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- PDB-5z2f: NADPH/PDA bound Dihydrodipicolinate reductase from Paenisporosarc... -

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Basic information

Entry
Database: PDB / ID: 5z2f
TitleNADPH/PDA bound Dihydrodipicolinate reductase from Paenisporosarcina sp. TG-14
ComponentsDihydrodipicolinate reductase
KeywordsOXIDOREDUCTASE / dihydrodipicolinate reductase / Paenisporosarcina sp. TG-14
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 / : / : / NAD binding / NADP binding / 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 / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / PYRIDINE-2,6-DICARBOXYLIC ACID / 4-hydroxy-tetrahydrodipicolinate reductase
Similarity search - Component
Biological speciesPaenisporosarcina sp. TG-14 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsLee, J.H. / Lee, C.W. / Park, S.
CitationJournal: Sci Rep / Year: 2018
Title: Crystal structure of dihydrodipicolinate reductase (PaDHDPR) from Paenisporosarcina sp. TG-14: structural basis for NADPH preference as a cofactor
Authors: Lee, C.W. / Park, S.H. / Lee, S.G. / Park, H.H. / Kim, H.J. / Park, H. / Park, H. / Lee, J.H.
History
DepositionJan 2, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 27, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Dihydrodipicolinate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,1953
Polymers29,2851
Non-polymers9112
Water2,252125
1
A: Dihydrodipicolinate reductase
hetero molecules

A: Dihydrodipicolinate reductase
hetero molecules

A: Dihydrodipicolinate reductase
hetero molecules

A: Dihydrodipicolinate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,78112
Polymers117,1384
Non-polymers3,6428
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation7_555y,x,-z1
crystal symmetry operation8_555-y,-x,-z1
Buried area18940 Å2
ΔGint-61 kcal/mol
Surface area38170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.942, 79.942, 83.835
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212
Components on special symmetry positions
IDModelComponents
11A-429-

HOH

21A-457-

HOH

31A-510-

HOH

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Components

#1: Protein Dihydrodipicolinate reductase


Mass: 29284.623 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Paenisporosarcina sp. TG-14 (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A3B6UER2*PLUS
#2: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Chemical ChemComp-PDC / PYRIDINE-2,6-DICARBOXYLIC ACID / DIPICOLINIC ACID


Mass: 167.119 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H5NO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 125 / 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: 2.29 Å3/Da / Density % sol: 46.22 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2M Ammonium Sulfate, 0.1M Tris:HCl pH 8.5, and 25%(w/v) PEG 3350

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9796 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 11, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 2.1→50.01 Å / Num. obs: 16378 / % possible obs: 99.3 % / Redundancy: 13.3 % / Net I/σ(I): 40.9
Reflection shellResolution: 2.1→2.15 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→50.01 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.925 / SU B: 6.806 / SU ML: 0.168 / Cross valid method: THROUGHOUT / ESU R: 0.233 / ESU R Free: 0.208 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25657 783 4.8 %RANDOM
Rwork0.18701 ---
obs0.19021 15536 99.23 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 41.853 Å2
Baniso -1Baniso -2Baniso -3
1--3.09 Å20 Å20 Å2
2---3.09 Å20 Å2
3---6.17 Å2
Refinement stepCycle: 1 / Resolution: 2.1→50.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2051 0 60 125 2236
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0192157
X-RAY DIFFRACTIONr_bond_other_d0.0020.021970
X-RAY DIFFRACTIONr_angle_refined_deg1.8071.9962934
X-RAY DIFFRACTIONr_angle_other_deg1.01434587
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9215264
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.70825.21394
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.21115360
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.982158
X-RAY DIFFRACTIONr_chiral_restr0.0950.2333
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0212371
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02405
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_it2.7544.0371059
X-RAY DIFFRACTIONr_mcbond_other2.7494.0331058
X-RAY DIFFRACTIONr_mcangle_it3.736.0421322
X-RAY DIFFRACTIONr_mcangle_other3.7336.0471323
X-RAY DIFFRACTIONr_scbond_it3.7134.4181098
X-RAY DIFFRACTIONr_scbond_other3.7164.4211095
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.5766.4961610
X-RAY DIFFRACTIONr_long_range_B_refined6.92349.472411
X-RAY DIFFRACTIONr_long_range_B_other6.83149.1822378
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.099→2.153 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.334 55 -
Rwork0.288 1092 -
obs--98.45 %

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