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- PDB-1c3v: DIHYDRODIPICOLINATE REDUCTASE FROM MYCOBACTERIUM TUBERCULOSIS COM... -

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Basic information

Entry
Database: PDB / ID: 1c3v
TitleDIHYDRODIPICOLINATE REDUCTASE FROM MYCOBACTERIUM TUBERCULOSIS COMPLEXED WITH NADPH AND PDC
ComponentsDIHYDRODIPICOLINATE REDUCTASE4-hydroxy-tetrahydrodipicolinate reductase
KeywordsOXIDOREDUCTASE / TWO-DOMAIN STRUCTURE / 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 / NADH binding / cell wall / diaminopimelate biosynthetic process / 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
Chem-NDP / PYRIDINE-2,6-DICARBOXYLIC ACID / 4-hydroxy-tetrahydrodipicolinate reductase / 4-hydroxy-tetrahydrodipicolinate reductase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2.39 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
DepositionJul 28, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 26, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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)53,6067
Polymers51,5872
Non-polymers2,0195
Water45025
1
A: DIHYDRODIPICOLINATE REDUCTASE
B: DIHYDRODIPICOLINATE REDUCTASE
hetero molecules

A: DIHYDRODIPICOLINATE REDUCTASE
B: DIHYDRODIPICOLINATE REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,21214
Polymers103,1744
Non-polymers4,03910
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_755-x+2,-y+1/2,z1
Buried area19130 Å2
ΔGint-47 kcal/mol
Surface area34580 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)118.831, 118.257, 79.377
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number24
Space group name H-MI212121
DetailsThe biological assembly is a dimer constructed from chain A by a non-crystallographic binary axis.

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Components

#1: Protein DIHYDRODIPICOLINATE REDUCTASE / 4-hydroxy-tetrahydrodipicolinate reductase


Mass: 25793.383 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Plasmid: PET23A / Production host: Escherichia coli (E. coli)
References: UniProt: P72024, UniProt: P9WP23*PLUS, EC: 1.3.1.26
#2: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Nicotinamide adenine dinucleotide phosphate


Mass: 745.421 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#3: Chemical ChemComp-PDC / PYRIDINE-2,6-DICARBOXYLIC ACID / DIPICOLINIC ACID / Dipicolinic acid


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


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


Mass: 18.015 Da / Num. of mol.: 25 / 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: 2.7 Å3/Da / Density % sol: 54.47 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: ammonium sulfate, PEG400, HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 288.0K

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Data collection

DiffractionMean temperature: 288 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: XENTRONICS / Detector: AREA DETECTOR / Date: May 25, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→30.4 Å / Num. all: 19713 / Num. obs: 16553 / % possible obs: 87.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 4 / Redundancy: 3.29 % / Biso Wilson estimate: 41.9 Å2 / Rmerge(I) obs: 0.105 / Net I/σ(I): 7.11
Reflection shellResolution: 2.54→2.63 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.395 / Num. unique all: 3306 / % possible all: 88.68

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Processing

Software
NameVersionClassification
X-GENdata scaling
X-GENdata reduction
X-PLORmodel building
X-PLOR3.851refinement
X-PLORphasing
RefinementResolution: 2.39→30.4 Å / σ(F): 2 / σ(I): 4 / Stereochemistry target values: Engh & Huber
Details: Used torsion-angle molecular dynamics slowcool followed by B factor and positional refinements as implemented in X-PLOR.
RfactorNum. reflectionSelection details
Rfree0.243 736 random
Rwork0.193 --
all0.212 19713 -
obs0.197 16553 -
Refinement stepCycle: LAST / Resolution: 2.39→30.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3620 0 133 25 3778
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.006
X-RAY DIFFRACTIONx_angle_deg1.452
X-RAY DIFFRACTIONx_dihedrals_deg26.252
X-RAY DIFFRACTIONx_impropers_deg1.098

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