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- PDB-7lgp: DapE enzyme from Shigella flexneri -

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Basic information

Entry
Database: PDB / ID: 7lgp
TitleDapE enzyme from Shigella flexneri
ComponentsSuccinyl-diaminopimelate desuccinylase
KeywordsHYDROLASE / dapE / M20 peptidase / structural genomics / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homology
Function and homology information


succinyl-diaminopimelate desuccinylase / succinyl-diaminopimelate desuccinylase activity / diaminopimelate biosynthetic process / cobalt ion binding / L-lysine biosynthetic process via diaminopimelate / zinc ion binding
Similarity search - Function
Succinyl-diaminopimelate desuccinylase, proteobacteria / ArgE / dapE / ACY1 / CPG2 / yscS family signature 1. / ArgE / dapE / ACY1 / CPG2 / yscS family signature 2. / ArgE/DapE/ACY1/CPG2/YscS, conserved site / : / Bacterial exopeptidase dimerisation domain / Peptidase M20, dimerisation domain / Peptidase dimerisation domain / Peptidase M20 / Peptidase family M20/M25/M40
Similarity search - Domain/homology
Succinyl-diaminopimelate desuccinylase / Succinyl-diaminopimelate desuccinylase
Similarity search - Component
Biological speciesShigella flexneri 2a str. 301 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.91 Å
AuthorsOsipiuk, J. / Endres, M. / Becker, D.P. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)HHSN272201200026C United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)HHSN272201700060C United States
CitationJournal: To Be Published
Title: DapE enzyme from Shigella flexneri
Authors: Osipiuk, J. / Endres, M. / Becker, D.P. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionJan 20, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 27, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Succinyl-diaminopimelate desuccinylase
B: Succinyl-diaminopimelate desuccinylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,89622
Polymers83,1642
Non-polymers73220
Water11,187621
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5690 Å2
ΔGint-268 kcal/mol
Surface area29750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)180.141, 180.141, 200.091
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32

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Components

#1: Protein Succinyl-diaminopimelate desuccinylase / SDAP desuccinylase / N-succinyl-LL-2 / 6-diaminoheptanedioate amidohydrolase


Mass: 41582.102 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shigella flexneri 2a str. 301 (bacteria)
Gene: dapE / Plasmid: pMCSG53 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: D2AGR7, UniProt: P0AED8*PLUS, succinyl-diaminopimelate desuccinylase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 621 / 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: 3.76 Å3/Da / Density % sol: 67.26 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 2.8 M ammonium sulfate, 150 mM Tris buffer pH 8.0, 10 mM sodium potassium tartrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 16, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.91→47.68 Å / Num. obs: 95874 / % possible obs: 99.8 % / Redundancy: 8.1 % / CC1/2: 0.997 / CC star: 0.999 / Rmerge(I) obs: 0.146 / Rpim(I) all: 0.053 / Rrim(I) all: 0.155 / Χ2: 1.555 / Net I/av σ(I): 16.1 / Net I/σ(I): 7.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
1.91-1.944.91.2671.0346130.5090.8210.6181.4150.80896.6
1.94-1.986.11.11547140.5860.481.2170.84699.2
1.98-2.027.50.99947860.7220.3821.0710.885100
2.02-2.068.20.83647670.8050.3030.8910.96100
2.06-2.18.30.71747720.860.2590.7641.081100
2.1-2.158.40.60547650.8860.2180.6441.15100
2.15-2.28.40.51348080.9140.1850.5471.282100
2.2-2.268.40.44747590.9290.1610.4761.41299.9
2.26-2.338.50.39747690.9460.1430.4231.473100
2.33-2.418.50.35347860.9530.1270.3761.618100
2.41-2.498.50.30547930.9630.110.3251.784100
2.49-2.598.50.27647830.9630.0990.2941.849100
2.59-2.718.50.24547890.970.0880.261.965100
2.71-2.858.40.2147980.9770.0750.2241.962100
2.85-3.038.40.18648270.9820.0670.1981.956100
3.03-3.278.40.16448090.9860.0590.1751.931100
3.27-3.598.40.14948340.9860.0530.1581.89100
3.59-4.118.30.13348390.9880.0480.1411.87799.9
4.11-5.188.10.10548660.9930.0390.1131.83699.9
5.18-47.688.10.06649970.9980.0240.071.821100

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
HKL-3000data scaling
PDB_EXTRACT3.27data extraction
HKL-3000data reduction
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4O23

4o23


Resolution: 1.91→47.68 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.966 / SU B: 5.564 / SU ML: 0.079 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.1 / ESU R Free: 0.099 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1867 4855 5.1 %RANDOM
Rwork0.1588 ---
obs0.1603 91019 99.69 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 95.28 Å2 / Biso mean: 36.907 Å2 / Biso min: 21.81 Å2
Baniso -1Baniso -2Baniso -3
1--0.47 Å2-0.24 Å20 Å2
2---0.47 Å20 Å2
3---1.53 Å2
Refinement stepCycle: final / Resolution: 1.91→47.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5811 0 20 622 6453
Biso mean--49.38 47.66 -
Num. residues----751
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0136282
X-RAY DIFFRACTIONr_bond_other_d0.0010.0175965
X-RAY DIFFRACTIONr_angle_refined_deg1.5611.6378620
X-RAY DIFFRACTIONr_angle_other_deg1.4061.57313720
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6835844
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.57722.299374
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.314151047
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.2061552
X-RAY DIFFRACTIONr_chiral_restr0.0770.2826
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.027422
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021534
LS refinement shellResolution: 1.91→1.96 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.281 332 -
Rwork0.283 6515 -
all-6847 -
obs--96.74 %
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)
10.45130.0664-0.37770.357-0.01860.4421-0.00330.0446-0.02430.0408-0.02960.13670.0053-0.05760.03290.01-0.01240.010.053-0.02880.085621.886416.039845.1513
20.1741-0.0526-0.1270.2340.52951.31650.00930.0164-0.0112-0.0523-0.02130.0166-0.0245-0.0590.0120.0956-0.007-0.01720.01990.0020.013342.521710.9074-10.937
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 509
2X-RAY DIFFRACTION2B-1 - 511

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