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- PDB-9o8n: Crystal structure of 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate... -

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Basic information

Entry
Database: PDB / ID: 9o8n
TitleCrystal structure of 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase (DapD) from Bordetella pertussis
Components2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase
KeywordsTRANSFERASE / SSGCID / STRUCTURAL GENOMICS / SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE / dapD / Bordetella pertussis
Function / homology
Function and homology information


2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase / 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase activity / diaminopimelate biosynthetic process / L-lysine biosynthetic process via diaminopimelate / nucleotidyltransferase activity / cytoplasm
Similarity search - Function
Tetrahydrodipicolinate N-succinyltransferase, transferase hexapeptide repeat family / Tetrahydrodipicolinate-N-succinyltransferase, chain A, domain 1 / Tetrahydrodipicolinate-N-succinyltransferase, N-terminal domain superfamily / Tetrahydrodipicolinate N-succinyltransferase N-terminal / Hexapeptide repeat of succinyl-transferase / Hexapeptide transferase, conserved site / Hexapeptide-repeat containing-transferases signature. / Hexapeptide repeat / Trimeric LpxA-like superfamily
Similarity search - Domain/homology
2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase
Similarity search - Component
Biological speciesBordetella pertussis Tohama I (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.59 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)75N93022C00036 United States
National Institutes of Health/Office of the DirectorS10OD030394 United States
CitationJournal: To be published
Title: Crystal structure of 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase (dapD) from Bordetella pertussis
Authors: Ung, A.R. / Lovell, S. / Cooper, A. / Battaile, K.P.
History
DepositionApr 16, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 23, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,2868
Polymers29,9671
Non-polymers3197
Water4,179232
1
A: 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase
hetero molecules

A: 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase
hetero molecules

A: 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,85724
Polymers89,9013
Non-polymers95621
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-y,x-y-1,z1
crystal symmetry operation3_655-x+y+1,-x,z1
Buried area12750 Å2
ΔGint-268 kcal/mol
Surface area29780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.696, 97.696, 78.288
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63
Components on special symmetry positions
IDModelComponents
11A-424-

HOH

21A-622-

HOH

31A-623-

HOH

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Components

#1: Protein 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase / Tetrahydrodipicolinate N-succinyltransferase / THDP succinyltransferase / THP succinyltransferase / ...Tetrahydrodipicolinate N-succinyltransferase / THDP succinyltransferase / THP succinyltransferase / Tetrahydropicolinate succinylase


Mass: 29966.992 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bordetella pertussis Tohama I (bacteria)
Gene: dapD, BP1764 / Plasmid: BopeA.00002.a.B2 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P0A4U8, 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 232 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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: 3.6 Å3/Da / Density % sol: 65.82 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4
Details: Berkeley A1: 2200 mM Sodium chloride, 100 mM Tris HCl/ Sodium hydroxide pH 8.0, 50 mM Calcium chloride. BopeA.00002.a.B2.PW39337 at 16.9 mg/mL. plate 19707 A1 drop 1, Puck: PSL1213, Cryo: ...Details: Berkeley A1: 2200 mM Sodium chloride, 100 mM Tris HCl/ Sodium hydroxide pH 8.0, 50 mM Calcium chloride. BopeA.00002.a.B2.PW39337 at 16.9 mg/mL. plate 19707 A1 drop 1, Puck: PSL1213, Cryo: 80% crystallant + 20% glycerol.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 19-ID / Wavelength: 0.9786 Å
DetectorType: DECTRIS EIGER2 XE 9M / Detector: PIXEL / Date: Mar 15, 2025
RadiationMonochromator: Double Crystal Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 1.59→48.85 Å / Num. obs: 57075 / % possible obs: 100 % / Redundancy: 20.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.196 / Rpim(I) all: 0.044 / Rrim(I) all: 0.201 / Χ2: 0.99 / Net I/σ(I): 13.3 / Num. measured all: 1173267
Reflection shellResolution: 1.59→1.62 Å / % possible obs: 100 % / Redundancy: 21.4 % / Rmerge(I) obs: 2.87 / Num. measured all: 60173 / Num. unique obs: 2815 / CC1/2: 0.308 / Rpim(I) all: 0.63 / Rrim(I) all: 2.939 / Χ2: 0.99 / Net I/σ(I) obs: 1.6

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Processing

Software
NameVersionClassification
PHENIXdev_5660refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.59→48.85 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.57 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1795 2873 5.04 %
Rwork0.1577 --
obs0.1587 57023 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.59→48.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2023 0 12 232 2267
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082093
X-RAY DIFFRACTIONf_angle_d0.9172853
X-RAY DIFFRACTIONf_dihedral_angle_d17.619756
X-RAY DIFFRACTIONf_chiral_restr0.065331
X-RAY DIFFRACTIONf_plane_restr0.009373
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.59-1.620.34221260.30852547X-RAY DIFFRACTION100
1.62-1.640.31821300.29522569X-RAY DIFFRACTION100
1.64-1.670.27291600.2792544X-RAY DIFFRACTION100
1.67-1.710.29661470.26112567X-RAY DIFFRACTION100
1.71-1.740.28061500.2432581X-RAY DIFFRACTION100
1.74-1.780.25331280.22512582X-RAY DIFFRACTION100
1.78-1.820.21361500.20442551X-RAY DIFFRACTION100
1.82-1.870.19271340.17032568X-RAY DIFFRACTION100
1.87-1.920.16451370.16882587X-RAY DIFFRACTION100
1.92-1.970.19481220.16072553X-RAY DIFFRACTION100
1.97-2.040.17461360.15372591X-RAY DIFFRACTION100
2.04-2.110.15051260.14022564X-RAY DIFFRACTION100
2.11-2.190.15491290.13242622X-RAY DIFFRACTION100
2.19-2.290.15091560.13062532X-RAY DIFFRACTION100
2.29-2.410.14711350.12432577X-RAY DIFFRACTION100
2.41-2.570.19211380.1382598X-RAY DIFFRACTION100
2.57-2.760.1761330.14642570X-RAY DIFFRACTION100
2.76-3.040.15331400.14992597X-RAY DIFFRACTION100
3.04-3.480.17821520.14622577X-RAY DIFFRACTION100
3.48-4.390.13721270.12962613X-RAY DIFFRACTION100
4.39-48.850.19031170.16272660X-RAY DIFFRACTION99
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)
16.38770.89572.56358.0153-1.29516.7796-0.013-0.11240.21110.2499-0.0710.0194-0.2924-0.15510.04940.2393-0.00430.02820.1084-0.05610.134552.00475.994211.8259
29.0447.05938.11755.56466.52817.91940.3039-0.3599-0.01480.4666-0.35230.21320.0729-0.33470.0260.29790.01110.04870.181-0.02390.192744.0208-1.26215.4605
36.82780.99822.453.51311.74693.6002-0.23460.19710.3807-0.3587-0.01040.4101-0.4902-0.13030.23730.28320.0335-0.00730.1263-0.01680.204241.6116-1.73852.3366
48.026-1.3290.13451.3890.45563.3878-0.1218-0.3524-0.30480.28330.03840.06130.147-0.14140.07450.2451-0.0060.00950.1846-0.03960.130151.4122-17.176717.614
53.3578-1.208-0.08574.18510.66654.19320.0727-0.196-0.0190.2739-0.10910.3217-0.0938-0.49850.02390.1949-0.00930.05270.209-0.01180.145435.4264-22.092614.5412
64.75720.1929-0.39443.7156-0.21951.9664-0.0714-0.15890.1670.31040.07040.1384-0.1629-0.17230.01280.18480.01840.02880.1542-0.00760.095738.7141-17.67948.5452
71.7092-0.15640.14653.05640.21182.346-0.0278-0.07490.0772-0.04110.03930.0767-0.1925-0.0541-0.0040.14560.01770.01210.1282-0.00760.111439.7854-15.0456-1.1788
81.69930.7435-0.23571.92050.21674.6408-0.0612-0.00570.0285-0.1094-0.02480.1178-0.1207-0.02830.08330.16080.0122-0.01830.12160.00710.144440.0914-17.2568-15.6975
95.4584-1.2911-0.63062.88531.02552.2918-0.04150.0053-0.2013-0.0195-0.1970.57540.0057-0.42260.17360.1631-0.006-0.02950.1873-0.02510.219837.2806-23.186-20.9648
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 25 )
2X-RAY DIFFRACTION2chain 'A' and (resid 26 through 41 )
3X-RAY DIFFRACTION3chain 'A' and (resid 42 through 69 )
4X-RAY DIFFRACTION4chain 'A' and (resid 70 through 95 )
5X-RAY DIFFRACTION5chain 'A' and (resid 96 through 112 )
6X-RAY DIFFRACTION6chain 'A' and (resid 113 through 129 )
7X-RAY DIFFRACTION7chain 'A' and (resid 130 through 182 )
8X-RAY DIFFRACTION8chain 'A' and (resid 183 through 231 )
9X-RAY DIFFRACTION9chain 'A' and (resid 232 through 271 )

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