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- PDB-3r5a: Pseudomonas aeruginosa DapD (PA3666) in complex with D-2-aminopimelate -

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Basic information

Entry
Database: PDB / ID: 3r5a
TitlePseudomonas aeruginosa DapD (PA3666) in complex with D-2-aminopimelate
ComponentsTetrahydrodipicolinate N-succinyletransferase
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / TRANSFERASE-TRANSFERASE INHIBITOR complex
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
(2R)-2-aminoheptanedioic 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 / FOURIER SYNTHESIS / Resolution: 1.89 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 1.3Mar 7, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)218,96614
Polymers217,7306
Non-polymers1,2358
Water18,3571019
1
A: Tetrahydrodipicolinate N-succinyletransferase
B: Tetrahydrodipicolinate N-succinyletransferase
C: Tetrahydrodipicolinate N-succinyletransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,4837
Polymers108,8653
Non-polymers6184
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10210 Å2
ΔGint-31 kcal/mol
Surface area33950 Å2
MethodPISA
2
D: Tetrahydrodipicolinate N-succinyletransferase
E: Tetrahydrodipicolinate N-succinyletransferase
F: Tetrahydrodipicolinate N-succinyletransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,4837
Polymers108,8653
Non-polymers6184
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9720 Å2
ΔGint-27 kcal/mol
Surface area34370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.343, 101.931, 135.686
Angle α, β, γ (deg.)90.00, 89.97, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
12D
22E
32F

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1114A1 - 329
2114B1 - 329
3114C1 - 329
1124D1 - 329
2124E1 - 329
3124F1 - 329

NCS ensembles :
ID
1
2

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Components

#1: Protein
Tetrahydrodipicolinate N-succinyletransferase / Tetrahydrodipicolinate succinylase


Mass: 36288.379 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: PAO1 / Gene: dapD, PA3666 / Plasmid: pET28a / 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-P0A / (2R)-2-aminoheptanedioic acid


Type: D-peptide linking / Mass: 175.182 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C7H13NO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1019 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.65 Å3/Da / Density % sol: 53.53 %
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: MAX II / Beamline: I911-2 / Wavelength: 1.04 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Oct 8, 2009
RadiationMonochromator: Bent Si (111) crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.04 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.509
11h,-k,-l20.491
ReflectionResolution: 1.88→22 Å / Num. all: 173938 / Num. obs: 173938 / % possible obs: 91.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.5 % / Rmerge(I) obs: 0.059 / Rsym value: 0.059 / Net I/σ(I): 9.8
Reflection shellResolution: 1.88→1.98 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.333 / Mean I/σ(I) obs: 2.3 / Rsym value: 0.333 / % possible all: 72.8

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Processing

Software
NameVersionClassification
MxCuBEdata collection
PHASERphasing
REFMAC5.5.0109refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.89→21.83 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.928 / SU B: 2.698 / SU ML: 0.076 / Cross valid method: THROUGHOUT / ESU R: 0.031 / ESU R Free: 0.029 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23532 8767 5 %RANDOM
Rwork0.19557 ---
obs0.19755 165139 96.06 %-
all-165139 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.44 Å2
Baniso -1Baniso -2Baniso -3
1--6.02 Å20 Å2-0.88 Å2
2---5.27 Å20 Å2
3---11.29 Å2
Refinement stepCycle: LAST / Resolution: 1.89→21.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14092 0 84 1019 15195
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.02214385
X-RAY DIFFRACTIONr_bond_other_d0.0030.029471
X-RAY DIFFRACTIONr_angle_refined_deg1.1451.98319507
X-RAY DIFFRACTIONr_angle_other_deg0.8743.00123196
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.05651896
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.00824.731539
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.064152336
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.5791570
X-RAY DIFFRACTIONr_chiral_restr0.0670.22320
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02116110
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022704
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.3911.59454
X-RAY DIFFRACTIONr_mcbond_other0.131.53950
X-RAY DIFFRACTIONr_mcangle_it0.676215014
X-RAY DIFFRACTIONr_scbond_it0.98934931
X-RAY DIFFRACTIONr_scangle_it1.5494.54493
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A3908MEDIUM POSITIONAL0.260.5
12B3908MEDIUM POSITIONAL0.290.5
13C3908MEDIUM POSITIONAL0.280.5
11A3908MEDIUM THERMAL0.392
12B3908MEDIUM THERMAL0.632
13C3908MEDIUM THERMAL0.732
21D3807MEDIUM POSITIONAL0.290.5
22E3807MEDIUM POSITIONAL0.320.5
23F3807MEDIUM POSITIONAL0.290.5
21D3807MEDIUM THERMAL0.432
22E3807MEDIUM THERMAL0.682
23F3807MEDIUM THERMAL0.82
LS refinement shellResolution: 1.89→1.939 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.314 573 -
Rwork0.237 9793 -
obs--78.32 %

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