONr_long_range_B_other5.02820.1810069
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.305→2.364 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.351 216 -
Rwork0.334 3747 -
obs--91.99 %
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)
13.03470.2254-0.22021.8081-0.00641.46230.0156-0.05430.16660.2373-0.03890.1045-0.0428-0.09580.02340.1990.00290.08620.0086-0.0050.04780.642-0.0091.214
22.117-0.5366-0.44111.52890.32481.42420.06010.12960.4013-0.2329-0.0774-0.0414-0.07690.03590.01740.1988-0.04490.08450.0439-0.01150.138615.66738.145-38.809
32.0155-0.3620.13182.2901-0.57811.98710.0690.1793-0.2916-0.5041-0.11960.30750.29290.0240.05070.3375-0.0140.06260.0459-0.07210.155810.4847.572-40.048
41.57070.43160.21051.81760.86371.89940.053-0.1697-0.49160.3872-0.043-0.10390.3145-0.0612-0.010.3203-0.00590.11080.03070.03430.24875.808-30.562.579
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-4 - 283
2X-RAY DIFFRACTION2B-4 - 283
3X-RAY DIFFRACTION3C-4 - 283
4X-RAY DIFFRACTION4D-4 - 283

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