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- PDB-3tdt: COMPLEX OF TETRAHYDRODIPICOLINATE N-SUCCINYLTRANSFERASE WITH 2-AM... -

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Basic information

Entry
Database: PDB / ID: 3tdt
TitleCOMPLEX OF TETRAHYDRODIPICOLINATE N-SUCCINYLTRANSFERASE WITH 2-AMINO-6-OXOPIMELATE AND COENZYME A
ComponentsTETRAHYDRODIPICOLINATE N-SUCCINYLTRANSFERASE
KeywordsACYLTRANSFERASE / LYSINE BIOSYNTHESIS
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 / nucleotidyltransferase activity / 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 ...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 / Hexapeptide repeat proteins / UDP N-Acetylglucosamine Acyltransferase; domain 1 / Bacterial transferase hexapeptide (six repeats) / Trimeric LpxA-like superfamily / 3 Solenoid / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
2-AMINO-6-OXOPIMELIC ACID / COENZYME A / 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase
Similarity search - Component
Biological speciesMycobacterium bovis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsBeaman, T.W. / Blanchard, J.S. / Roderick, S.L.
Citation
Journal: Biochemistry / Year: 1998
Title: The conformational change and active site structure of tetrahydrodipicolinate N-succinyltransferase.
Authors: Beaman, T.W. / Blanchard, J.S. / Roderick, S.L.
#1: Journal: Biochemistry / Year: 1997
Title: Three-Dimensional Structure of Tetrahydrodipicolinate N-Succinyltransferase
Authors: Beaman, T.W. / Binder, D.A. / Blanchard, J.S. / Roderick, S.L.
#2: Journal: Proteins / Year: 1996
Title: Crystallization and Preliminary Crystallographic Analysis of Tetrahydrodipicolinate-N-Succinyltransferase
Authors: Binder, D.A. / Blanchard, J.S. / Roderick, S.L.
History
DepositionMay 6, 1998Processing site: BNL
Revision 1.0Oct 14, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Aug 9, 2023Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Refinement description
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TETRAHYDRODIPICOLINATE N-SUCCINYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,8763
Polymers29,9191
Non-polymers9572
Water1,63991
1
A: TETRAHYDRODIPICOLINATE N-SUCCINYLTRANSFERASE
hetero molecules

A: TETRAHYDRODIPICOLINATE N-SUCCINYLTRANSFERASE
hetero molecules

A: TETRAHYDRODIPICOLINATE N-SUCCINYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,6279
Polymers89,7573
Non-polymers2,8706
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area18540 Å2
ΔGint-42 kcal/mol
Surface area26790 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)96.000, 96.000, 72.300
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

#1: Protein TETRAHYDRODIPICOLINATE N-SUCCINYLTRANSFERASE / DAPD


Mass: 29918.990 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium bovis (bacteria) / Cell line: BL21 / Gene: DAPD / Plasmid: PET3A / Species (production host): Escherichia coli / Gene (production host): DAPD / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3)
References: UniProt: P56220, 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase
#2: Chemical ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#3: Chemical ChemComp-26P / 2-AMINO-6-OXOPIMELIC ACID


Mass: 189.166 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H11NO5
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 91 / 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: 2.15 Å3/Da / Density % sol: 43 %
Crystal growpH: 8
Details: 16 % (W/V) POLYETHYLENE GLYCOL 4000 100 MM TRIS, PH 8.0 200 MM AMMONIUM SULFATE 5 % (V/V) 2-PROPANOL 5 MM 2,3,4,5-TETRAHYDRODIPICOLINATE 20 MM COENZYME A
Crystal
*PLUS
Crystal grow
*PLUS
pH: 6.4 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110-13 %(w/v)PEG40001drop
294 mMMES1drop
394 mMammonium sulfate1drop
44.7 %(v/v)2-propanol1drop
516 mM(D,L)-2-aminopimelate1reservoir
62.5 mMCoA1reservoir

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Data collection

DiffractionMean temperature: 295 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: SIEMENS / Detector: AREA DETECTOR / Date: Feb 1, 1997
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionHighest resolution: 2 Å / Num. obs: 48370 / % possible obs: 97.1 % / Redundancy: 3 % / Rmerge(I) obs: 0.045 / Rsym value: 0.045 / Net I/σ(I): 31.2
Reflection shellResolution: 2→2.1 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.103 / Mean I/σ(I) obs: 6.9 / Rsym value: 0.103 / % possible all: 87.2
Reflection shell
*PLUS
% possible obs: 87.2 %

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Processing

Software
NameVersionClassification
X-PLORmodel building
TNT5Erefinement
X-PLORrefinement
XDSdata reduction
XSCALEdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2TDT

2tdt


Resolution: 2→99 Å / Isotropic thermal model: TNT BCORREL / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: TNT PROTGEO
RfactorNum. reflection% reflectionSelection details
Rfree0.22 886 5 %SHELLS
Rwork0.152 ---
all0.154 15867 --
obs0.154 15867 97.1 %-
Solvent computationBsol: 185 Å2 / ksol: 0.64 e/Å3
Refinement stepCycle: LAST / Resolution: 2→99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2078 0 61 91 2230
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.01921740.8
X-RAY DIFFRACTIONt_angle_deg1.7129441.3
X-RAY DIFFRACTIONt_dihedral_angle_d23.212810
X-RAY DIFFRACTIONt_incorr_chiral_ct0
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes0.011542
X-RAY DIFFRACTIONt_gen_planes0.0173155
X-RAY DIFFRACTIONt_it4.6742783
X-RAY DIFFRACTIONt_nbd0.025810
Software
*PLUS
Name: TNT / Version: 5E / Classification: refinement
Refinement
*PLUS
Rfactor Rfree: 0.225
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev idealWeight
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_dihedral_angle_deg23.20
X-RAY DIFFRACTIONt_planar_d0.0112
X-RAY DIFFRACTIONt_plane_restr0.0175
LS refinement shell
*PLUS
Rfactor Rfree: 0.27 / Rfactor obs: 0.21

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