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- PDB-1p9l: Structure of M. tuberculosis dihydrodipicolinate reductase in com... -

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Basic information

Entry
Database: PDB / ID: 1p9l
TitleStructure of M. tuberculosis dihydrodipicolinate reductase in complex with NADH and 2,6 PDC
Componentsdihydrodipicolinate reductase
KeywordsOXIDOREDUCTASE / REDUCTASE / LYSINE BIOSYNTHESIS / NADH BINDING SPECIFICITY / TB Structural Genomics Consortium / TBSGC / Structural Genomics / PSI / Protein Structure Initiative
Function / homology
Function and homology information


4-hydroxy-tetrahydrodipicolinate reductase / oxidoreductase activity, acting on CH or CH2 groups, NAD or NADP as acceptor / 4-hydroxy-tetrahydrodipicolinate reductase activity / cell wall / NADH binding / diaminopimelate biosynthetic process / L-lysine biosynthetic process via diaminopimelate / NADPH binding / peptidoglycan-based cell wall / plasma membrane / cytosol
Similarity search - Function
Dihydrodipicolinate reductase, conserved site / Dihydrodipicolinate reductase signature. / Dihydrodipicolinate reductase, C-terminal / Dihydrodipicolinate reductase / Dihydrodipicolinate reductase, C-terminus / Dihydrodipicolinate reductase, N-terminal / Dihydrodipicolinate reductase, N-terminus / Dihydrodipicolinate Reductase; domain 2 / Dihydrodipicolinate Reductase; domain 2 / NAD(P)-binding Rossmann-like Domain ...Dihydrodipicolinate reductase, conserved site / Dihydrodipicolinate reductase signature. / Dihydrodipicolinate reductase, C-terminal / Dihydrodipicolinate reductase / Dihydrodipicolinate reductase, C-terminus / Dihydrodipicolinate reductase, N-terminal / Dihydrodipicolinate reductase, N-terminus / Dihydrodipicolinate Reductase; domain 2 / Dihydrodipicolinate Reductase; domain 2 / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / PYRIDINE-2,6-DICARBOXYLIC ACID / 4-hydroxy-tetrahydrodipicolinate reductase / 4-hydroxy-tetrahydrodipicolinate reductase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsCirilli, M. / Zheng, R. / Scapin, G. / Blanchard, J.S. / TB Structural Genomics Consortium (TBSGC)
CitationJournal: Biochemistry / Year: 2003
Title: The three-dimensional structures of the Mycobacterium tuberculosis dihydrodipicolinate reductase-NADH-2,6-PDC and -NADPH-2,6-PDC complexes. Structural and mutagenic analysis of relaxed nucleotide specificity.
Authors: Cirilli, M. / Zheng, R. / Scapin, G. / Blanchard, J.S.
History
DepositionMay 12, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 26, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Nov 6, 2013Group: Non-polymer description
Revision 1.4Aug 16, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: dihydrodipicolinate reductase
B: dihydrodipicolinate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,4467
Polymers51,5872
Non-polymers1,8595
Water2,108117
1
A: dihydrodipicolinate reductase
B: dihydrodipicolinate reductase
hetero molecules

A: dihydrodipicolinate reductase
B: dihydrodipicolinate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,89214
Polymers103,1744
Non-polymers3,71910
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_755-x+2,-y+1/2,z1
Buried area18820 Å2
ΔGint-54 kcal/mol
Surface area34290 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)119.290, 117.280, 78.540
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number24
Space group name H-MI212121
DetailsThe biological assembly is a tetramer, generated by a crystallographic two-fold axis

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Components

#1: Protein dihydrodipicolinate reductase


Mass: 25793.383 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: dapB / Plasmid: pET23a(+) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P72024, UniProt: P9WP23*PLUS, EC: 1.3.1.26
#2: Chemical ChemComp-NAI / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / NADH


Mass: 665.441 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H29N7O14P2
#3: Chemical ChemComp-PDC / PYRIDINE-2,6-DICARBOXYLIC ACID / DIPICOLINIC ACID


Mass: 167.119 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H5NO4
#4: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 117 / 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: 2.66 Å3/Da / Density % sol: 53.78 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: ammonium Sulfate, PEG 400, Hepes, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
120 mg/mlprotein1drop
22 mMNADH1drop
330 mM2,6-PDC1drop
42.2 Mammonium sulfate1reservoir
50.1 MHEPES1reservoirpH7.5
63 %PEG4001reservoir

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: SIEMENS / Detector: AREA DETECTOR / Date: Sep 12, 1996
RadiationMonochromator: Ni filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→25 Å / Num. all: 24785 / Num. obs: 24502 / % possible obs: 98.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.2 % / Biso Wilson estimate: 28.7 Å2 / Rsym value: 0.078 / Net I/σ(I): 13.6
Reflection shellResolution: 2.3→2.4 Å / Redundancy: 3.2 % / Mean I/σ(I) obs: 3.3 / Num. unique all: 2353 / Rsym value: 0.206 / % possible all: 95.1
Reflection
*PLUS
Lowest resolution: 25 Å / Num. measured all: 77959 / Rmerge(I) obs: 0.078
Reflection shell
*PLUS
% possible obs: 95.1 % / Redundancy: 2.1 % / Num. unique obs: 2353 / Num. measured obs: 4910 / Rmerge(I) obs: 0.206

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Processing

Software
NameVersionClassification
Sadiedata collection
SAINTdata reduction
AMoREphasing
X-PLOR3.843refinement
SADIEdata reduction
SAINTdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ARZ

1arz


Resolution: 2.3→25 Å / Data cutoff high absF: 0.001 / Data cutoff low absF: 10000000 / Isotropic thermal model: restrained / Cross valid method: THROUGHOUT / σ(F): 1 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.25 2379 9.6 %random
Rwork0.193 ---
obs0.197 24147 97.4 %-
all-24785 --
Displacement parametersBiso mean: 26.8 Å2
Refinement stepCycle: LAST / Resolution: 2.3→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3624 0 125 117 3866
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.011
X-RAY DIFFRACTIONx_angle_deg1.63
X-RAY DIFFRACTIONx_dihedral_angle_d26.9
X-RAY DIFFRACTIONx_improper_angle_d0.749
X-RAY DIFFRACTIONx_mcbond_it2.91.5
X-RAY DIFFRACTIONx_mcangle_it4.42.5
X-RAY DIFFRACTIONx_scbond_it3.72
X-RAY DIFFRACTIONx_scangle_it5.62.5
LS refinement shellResolution: 2.3→2.4 Å
RfactorNum. reflection% reflection
Rfree0.309 273 8.9 %
Rwork0.262 2528 -
obs-2801 91.5 %
Refinement
*PLUS
Rfactor Rfree: 0.25
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg26.9
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.749

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