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- PDB-3r5c: Pseudomonas aeruginosa DapD (PA3666) in complex with CoA and succinate -

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Basic information

Entry
Database: PDB / ID: 3r5c
TitlePseudomonas aeruginosa DapD (PA3666) in complex with CoA and succinate
ComponentsTetrahydrodipicolinate N-succinyletransferase
KeywordsTRANSFERASE
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 / magnesium ion binding / cytoplasm
Similarity search - Function
2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase, gammaproteobacteria / Tetrahydrodipicolinate N-succinyltransferase N-terminal / Trimeric LpxA-like enzymes / Alpha-Beta Plaits - #2010 / Type 2 tetrahydrodipicolinate N-succinyltransferase family / 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase, middle domain / 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase, middle domain superfamily / Tetrahydrodipicolinate N-succinyltransferase middle / Hexapeptide repeat of succinyl-transferase / Wheat Germ Agglutinin (Isolectin 2); domain 1 ...2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase, gammaproteobacteria / Tetrahydrodipicolinate N-succinyltransferase N-terminal / Trimeric LpxA-like enzymes / Alpha-Beta Plaits - #2010 / Type 2 tetrahydrodipicolinate N-succinyltransferase family / 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase, middle domain / 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase, middle domain superfamily / Tetrahydrodipicolinate N-succinyltransferase middle / Hexapeptide repeat of succinyl-transferase / Wheat Germ Agglutinin (Isolectin 2); domain 1 / Hexapeptide repeat proteins / UDP N-Acetylglucosamine Acyltransferase; domain 1 / Hexapeptide repeat / Trimeric LpxA-like superfamily / 3 Solenoid / Alpha-Beta Plaits / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
COENZYME A / SUCCINIC ACID / 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase / 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsSandalova, T. / Schnell, R. / Schneider, G.
CitationJournal: Plos One / Year: 2012
Title: Tetrahydrodipicolinate N-succinyltransferase and dihydrodipicolinate synthase from Pseudomonas aeruginosa: structure analysis and gene deletion.
Authors: Schnell, R. / Oehlmann, W. / Sandalova, T. / Braun, Y. / Huck, C. / Maringer, M. / Singh, M. / Schneider, G.
History
DepositionMar 18, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 25, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 1, 2012Group: Structure summary
Revision 1.2Mar 30, 2016Group: Database references
Revision 1.3Sep 13, 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Tetrahydrodipicolinate N-succinyletransferase
B: Tetrahydrodipicolinate N-succinyletransferase
C: Tetrahydrodipicolinate N-succinyletransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,5229
Polymers108,8653
Non-polymers2,6576
Water2,576143
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9910 Å2
ΔGint-23 kcal/mol
Surface area36940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)123.282, 123.282, 198.763
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1112A1 - 352
2112B - A1 - 352
3112C1 - 352

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Components

#1: Protein Tetrahydrodipicolinate N-succinyletransferase / Tetrahydrodipicolinate succinylase


Mass: 36288.379 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: PAO1 / Gene: dapD, PA3666 / Plasmid: pET28a (Novagen) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q9Z9H2, UniProt: G3XD76*PLUS, 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase
#2: Chemical ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#3: Chemical ChemComp-SIN / SUCCINIC ACID


Mass: 118.088 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H6O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 143 / 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: 3.47 Å3/Da / Density % sol: 64.54 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: 19-20% of PEG3350, 0.3-0.4M succinate, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.9334 Å
DetectorType: ADSC QUANTUM 4r / Detector: CCD / Date: Apr 5, 2009
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9334 Å / Relative weight: 1
ReflectionResolution: 2.4→66 Å / Num. all: 60616 / Num. obs: 60616 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.6 % / Biso Wilson estimate: 42.1 Å2 / Rmerge(I) obs: 0.113 / Rsym value: 0.113 / Net I/σ(I): 17.1
Reflection shellResolution: 2.4→2.53 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.654 / Mean I/σ(I) obs: 2.6 / Num. unique all: 8713 / Rsym value: 0.654 / % possible all: 100

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Processing

Software
NameVersionClassification
MxCuBEdata collection
PHASESphasing
REFMAC5.5.0109refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: polyAla model of 2RIJ.pdb

2rij


Resolution: 2.4→53.13 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.889 / SU B: 6.981 / SU ML: 0.166 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(I): 0 / ESU R Free: 0.24 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26748 3101 5.1 %RANDOM
Rwork0.22454 ---
all0.22627 57431 --
obs0.22671 57431 99.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.91 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2--0.01 Å20 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 2.4→53.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7459 0 168 143 7770
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0227749
X-RAY DIFFRACTIONr_bond_other_d0.0020.025041
X-RAY DIFFRACTIONr_angle_refined_deg1.4251.99910534
X-RAY DIFFRACTIONr_angle_other_deg0.8873.00212299
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.46851004
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.74524.897292
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.83151248
X-RAY DIFFRACTIONr_dihedral_angle_4_deg27.4621536
X-RAY DIFFRACTIONr_chiral_restr0.0790.21250
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0218611
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021428
X-RAY DIFFRACTIONr_mcbond_it0.5791.54981
X-RAY DIFFRACTIONr_mcbond_other0.1421.52080
X-RAY DIFFRACTIONr_mcangle_it1.11427921
X-RAY DIFFRACTIONr_scbond_it1.64432768
X-RAY DIFFRACTIONr_scangle_it2.8244.52613
Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Auth asym-IDNumberTypeRms dev position (Å)Weight position
A1956tight positional0.20.05
B1956tight positional0.140.05
C1956tight positional0.170.05
A2233medium positional0.360.5
B2233medium positional0.320.5
C2233medium positional0.310.5
A1956tight thermal0.570.5
B1956tight thermal0.740.5
C1956tight thermal0.980.5
A2233medium thermal0.582
B2233medium thermal0.662
C2233medium thermal0.842
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.354 217 -
Rwork0.297 4196 -
obs-57431 100 %

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