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- PDB-5vo3: Crystal structure of DapE in complex with the products (succinic ... -

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Basic information

Entry
Database: PDB / ID: 5vo3
TitleCrystal structure of DapE in complex with the products (succinic acid and diaminopimelic acid)
ComponentsSuccinyl-diaminopimelate desuccinylase
KeywordsHYDROLASE / DapE / hydrolaze / Succinic acid / diaminopimelic acid / M28 / Structural Genomics / PSI-Biology
Function / homology
Function and homology information


succinyl-diaminopimelate desuccinylase / succinyl-diaminopimelate desuccinylase activity / diaminopimelate biosynthetic process / lysine biosynthetic process via diaminopimelate / cobalt ion binding / zinc ion binding / cytosol
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 / Alpha-Beta Plaits - #360 / Peptidase M20, dimerisation domain / Bacterial exopeptidase dimerisation domain / Peptidase dimerisation domain / Peptidase M20 ...: / 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 / Alpha-Beta Plaits - #360 / Peptidase M20, dimerisation domain / Bacterial exopeptidase dimerisation domain / Peptidase dimerisation domain / Peptidase M20 / Peptidase family M20/M25/M40 / Zn peptidases / Aminopeptidase / Alpha-Beta Plaits / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
2,6-DIAMINOPIMELIC ACID / SUCCINIC ACID / Succinyl-diaminopimelate desuccinylase
Similarity search - Component
Biological speciesHaemophilus influenzae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.954 Å
AuthorsNocek, B.
CitationJournal: Biochemistry / Year: 2018
Title: Structural Evidence of a Major Conformational Change Triggered by Substrate Binding in DapE Enzymes: Impact on the Catalytic Mechanism.
Authors: Nocek, B. / Reidl, C. / Starus, A. / Heath, T. / Bienvenue, D. / Osipiuk, J. / Jedrzejczak, R. / Joachimiak, A. / Becker, D.P. / Holz, R.C.
History
DepositionMay 1, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 25, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Category: atom_site / chem_comp_atom / chem_comp_bond
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2

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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)42,0935
Polymers41,6541
Non-polymers4394
Water4,125229
1
A: Succinyl-diaminopimelate desuccinylase
hetero molecules

A: Succinyl-diaminopimelate desuccinylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,18710
Polymers83,3082
Non-polymers8788
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_455-x-1,y,-z1
Buried area6840 Å2
ΔGint-151 kcal/mol
Surface area27930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.648, 135.536, 149.613
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-691-

HOH

21A-824-

HOH

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Components

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


Mass: 41654.211 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haemophilus influenzae (bacteria) / Gene: dapE, HI_0102
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P44514, succinyl-diaminopimelate desuccinylase
#2: Chemical ChemComp-SIN / SUCCINIC ACID


Mass: 118.088 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C4H6O4
#3: Chemical ChemComp-API / 2,6-DIAMINOPIMELIC ACID


Type: L-peptide linking / Mass: 190.197 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C7H14N2O4
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: Zn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 229 / Source method: isolated from a natural source / Formula: H2O

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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: 3.43 Å3/Da / Density % sol: 64.12 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.15 M Hepes pH 7.5, 0.06 M Sodium potassium tartrate, 26 % Peg 8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 8, 2016 / Details: mirrors
RadiationMonochromator: double crystals / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.95→40 Å / Num. obs: 60902 / % possible obs: 99.5 % / Redundancy: 4 % / Rmerge(I) obs: 0.073 / Net I/σ(I): 16
Reflection shellResolution: 1.9539→1.9844 Å

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Processing

Software
NameVersionClassification
PHENIXdev_1888refinement
HKL-3000data reduction
HKL-3000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ISZ

3isz


Resolution: 1.954→35.321 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.35
RfactorNum. reflection% reflection
Rfree0.1846 3023 5.11 %
Rwork0.1623 --
obs0.1634 59180 73.38 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.954→35.321 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2929 0 2 229 3160
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083019
X-RAY DIFFRACTIONf_angle_d1.1744105
X-RAY DIFFRACTIONf_dihedral_angle_d13.9251110
X-RAY DIFFRACTIONf_chiral_restr0.115467
X-RAY DIFFRACTIONf_plane_restr0.005537
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9539-1.98440.1799760.18071232X-RAY DIFFRACTION36
1.9844-2.0170.2275760.17341413X-RAY DIFFRACTION40
2.017-2.05170.2269920.18311487X-RAY DIFFRACTION44
2.0517-2.0890.2054810.17911677X-RAY DIFFRACTION48
2.089-2.12920.2185880.17941904X-RAY DIFFRACTION54
2.1292-2.17270.1902780.17452074X-RAY DIFFRACTION59
2.1727-2.21990.1871170.18572202X-RAY DIFFRACTION63
2.2199-2.27150.19971290.18252276X-RAY DIFFRACTION65
2.2715-2.32830.20531240.18092324X-RAY DIFFRACTION67
2.3283-2.39130.19921270.18682350X-RAY DIFFRACTION68
2.3913-2.46160.20131280.18372477X-RAY DIFFRACTION70
2.4616-2.5410.16521360.16832526X-RAY DIFFRACTION73
2.541-2.63180.18881360.17862606X-RAY DIFFRACTION75
2.6318-2.73720.2051530.17072825X-RAY DIFFRACTION81
2.7372-2.86170.16371910.17773007X-RAY DIFFRACTION87
2.8617-3.01250.18611890.1733258X-RAY DIFFRACTION93
3.0125-3.20110.2281780.17183352X-RAY DIFFRACTION97
3.2011-3.44810.21292060.16393415X-RAY DIFFRACTION99
3.4481-3.79470.1871670.1543494X-RAY DIFFRACTION99
3.7947-4.3430.15842020.133411X-RAY DIFFRACTION98
4.343-5.46840.15221560.12563484X-RAY DIFFRACTION100
5.4684-35.32680.1681930.17523363X-RAY DIFFRACTION96
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)
13.57851.29260.36583.1920.10861.7476-0.090.3472-0.80930.03910.1684-0.29430.45030.04140.03010.2379-0.03950.05440.0544-0.09060.2508-16.385810.810130.9508
20.3346-0.03780.61770.21620.06932.62050.0409-0.0623-0.0180.0219-0.01740.0442-0.0084-0.4399-0.02490.0791-0.01930.0320.15320.01440.111-30.563730.993413.7888
31.77670.84530.30031.77080.16012.2171-0.01220.1813-0.12180.01110.0727-0.1060.04730.0807-0.10050.1116-0.01330.01730.0905-0.02310.1065-13.008922.057732.1952
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid -3 through 172 )
2X-RAY DIFFRACTION2chain 'A' and (resid 173 through 313 )
3X-RAY DIFFRACTION3chain 'A' and (resid 314 through 376 )

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