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- PDB-6amy: Crystal structure of a 2,3,4,5-tetrahydropyridine-2,6-dicarboxyla... -

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Basic information

Entry
Database: PDB / ID: 6amy
TitleCrystal structure of a 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase from Acinetobacter baumannii
Components2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase
KeywordsTRANSFERASE / NIAID / structural genomics / dapD / hospital-derived bacterial infection / Seattle Structural Genomics Center for Infectious Disease / SSGCID
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 / lysine biosynthetic process via diaminopimelate / cytoplasm
Similarity search - Function
Tetrahydrodipicolinate-N-succinyltransferase; Chain A, domain 1 / Tetrahydrodipicolinate-N-succinyltransferase, N-terminal domain / 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 proteins ...Tetrahydrodipicolinate-N-succinyltransferase; Chain A, domain 1 / Tetrahydrodipicolinate-N-succinyltransferase, N-terminal domain / 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 proteins / UDP N-Acetylglucosamine Acyltransferase; domain 1 / Hexapeptide repeat / Bacterial transferase hexapeptide (six repeats) / Trimeric LpxA-like superfamily / 3 Solenoid / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase
Similarity search - Component
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.85 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease / Edwards, T.E. / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: To Be Published
Title: Crystal structure of a 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase from Acinetobacter baumannii
Authors: Edwards, T.E. / Horanyi, P.S. / Lorimer, D.D. / Seattle Structural Genomics Center for Infectious Disease
History
DepositionAug 11, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 6, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 4, 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

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Assembly

Deposited unit
A: 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase
B: 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase
C: 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase


Theoretical massNumber of molelcules
Total (without water)91,8383
Polymers91,8383
Non-polymers00
Water34219
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9830 Å2
ΔGint-68 kcal/mol
Surface area28360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.360, 83.210, 148.040
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 30612.654 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii (bacteria) / Gene: dapD / Production host: Escherichia coli (E. coli)
References: UniProt: Q5DL43, 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 19 / 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: 2.16 Å3/Da / Density % sol: 43.01 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: AcbaC.00002.a.B1.PS02398 at 23.06 mg/mL against MCSG1 condition C12 0.1 M BisTris pH 6.5, 25% PEG 3350, crystal tracking ID 263652c12, unique puck ID tvb4-5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 21, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.85→41.946 Å / Num. obs: 19263 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 8.11 % / Biso Wilson estimate: 64.1 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.06 / Rrim(I) all: 0.065 / Χ2: 0.98 / Net I/σ(I): 24.34 / Num. measured all: 156216 / Scaling rejects: 0
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.85-2.928.3180.5263.9714230.9040.561100
2.92-38.3050.3715.513440.9610.396100
3-3.098.2730.2677.4113360.9820.285100
3.09-3.198.3270.248.3612860.9860.256100
3.19-3.298.2580.18610.7512380.9890.198100
3.29-3.418.2620.15312.9312120.9920.163100
3.41-3.548.2530.11216.7511660.9960.12100
3.54-3.688.2660.08322.1211270.9970.088100
3.68-3.848.1550.06726.7510870.9990.071100
3.84-4.038.1820.05731.1310600.9980.061100
4.03-4.258.1570.05433.389900.9990.057100
4.25-4.518.0910.04439.369350.9990.047100
4.51-4.828.0180.0443.388840.9990.042100
4.82-5.27.9740.03942.968460.9990.042100
5.2-5.77.9060.04241.117640.9990.04599.9
5.7-6.377.8420.0441.17080.9990.043100
6.37-7.367.7940.03545.776250.9990.038100
7.36-9.017.5740.02852.655450.9990.03100
9.01-12.757.170.02755.164360.9990.029100
12.75-41.9466.1830.02752.862510.9990.02993.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
XSCALEdata scaling
MOLREPphasing
PDB_EXTRACT3.22data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3gos

3gos


Resolution: 2.85→41.946 Å / SU ML: 0.42 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 25.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.255 1113 5.97 %
Rwork0.1767 --
obs0.1813 18628 96.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.85→41.946 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5642 0 0 19 5661
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085748
X-RAY DIFFRACTIONf_angle_d1.0077844
X-RAY DIFFRACTIONf_dihedral_angle_d11.8443366
X-RAY DIFFRACTIONf_chiral_restr0.063928
X-RAY DIFFRACTIONf_plane_restr0.0061014
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8501-2.97980.39431260.252016X-RAY DIFFRACTION91
2.9798-3.13680.27841370.21362084X-RAY DIFFRACTION94
3.1368-3.33330.3041450.19372127X-RAY DIFFRACTION96
3.3333-3.59050.28971420.19222165X-RAY DIFFRACTION97
3.5905-3.95160.23371380.16632223X-RAY DIFFRACTION99
3.9516-4.52280.24241360.14692238X-RAY DIFFRACTION99
4.5228-5.6960.21721350.15142288X-RAY DIFFRACTION100
5.696-41.95030.24571540.192374X-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)
13.88790.4808-0.61332.58740.97891.856-0.03310.5686-1.0811-0.49790.05871.20930.4905-0.86750.20570.8789-0.6025-0.54510.78510.26611.2473-26.5847-25.461218.9829
21.8452-0.29260.97663.45580.74912.138-0.015-0.5917-0.0816-0.12650.28470.85570.3909-0.4189-0.180.3803-0.16720.00650.69960.21180.5569-16.9882-12.084230.5244
32.0067-0.56340.68041.912-2.00422.11170.27030.4913-0.3136-1.8250.005-0.49210.38670.2832-0.00421.2198-0.1280.18840.5862-0.03560.4005-4.4257-12.61419.4761
43.5478-1.57153.78773.0975-3.52087.0472-0.394-0.2684-0.1734-0.22130.2261-0.487-0.7690.54970.06391.05090.06380.60110.85350.11980.72526.8817-10.38269.1438
51.9781-0.13340.38315.2295-1.16412.4875-0.3356-0.31750.06750.45920.3365-0.7894-0.0878-0.13310.01690.32930.0455-0.02960.4878-0.09620.4242-0.3633.095937.793
60.9266-0.0767-1.28410.5657-1.32795.7368-0.10660.54380.2185-0.92020.2924-1.1702-0.05320.6083-0.01690.7185-0.20980.39720.7044-0.03490.92066.86848.132313.827
70.59530.30090.02780.4467-0.56231.1175-0.36080.4168-0.3331-0.66150.4739-0.5249-0.0467-0.2925-0.38381.086-0.13460.67070.6441-0.01910.6038.19757.25535.0918
86.8342.5471-2.54283.76980.82776.77820.0121-0.38910.07090.40191.15430.821-0.7985-0.7239-0.6461.05010.3353-0.3370.73650.10611.0162-27.805432.089427.3574
91.0024-0.7480.64284.0706-1.42673.2518-0.2274-0.32720.1574-0.20670.4721.0554-0.2018-0.9968-0.13950.36360.0952-0.11980.82930.09230.8399-26.89916.712725.7563
101.52290.69720.80410.62040.6630.8033-0.0726-0.00010.284-0.1004-0.01441.49280.0141-0.58060.19350.327-0.2007-0.05220.94380.19341.0291-31.2187-0.4625.6916
111.0854-0.26420.0483.4704-0.46171.0042-0.1408-0.1426-0.0453-1.120.16611.02770.2579-0.87990.04730.566-0.1051-0.23350.73080.11780.6-24.57125.091217.2085
124.1124-2.1919-2.39533.20861.66664.9520.18840.21740.0398-1.7560.16810.20750.17710.0961-0.28951.033-0.1785-0.06360.54960.05110.5027-15.88159.79516.7589
133.936-1.1608-1.35251.4616-0.132.82480.34761.03630.2601-1.351-0.1223-0.1148-0.13250.2098-0.09691.7402-0.24540.16660.85070.04010.4302-7.64286.3253-3.4299
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 69 )
2X-RAY DIFFRACTION2chain 'A' and (resid 70 through 143 )
3X-RAY DIFFRACTION3chain 'A' and (resid 144 through 245 )
4X-RAY DIFFRACTION4chain 'A' and (resid 246 through 271 )
5X-RAY DIFFRACTION5chain 'B' and (resid 2 through 181 )
6X-RAY DIFFRACTION6chain 'B' and (resid 182 through 239 )
7X-RAY DIFFRACTION7chain 'B' and (resid 240 through 259 )
8X-RAY DIFFRACTION8chain 'C' and (resid 2 through 24 )
9X-RAY DIFFRACTION9chain 'C' and (resid 25 through 94 )
10X-RAY DIFFRACTION10chain 'C' and (resid 95 through 111 )
11X-RAY DIFFRACTION11chain 'C' and (resid 112 through 161 )
12X-RAY DIFFRACTION12chain 'C' and (resid 162 through 216 )
13X-RAY DIFFRACTION13chain 'C' and (resid 217 through 270 )

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