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- PDB-7uoi: Crystallographic structure of DapE from Enterococcus faecium -

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Basic information

Entry
Database: PDB / ID: 7uoi
TitleCrystallographic structure of DapE from Enterococcus faecium
Componentssuccinyl-diaminopimelate desuccinylase
KeywordsHYDROLASE / DapE / desuccinylase / Metalloenzymes
Function / homology:
Function and homology information
Biological speciesEnterococcus faecium 1
231
410
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsGonzalez-Segura, L. / Diaz-Vilchis, A. / Terrazas-Lopez, M. / Diaz-Sanchez, A.G.
Funding support Mexico, 3items
OrganizationGrant numberCountry
Consejo Nacional de Ciencia y Tecnologia (CONACYT)PN-2015-587 Mexico
Facultad de QuimicaUNAM 5000-9129 Mexico
Programa de Apoyo a Proyectos de Investigacion e Innovacion Tecnologica (PAPIIT)IN227920 Mexico
CitationJournal: Int.J.Biol.Macromol. / Year: 2024
Title: The three-dimensional structure of DapE from Enterococcus faecium reveals new insights into DapE/ArgE subfamily ligand specificity.
Authors: Terrazas-Lopez, M. / Gonzalez-Segura, L. / Diaz-Vilchis, A. / Aguirre-Mendez, K.A. / Lobo-Galo, N. / Martinez-Martinez, A. / Diaz-Sanchez, A.G.
History
DepositionApr 12, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 12, 2023Provider: repository / Type: Initial release
Revision 1.1Apr 19, 2023Group: Author supporting evidence / Category: pdbx_audit_support
Revision 1.2May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.3Jun 12, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: succinyl-diaminopimelate desuccinylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,2314
Polymers43,9811
Non-polymers2503
Water9,062503
1
A: succinyl-diaminopimelate desuccinylase
hetero molecules

A: succinyl-diaminopimelate desuccinylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,4628
Polymers87,9632
Non-polymers4996
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area3790 Å2
ΔGint-87 kcal/mol
Surface area30880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)132.486, 45.378, 78.751
Angle α, β, γ (deg.)90.000, 103.650, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-502-

HOH

21A-971-

HOH

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Components

#1: Protein succinyl-diaminopimelate desuccinylase


Mass: 43981.395 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterococcus faecium 1,231,410 (bacteria)
Gene: EFTG_01132 / Variant: Enterococcus faecium / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): Bl21-DE3
References: UniProt: A0A7U8IMK7, succinyl-diaminopimelate desuccinylase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 503 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.74 Å3/Da / Density % sol: 55.14 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4.6 / Details: 100 mM sodium acetate, 8% PEG4000, pH 4.6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.85 Å
DetectorType: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: Jun 13, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.85 Å / Relative weight: 1
ReflectionResolution: 1.6→44.37 Å / Num. obs: 58807 / % possible obs: 97.7 % / Redundancy: 5.5 % / Biso Wilson estimate: 20.18 Å2 / CC1/2: 0.96 / Rmerge(I) obs: 0.073 / Net I/σ(I): 11.2
Reflection shellResolution: 1.6→1.69 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 2.9 / Num. unique obs: 7861 / CC1/2: 0.85 / % possible all: 90

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Starting model: 0 / Resolution: 1.6→38.263 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.41 / Phase error: 17.68 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1807 2945 5.03 %
Rwork0.1528 55553 -
obs0.1542 58498 96.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 97.88 Å2 / Biso mean: 25 Å2 / Biso min: 9.59 Å2
Refinement stepCycle: final / Resolution: 1.6→38.263 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2948 0 13 505 3466
Biso mean--46.91 39.38 -
Num. residues----383
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0123279
X-RAY DIFFRACTIONf_angle_d1.0984485
X-RAY DIFFRACTIONf_chiral_restr0.077496
X-RAY DIFFRACTIONf_plane_restr0.008604
X-RAY DIFFRACTIONf_dihedral_angle_d3.0352621
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.6004-1.62670.2881340.2331226383
1.6267-1.65470.23031300.2014240390
1.6547-1.68480.20291300.1745261195
1.6848-1.71720.21671390.1698265499
1.7172-1.75230.21881270.1631254693
1.7523-1.79040.20591520.1634264098
1.7904-1.8320.19121260.169265399
1.832-1.87780.19461390.1668269899
1.8778-1.92860.24071530.2141259797
1.9286-1.98530.19221410.1766269999
1.9853-2.04940.20061380.1545268799
2.0494-2.12270.17921310.1547272099
2.1227-2.20760.17961570.1551264498
2.2076-2.30810.21971380.1771265898
2.3081-2.42980.1871620.154265198
2.4298-2.5820.1841390.1514275099
2.582-2.78130.19191370.1555271099
2.7813-3.06110.18121450.1562268298
3.0611-3.50370.16521470.13942751100
3.5037-4.41330.1451520.125269598
4.4133-5.420.15661280.1401284199

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