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- PDB-5kt0: Dihydrodipicolinate reductase from the industrial and evolutionar... -

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Basic information

Entry
Database: PDB / ID: 5kt0
TitleDihydrodipicolinate reductase from the industrial and evolutionarily important cyanobacteria Anabaena variabilis.
Components4-hydroxy-tetrahydrodipicolinate reductase
KeywordsOXIDOREDUCTASE / DHDPR / Diaminopimelate biosynthesis pathway / enzyme / cyanobacteria
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 / cytoplasm
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 speciesAnabaena variabilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.83 Å
AuthorsChristensen, J.B. / Soares da Costa, T.P. / Faou, P. / Pearce, F.G. / Panjikar, S. / Perugini, M.A.
CitationJournal: To Be Published
Title: Dihydrodipicolinate Reductase from the industrial and evolutionarily important cyanobacteria Anabaena variabilis.
Authors: Christensen, J.B. / Soares da Costa, T.P. / Faou, P. / Pearce, F.G. / Panjikar, S. / Perugini, M.A.
History
DepositionJul 10, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 7, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 6, 2017Group: Data collection / Derived calculations
Category: diffrn_detector / diffrn_source / pdbx_struct_oper_list
Item: _diffrn_detector.detector / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Mar 6, 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

Downloads & links

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Assembly

Deposited unit
A: 4-hydroxy-tetrahydrodipicolinate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,1342
Polymers33,1101
Non-polymers241
Water181
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area100 Å2
ΔGint-6 kcal/mol
Surface area13790 Å2
2
A: 4-hydroxy-tetrahydrodipicolinate reductase
hetero molecules

A: 4-hydroxy-tetrahydrodipicolinate reductase
hetero molecules

A: 4-hydroxy-tetrahydrodipicolinate reductase
hetero molecules

A: 4-hydroxy-tetrahydrodipicolinate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)132,5358
Polymers132,4384
Non-polymers974
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation3_656-x+1,y,-z+11
crystal symmetry operation4_566x,-y+1,-z+11
Buried area11990 Å2
ΔGint-107 kcal/mol
Surface area43580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.728, 89.361, 95.917
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-501-

HOH

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Components

#1: Protein 4-hydroxy-tetrahydrodipicolinate reductase / HTPA reductase


Mass: 33109.555 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Anabaena variabilis (strain ATCC 29413 / PCC 7937) (bacteria)
Strain: ATCC 29413 / PCC 7937 / Gene: dapB, Ava_0474 / Plasmid: pLys / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q3MFY8, 4-hydroxy-tetrahydrodipicolinate reductase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / 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: 2.35 Å3/Da / Density % sol: 47.74 %
Crystal growTemperature: 281 K / Method: vapor diffusion, hanging drop
Details: 21% PEG3350, 0.2 M lithium sulphate, 0.1 M bis-tris chloride pH 5.5.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 5, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.82→55.5 Å / Num. obs: 7762 / % possible obs: 99.7 % / Redundancy: 14.18 % / Net I/σ(I): 25.76

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.83→2.899 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.905 / SU B: 15.37 / SU ML: 0.301 / Cross valid method: THROUGHOUT / ESU R Free: 0.373 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24346 452 5.8 %RANDOM
Rwork0.18263 ---
obs0.18629 7280 99.36 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 42.395 Å2
Baniso -1Baniso -2Baniso -3
1-0.32 Å2-0 Å20 Å2
2--0.01 Å20 Å2
3----0.34 Å2
Refinement stepCycle: 1 / Resolution: 2.83→2.899 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2040 0 1 1 2042
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0192078
X-RAY DIFFRACTIONr_bond_other_d0.0010.022047
X-RAY DIFFRACTIONr_angle_refined_deg1.5031.9812827
X-RAY DIFFRACTIONr_angle_other_deg0.81334716
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1955273
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.442582
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.68815340
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.3561510
X-RAY DIFFRACTIONr_chiral_restr0.0720.2332
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212369
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02429
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_it2.6744.1011095
X-RAY DIFFRACTIONr_mcbond_other2.6734.11094
X-RAY DIFFRACTIONr_mcangle_it4.4226.1461367
X-RAY DIFFRACTIONr_mcangle_other4.4216.1461368
X-RAY DIFFRACTIONr_scbond_it2.6774.441983
X-RAY DIFFRACTIONr_scbond_other2.6764.441984
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.5536.5121461
X-RAY DIFFRACTIONr_long_range_B_refined7.0632.6462207
X-RAY DIFFRACTIONr_long_range_B_other7.05932.6522208
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.827→2.899 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.288 32 -
Rwork0.279 520 -
obs--97.01 %

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