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- PDB-9mm2: Crystal structure of bacterial pectin methylesterase PmeC5 from B... -

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Basic information

Entry
Database: PDB / ID: 9mm2
TitleCrystal structure of bacterial pectin methylesterase PmeC5 from B. fibrisolvens D1T
ComponentsPutative cell wall binding repeat-containing protein
KeywordsSUGAR BINDING PROTEIN / Pectin methylesterase
Function / homology
Function and homology information


carbon-oxygen lyase activity, acting on polysaccharides / pectinesterase activity / cell wall modification / extracellular region
Similarity search - Function
: / Pel9A-like, right handed beta helix region / : / Pectinesterase, Asp active site / Pectinesterase signature 2. / Pectinesterase, catalytic / Pectinesterase / Parallel beta-helix repeat / Parallel beta-helix repeats / Choline-binding repeat ...: / Pel9A-like, right handed beta helix region / : / Pectinesterase, Asp active site / Pectinesterase signature 2. / Pectinesterase, catalytic / Pectinesterase / Parallel beta-helix repeat / Parallel beta-helix repeats / Choline-binding repeat / Cell wall/choline-binding repeat / Cell wall-binding repeat profile. / Pectin lyase fold / Pectin lyase fold/virulence factor
Similarity search - Domain/homology
AMMONIUM ION / Putative cell wall binding repeat-containing protein
Similarity search - Component
Biological speciesButyrivibrio fibrisolvens DSM 3071 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.33 Å
AuthorsCarbone, V. / Reilly, K. / Sang, C. / Schofield, L. / Ronimus, R. / Attwood, G.T. / Palevich, N.
Funding support New Zealand, 1items
OrganizationGrant numberCountry
Other governmentIF_AgR_Methanol New Zealand
CitationJournal: Biomolecules / Year: 2025
Title: Crystal Structure of the Multidomain Pectin Methylesterase PmeC5 from Butyrivibrio fibrisolvens D1 T.
Authors: Carbone, V. / Reilly, K. / Sang, C. / Schofield, L.R. / Kelly, W.J. / Ronimus, R.S. / Attwood, G.T. / Palevich, N.
History
DepositionDec 19, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 15, 2025Provider: repository / Type: Initial release
Revision 1.1Jun 18, 2025Group: 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.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative cell wall binding repeat-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,09417
Polymers49,3761
Non-polymers71916
Water12,178676
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.297, 61.950, 77.369
Angle α, β, γ (deg.)90.00, 105.39, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Putative cell wall binding repeat-containing protein


Mass: 49375.812 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Butyrivibrio fibrisolvens DSM 3071 (bacteria)
Gene: SAMN02745229_04032 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1M6G673

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Non-polymers , 5 types, 692 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-NH4 / AMMONIUM ION


Mass: 18.038 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H4N
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 676 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
Has protein modificationN

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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: 2.03 Å3/Da / Density % sol: 39.29 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.2 M Ammonium chloride, 20 % w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.953722 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Jul 12, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.953722 Å / Relative weight: 1
ReflectionResolution: 1.33→47.66 Å / Num. obs: 89955 / % possible obs: 99.4 % / Redundancy: 6.9 % / CC1/2: 1 / Rmerge(I) obs: 0.049 / Rpim(I) all: 0.02 / Rrim(I) all: 0.053 / Χ2: 1.01 / Net I/σ(I): 23.3 / Num. measured all: 624009
Reflection shellResolution: 1.33→1.35 Å / % possible obs: 98.4 % / Redundancy: 6.8 % / Rmerge(I) obs: 0.301 / Num. measured all: 30348 / Num. unique obs: 4440 / CC1/2: 0.958 / Rpim(I) all: 0.123 / Rrim(I) all: 0.326 / Χ2: 1 / Net I/σ(I) obs: 5.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
Aimlessdata scaling
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.33→41.78 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.973 / SU B: 0.557 / SU ML: 0.024 / Cross valid method: THROUGHOUT / ESU R: 0.04 / ESU R Free: 0.042 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.14014 4444 4.9 %RANDOM
Rwork0.11966 ---
obs0.12068 85488 99.34 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 8.645 Å2
Baniso -1Baniso -2Baniso -3
1--0.27 Å20 Å2-0.17 Å2
2--0.51 Å20 Å2
3----0.13 Å2
Refinement stepCycle: 1 / Resolution: 1.33→41.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3228 0 43 676 3947
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0123486
X-RAY DIFFRACTIONr_bond_other_d0.0010.0163082
X-RAY DIFFRACTIONr_angle_refined_deg1.8991.84748
X-RAY DIFFRACTIONr_angle_other_deg0.6421.7427136
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2655460
X-RAY DIFFRACTIONr_dihedral_angle_2_deg8.469512
X-RAY DIFFRACTIONr_dihedral_angle_3_deg9.98710553
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0980.2521
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.024245
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02801
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_it0.8570.7991768
X-RAY DIFFRACTIONr_mcbond_other0.8420.7981767
X-RAY DIFFRACTIONr_mcangle_it1.2551.4382237
X-RAY DIFFRACTIONr_mcangle_other1.2581.4392238
X-RAY DIFFRACTIONr_scbond_it1.6640.9461718
X-RAY DIFFRACTIONr_scbond_other1.6630.9461719
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.4241.6522507
X-RAY DIFFRACTIONr_long_range_B_refined4.513.084285
X-RAY DIFFRACTIONr_long_range_B_other3.9279.44040
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.33→1.365 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.173 307 -
Rwork0.154 6328 -
obs--99.18 %

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