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- PDB-5z2d: Dihydrodipicolinate reductase from Paenisporosarcina sp. TG-14 -

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Basic information

Entry
Database: PDB / ID: 5z2d
TitleDihydrodipicolinate 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 / diaminopimelate biosynthetic process / lysine biosynthetic process via diaminopimelate / 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
4-hydroxy-tetrahydrodipicolinate reductase
Similarity search - Component
Biological speciesPaenisporosarcina sp. TG-14 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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 1.0Jan 2, 2019Provider: 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


Theoretical massNumber of molelcules
Total (without water)29,1531
Polymers29,1531
Non-polymers00
Water5,278293
1
A: dihydrodipicolinate reductase

A: dihydrodipicolinate reductase

A: dihydrodipicolinate reductase

A: dihydrodipicolinate reductase


Theoretical massNumber of molelcules
Total (without water)116,6144
Polymers116,6144
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_665-x+1,-y+1,z1
crystal symmetry operation7_555y,x,-z+1/31
crystal symmetry operation10_665-y+1,-x+1,-z+1/31
Buried area12220 Å2
ΔGint-78 kcal/mol
Surface area44940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.229, 106.229, 101.999
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number181
Space group name H-MP6422
Components on special symmetry positions
IDModelComponents
11A-350-

HOH

21A-484-

HOH

31A-539-

HOH

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Components

#1: Protein dihydrodipicolinate reductase


Mass: 29153.424 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 293 / 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: 2.85 Å3/Da / Density % sol: 56.83 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 30%(v/v) PEG 400, 100mM Tris-HCl (pH 8.5), and 200mM MgCl2

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 29, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 31125 / % possible obs: 97.2 % / Redundancy: 11.3 % / Net I/σ(I): 31.8
Reflection shellResolution: 1.8→1.847 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→47.11 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.931 / SU B: 1.819 / SU ML: 0.059 / Cross valid method: THROUGHOUT / ESU R: 0.105 / ESU R Free: 0.108 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20677 1596 5.1 %RANDOM
Rwork0.16652 ---
obs0.16861 29463 97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.072 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å2-0 Å2-0 Å2
2---0 Å2-0 Å2
3---0.01 Å2
Refinement stepCycle: 1 / Resolution: 1.8→47.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2043 0 0 293 2336
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0192085
X-RAY DIFFRACTIONr_bond_other_d0.0020.021936
X-RAY DIFFRACTIONr_angle_refined_deg2.1321.962827
X-RAY DIFFRACTIONr_angle_other_deg1.13734508
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9345263
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.04325.21394
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.21115357
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.302158
X-RAY DIFFRACTIONr_chiral_restr0.1420.2324
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0212317
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02387
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_it2.2391.9441055
X-RAY DIFFRACTIONr_mcbond_other2.2371.9431054
X-RAY DIFFRACTIONr_mcangle_it2.942.911317
X-RAY DIFFRACTIONr_mcangle_other2.942.9111318
X-RAY DIFFRACTIONr_scbond_it4.1342.4511030
X-RAY DIFFRACTIONr_scbond_other4.1322.4511031
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.1483.4961511
X-RAY DIFFRACTIONr_long_range_B_refined7.69526.7542331
X-RAY DIFFRACTIONr_long_range_B_other7.28825.3722228
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.243 111 -
Rwork0.164 2165 -
obs--98.57 %

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