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- PDB-5ees: Crystal structure of DapB in complex with NADP+ from Corynebacter... -

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Basic information

Entry
Database: PDB / ID: 5ees
TitleCrystal structure of DapB in complex with NADP+ from Corynebacterium glutamicum
Components4-hydroxy-tetrahydrodipicolinate reductase
KeywordsOXIDOREDUCTASE
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 / 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
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 4-hydroxy-tetrahydrodipicolinate reductase
Similarity search - Component
Biological speciesCorynebacterium glutamicum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsSagong, H.-Y. / Kim, K.-J.
CitationJournal: J. Microbiol. Biotechnol. / Year: 2016
Title: Structural Insight into Dihydrodipicolinate Reductase from Corybebacterium glutamicum for Lysine Biosynthesis.
Authors: Sagong, H.Y. / Kim, K.J.
History
DepositionOct 23, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 11, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 19, 2017Group: Database references / Derived calculations
Category: citation / citation_author / pdbx_struct_oper_list
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Sep 9, 2020Group: Structure summary / Category: struct / Item: _struct.title
Revision 1.3Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: 4-hydroxy-tetrahydrodipicolinate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,9445
Polymers25,9161
Non-polymers1,0284
Water2,162120
1
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)107,77520
Polymers103,6644
Non-polymers4,11016
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z1
crystal symmetry operation10_665-x+1,-y+1,z1
crystal symmetry operation15_555y,x,-z1
Buried area18980 Å2
ΔGint-203 kcal/mol
Surface area37870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.969, 107.969, 172.049
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number98
Space group name H-MI4122

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Components

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


Mass: 25916.117 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Corynebacterium glutamicum (strain ATCC 13032 / DSM 20300 / JCM 1318 / LMG 3730 / NCIMB 10025) (bacteria)
Strain: ATCC 13032 / DSM 20300 / JCM 1318 / LMG 3730 / NCIMB 10025
Gene: dapB, Cgl1973, cg2163 / Plasmid: pET30a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE)-T1R
References: UniProt: P40110, 4-hydroxy-tetrahydrodipicolinate reductase
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE / Nicotinamide adenine dinucleotide phosphate


Mass: 743.405 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 120 / 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: 4.84 Å3/Da / Density % sol: 74.57 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.75 / Details: Ammonium sulfate, Sodium acetate trihydrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.97934 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Jul 21, 2014
RadiationMonochromator: Double Crystal Monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 2.14→50 Å / Num. obs: 25394 / % possible obs: 95.1 % / Redundancy: 8.6 % / Net I/σ(I): 8.6
Reflection shellResolution: 2.14→2.18 Å / Redundancy: 3 % / % possible all: 85.4

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Processing

Software
NameVersionClassification
HKL-2000data collection
REFMAC5.8.0131refinement
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5EER

5eer


Resolution: 2.15→50 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.957 / SU B: 5.142 / SU ML: 0.118 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.135 / ESU R Free: 0.132 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2112 1364 5.1 %RANDOM
Rwork0.1786 ---
obs0.1803 25394 95.08 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 277.26 Å2 / Biso mean: 52.835 Å2 / Biso min: 3.13 Å2
Baniso -1Baniso -2Baniso -3
1-0.84 Å2-0 Å20 Å2
2--0.84 Å2-0 Å2
3----1.68 Å2
Refinement stepCycle: final / Resolution: 2.15→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1820 0 64 120 2004
Biso mean--63.11 64.86 -
Num. residues----247
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0191912
X-RAY DIFFRACTIONr_bond_other_d0.0020.021808
X-RAY DIFFRACTIONr_angle_refined_deg2.2031.9862606
X-RAY DIFFRACTIONr_angle_other_deg1.09334144
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8415246
X-RAY DIFFRACTIONr_dihedral_angle_2_deg43.39825.48882
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.35915292
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.538159
X-RAY DIFFRACTIONr_chiral_restr0.1080.2307
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022189
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02419
X-RAY DIFFRACTIONr_mcbond_it4.2924.916987
X-RAY DIFFRACTIONr_mcbond_other4.2574.913986
X-RAY DIFFRACTIONr_mcangle_it6.0897.3581232
LS refinement shellResolution: 2.147→2.203 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.392 101 -
Rwork0.404 1687 -
all-1788 -
obs--86.54 %

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