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- PDB-8vkt: Crystallographic structure of dimetalated DapE from Enterococcus ... -

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Basic information

Entry
Database: PDB / ID: 8vkt
TitleCrystallographic structure of dimetalated DapE from Enterococcus faecium
ComponentsProbable succinyl-diaminopimelate desuccinylase
KeywordsHYDROLASE / DapE / desuccinylase / Metalloenzymes
Function / homology
Function and homology information


succinyl-diaminopimelate desuccinylase / succinyl-diaminopimelate desuccinylase activity / lysine biosynthetic process via diaminopimelate / metal ion binding
Similarity search - Function
N-formyl-4-amino-5-aminomethyl-2-methylpyrimidine deformylase/Succinyl-diaminopimelate desuccinylase / ArgE / dapE / ACY1 / CPG2 / yscS family signature 1. / ArgE / dapE / ACY1 / CPG2 / yscS family signature 2. / ArgE/DapE/ACY1/CPG2/YscS, conserved site / Peptidase M20, dimerisation domain / Bacterial exopeptidase dimerisation domain / Peptidase dimerisation domain / Peptidase M20 / Peptidase family M20/M25/M40
Similarity search - Domain/homology
Probable succinyl-diaminopimelate desuccinylase
Similarity search - Component
Biological speciesEnterococcus faecium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.398 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
DepositionJan 9, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 29, 2024Provider: repository / Type: Initial release
Revision 1.1Jun 5, 2024Group: Database references / Category: citation / Item: _citation.journal_volume

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Probable succinyl-diaminopimelate desuccinylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,3586
Polymers43,9811
Non-polymers3775
Water10,215567
1
A: Probable succinyl-diaminopimelate desuccinylase
hetero molecules

A: Probable succinyl-diaminopimelate desuccinylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,71712
Polymers87,9632
Non-polymers75410
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area4550 Å2
ΔGint-166 kcal/mol
Surface area30270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)131.822, 44.914, 78.024
Angle α, β, γ (deg.)90.00, 104.28, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-503-

HOH

21A-1034-

HOH

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Components

#1: Protein Probable succinyl-diaminopimelate desuccinylase


Mass: 43981.395 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterococcus faecium (bacteria) / Gene: B1P95_14080, GBM44_10270, KT858_002121 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3)
References: UniProt: A0A1S8KJG1, succinyl-diaminopimelate desuccinylase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / 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: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 567 / 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: 2.53 Å3/Da / Density % sol: 51.4 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / 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. 97918
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 10, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
101
2979181
ReflectionResolution: 1.398→43.7 Å / Num. obs: 84770 / % possible obs: 96.7 % / Redundancy: 6.5 % / Biso Wilson estimate: 16.64 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.051 / Net I/σ(I): 18.2
Reflection shellResolution: 1.4→1.47 Å / Redundancy: 5 % / Rmerge(I) obs: 0.198 / Mean I/σ(I) obs: 5.6 / Num. unique obs: 10322 / CC1/2: 0.97 / % possible all: 81.4

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.398→42.372 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 17.58 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1762 4239 5 %
Rwork0.1538 --
obs0.1549 84712 96.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.398→42.372 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2948 0 18 568 3534
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0163276
X-RAY DIFFRACTIONf_angle_d1.4844482
X-RAY DIFFRACTIONf_dihedral_angle_d5.5261867
X-RAY DIFFRACTIONf_chiral_restr0.111498
X-RAY DIFFRACTIONf_plane_restr0.01598
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.398-1.41350.27051130.22141916X-RAY DIFFRACTION70
1.4135-1.43010.21431050.2072126X-RAY DIFFRACTION76
1.4301-1.44750.25491210.1962310X-RAY DIFFRACTION83
1.4475-1.46590.22171260.18972416X-RAY DIFFRACTION89
1.4659-1.48510.19561490.18462611X-RAY DIFFRACTION95
1.4851-1.50550.18471410.17652729X-RAY DIFFRACTION98
1.5055-1.5270.20291560.17312714X-RAY DIFFRACTION99
1.527-1.54980.21051400.17192763X-RAY DIFFRACTION98
1.5498-1.5740.21611220.16542693X-RAY DIFFRACTION99
1.574-1.59980.17331490.16642763X-RAY DIFFRACTION99
1.5998-1.62740.21081420.16352729X-RAY DIFFRACTION99
1.6274-1.6570.21061420.16982753X-RAY DIFFRACTION99
1.657-1.68890.17581300.17022723X-RAY DIFFRACTION99
1.6889-1.72330.16241490.16242728X-RAY DIFFRACTION99
1.7233-1.76080.18811370.16432764X-RAY DIFFRACTION99
1.7608-1.80180.18691490.16612776X-RAY DIFFRACTION99
1.8018-1.84680.20121590.16482703X-RAY DIFFRACTION99
1.8468-1.89680.17611420.15612780X-RAY DIFFRACTION99
1.8968-1.95260.18331290.16662806X-RAY DIFFRACTION99
1.9526-2.01560.17171390.15822729X-RAY DIFFRACTION99
2.0156-2.08770.20151440.15142762X-RAY DIFFRACTION99
2.0877-2.17120.18171690.15342759X-RAY DIFFRACTION100
2.1712-2.270.18371640.14762740X-RAY DIFFRACTION100
2.27-2.38970.16421520.1512793X-RAY DIFFRACTION100
2.3897-2.53940.17791520.15592774X-RAY DIFFRACTION99
2.5394-2.73550.20341340.15852758X-RAY DIFFRACTION99
2.7355-3.01070.18791450.15362836X-RAY DIFFRACTION100
3.0107-3.44620.16381440.14822798X-RAY DIFFRACTION100
3.4462-4.34110.1261350.1242836X-RAY DIFFRACTION99
4.3411-100.16451600.15082885X-RAY DIFFRACTION99

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