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- PDB-6m76: GH31 alpha-N-acetylgalactosaminidase from Enterococcus faecalis -

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Basic information

Entry
Database: PDB / ID: 6m76
TitleGH31 alpha-N-acetylgalactosaminidase from Enterococcus faecalis
ComponentsLPXTG-motif cell wall anchor domain protein
KeywordsHYDROLASE / GLYCOSIDE HYDROLASE / MUCIN / (BETA/ALPHA)8-BARREL / FIBRONECTIN-LIKE
Function / homologyDomain of unknown function (DUF5110) / Glycosyl hydrolases family 31 TIM-barrel domain
Function and homology information
Biological speciesEnterococcus faecalis ATCC 10100 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.4 Å
AuthorsMiyazaki, T.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)19K15748 Japan
CitationJournal: Febs Lett. / Year: 2020
Title: Crystal structure of the Enterococcus faecalis alpha-N-acetylgalactosaminidase, a member of the glycoside hydrolase family 31.
Authors: Miyazaki, T. / Park, E.Y.
History
DepositionMar 17, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 20, 2020Provider: repository / Type: Initial release
Revision 1.1Aug 12, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Sep 16, 2020Group: Database references / Source and taxonomy / Structure summary
Category: entity_src_gen / pdbx_entry_details ...entity_src_gen / pdbx_entry_details / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _entity_src_gen.gene_src_strain / _entity_src_gen.pdbx_gene_src_gene ..._entity_src_gen.gene_src_strain / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name / _pdbx_entry_details.sequence_details / _struct_ref.db_code / _struct_ref.db_name / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq.seq_align_beg
Revision 1.3Mar 27, 2024Group: Data collection / Database references / Derived calculations
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _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: LPXTG-motif cell wall anchor domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,18710
Polymers106,6291
Non-polymers5599
Water19,1501063
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1960 Å2
ΔGint31 kcal/mol
Surface area35000 Å2
Unit cell
Length a, b, c (Å)82.438, 82.971, 149.683
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein LPXTG-motif cell wall anchor domain protein


Mass: 106628.641 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterococcus faecalis ATCC 10100 (bacteria)
Strain: ATCC 10100 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1063 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Sequence detailsTHE SEQUENCE OF THIS PROTEIN WAS NOT AVAILABLE AT THE UNIPROT KNOWLEDGEBASE DATABASE (UNIPROTKB) AT ...THE SEQUENCE OF THIS PROTEIN WAS NOT AVAILABLE AT THE UNIPROT KNOWLEDGEBASE DATABASE (UNIPROTKB) AT THE TIME OF DEPOSITION. AUTHORS STATE THAT THE GENEBANK ACCESSION NUMBER IS EOK08638.1. FOR THE PROTEIN.

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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: 2.5 Å3/Da / Density % sol: 50.87 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 25% PEG3350, 0.2 M ammonium citrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 24, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.4→50 Å / Num. obs: 201712 / % possible obs: 100 % / Redundancy: 12.7 % / CC1/2: 1 / Rmerge(I) obs: 0.068 / Net I/σ(I): 18.3
Reflection shellResolution: 1.4→1.48 Å / Redundancy: 13.1 % / Rmerge(I) obs: 0.877 / Mean I/σ(I) obs: 2.7 / Num. unique obs: 29211 / CC1/2: 0.884 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.4→46.123 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.965 / SU B: 1.103 / SU ML: 0.043 / Cross valid method: FREE R-VALUE / ESU R: 0.056 / ESU R Free: 0.058
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1951 9974 4.963 %
Rwork0.1715 --
all0.173 --
obs-200987 99.67 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 22.259 Å2
Baniso -1Baniso -2Baniso -3
1-0.093 Å20 Å20 Å2
2---0.02 Å20 Å2
3----0.073 Å2
Refinement stepCycle: LAST / Resolution: 1.4→46.123 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7216 0 36 1063 8315
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0137518
X-RAY DIFFRACTIONr_bond_other_d0.0010.0176639
X-RAY DIFFRACTIONr_angle_refined_deg1.471.6510205
X-RAY DIFFRACTIONr_angle_other_deg1.4081.57815521
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3355946
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.41124.845386
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.078151223
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9011521
X-RAY DIFFRACTIONr_chiral_restr0.0730.2965
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.028593
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021526
X-RAY DIFFRACTIONr_nbd_refined0.2070.21401
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1790.26245
X-RAY DIFFRACTIONr_nbtor_refined0.1690.23654
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0760.23188
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1340.2759
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1190.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.260.217
X-RAY DIFFRACTIONr_nbd_other0.2410.243
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1690.238
X-RAY DIFFRACTIONr_mcbond_it1.3912.2183751
X-RAY DIFFRACTIONr_mcbond_other1.392.2173750
X-RAY DIFFRACTIONr_mcangle_it2.1083.3254708
X-RAY DIFFRACTIONr_mcangle_other2.1083.3264709
X-RAY DIFFRACTIONr_scbond_it2.0412.3953767
X-RAY DIFFRACTIONr_scbond_other2.0412.3963768
X-RAY DIFFRACTIONr_scangle_it3.0913.5115497
X-RAY DIFFRACTIONr_scangle_other3.0913.5115498
X-RAY DIFFRACTIONr_lrange_it4.69326.8958739
X-RAY DIFFRACTIONr_lrange_other4.4426.1018452
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4-1.4360.2866630.26314118X-RAY DIFFRACTION99.9729
1.436-1.4760.3036850.29413695X-RAY DIFFRACTION99.7434
1.476-1.5180.2717120.25813237X-RAY DIFFRACTION99.6357
1.518-1.5650.2986400.27112911X-RAY DIFFRACTION99.6104
1.565-1.6160.2226670.20212546X-RAY DIFFRACTION99.8791
1.616-1.6730.2156420.1912119X-RAY DIFFRACTION99.8045
1.673-1.7360.1986270.18211688X-RAY DIFFRACTION99.7812
1.736-1.8070.215990.18711248X-RAY DIFFRACTION99.6887
1.807-1.8870.2225480.18310871X-RAY DIFFRACTION99.6683
1.887-1.980.2225150.210171X-RAY DIFFRACTION97.893
1.98-2.0870.2095570.1779816X-RAY DIFFRACTION99.4917
2.087-2.2130.1894360.1619385X-RAY DIFFRACTION99.8983
2.213-2.3660.2025010.1668744X-RAY DIFFRACTION99.4086
2.366-2.5550.1774820.158162X-RAY DIFFRACTION99.9191
2.555-2.7990.1784150.1497592X-RAY DIFFRACTION99.9251
2.799-3.1280.1823440.1516901X-RAY DIFFRACTION99.9448
3.128-3.6110.183040.1526146X-RAY DIFFRACTION100
3.611-4.420.1612560.1415226X-RAY DIFFRACTION99.9635
4.42-6.240.1452410.1454068X-RAY DIFFRACTION100
6.24-46.1230.1871400.1672369X-RAY DIFFRACTION99.6426

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