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- PDB-1dap: C. GLUTAMICUM DAP DEHYDROGENASE IN COMPLEX WITH NADP+ -

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Basic information

Entry
Database: PDB / ID: 1dap
TitleC. GLUTAMICUM DAP DEHYDROGENASE IN COMPLEX WITH NADP+
ComponentsDIAMINOPIMELIC ACID DEHYDROGENASE
KeywordsOXIDOREDUCTASE / NADP / DEHYDROGENASE / D-AMINO ACID DEHYDROGENASE / LYSINE BIOSYNTHESIS / ASYMMETRIC DIMER
Function / homology
Function and homology information


diaminopimelate dehydrogenase / diaminopimelate dehydrogenase activity / diaminopimelate biosynthetic process / lysine biosynthetic process via diaminopimelate
Similarity search - Function
Diaminopimelate dehydrogenase, Ddh / Meso-diaminopimelate D-dehydrogenase, C-terminal / Diaminopimelic acid dehydrogenase C-terminal domain / 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
ACETATE ION / Chem-NDP / Meso-diaminopimelate D-dehydrogenase
Similarity search - Component
Biological speciesCorynebacterium glutamicum (bacteria)
MethodX-RAY DIFFRACTION / MIR / Resolution: 2.2 Å
AuthorsScapin, G. / Reddy, S.G. / Blanchard, J.S.
Citation
Journal: Biochemistry / Year: 1996
Title: Three-dimensional structure of meso-diaminopimelic acid dehydrogenase from Corynebacterium glutamicum.
Authors: Scapin, G. / Reddy, S.G. / Blanchard, J.S.
#1: Journal: Proteins / Year: 1996
Title: Expression, Purification, and Crystallization of Meso-Diaminopimelate Dehydrogenase from Corynebacterium Glutamicum
Authors: Reddy, S.G. / Scapin, G. / Blanchard, J.S.
History
DepositionJul 8, 1996Processing site: BNL
Revision 1.0Jul 7, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 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: DIAMINOPIMELIC ACID DEHYDROGENASE
B: DIAMINOPIMELIC ACID DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,0946
Polymers70,4852
Non-polymers1,6094
Water3,297183
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7950 Å2
ΔGint-47 kcal/mol
Surface area25210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.900, 65.800, 84.500
Angle α, β, γ (deg.)90.00, 106.60, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.494648, 0.102783, -0.862994), (0.105069, -0.992771, -0.058017), (-0.862719, -0.061976, -0.501872)19.8901, 83.1039, 44.27
2given(0.494648, 0.102783, -0.862994), (0.105069, -0.992771, -0.058017), (-0.862719, -0.061976, -0.501872)19.8901, 83.1039, 44.27

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Components

#1: Protein DIAMINOPIMELIC ACID DEHYDROGENASE / DAPDH


Mass: 35242.328 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Corynebacterium glutamicum (bacteria) / Strain: KY 10755 / Cell line: BL21 / Gene: DAPDH / Plasmid: PET23A / Species (production host): Escherichia coli / Gene (production host): DAPDH / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P04964, diaminopimelate dehydrogenase
#2: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 183 / 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: 2.8 Å3/Da / Density % sol: 65 %
Crystal growpH: 6.5
Details: 13-17% PEG 8000 IN 100 MM NA-CACODYLATE, PH 6.5, 150-300 MM MG-ACETATE CRYSTAL
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Details: Reddy, S.G., (1996) Proteins: Struct.,Funct., Genet., 25, 514.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
120 mg/mlDapDH1drop
220 mMHEPES1drop
31.5-2.0 MNADP+1drop
413-17 %PEG80001drop
5100 mMsodium cacodylate1drop
6150-300 mM1dropMg(OAc)2
713-17 %PEG80001reservoir
8100 mMsodium cacodylate1reservoir
9150-300 mM1reservoirMg(OAc)2

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Data collection

DiffractionMean temperature: 290 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: SIEMENS / Detector: AREA DETECTOR / Date: Sep 20, 1995
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→25 Å / Num. obs: 36359 / % possible obs: 89.2 % / Redundancy: 3.7 % / Rsym value: 0.078 / Net I/σ(I): 7.7
Reflection shellResolution: 2.2→2.3 Å / Redundancy: 2.6 % / Mean I/σ(I) obs: 2 / Rsym value: 0.221 / % possible all: 64.8
Reflection
*PLUS
Num. measured all: 135992 / Rmerge(I) obs: 0.078
Reflection shell
*PLUS
% possible obs: 64.8 % / Num. unique obs: 4374 / Num. measured obs: 11329 / Rmerge(I) obs: 0.221

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Processing

Software
NameClassification
PHASESphasing
TNTrefinement
XENGENdata reduction
XENGENdata scaling
RefinementMethod to determine structure: MIR / Resolution: 2.2→20 Å / σ(F): 2
RfactorNum. reflection% reflection
Rwork0.17 --
obs-36150 86 %
Refinement stepCycle: LAST / Resolution: 2.2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4927 0 104 183 5214
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.017
X-RAY DIFFRACTIONt_angle_deg1.765
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes
X-RAY DIFFRACTIONt_it
X-RAY DIFFRACTIONt_nbd
Software
*PLUS
Name: TNT / Classification: refinement
Refinement
*PLUS
Rfactor Rwork: 0.17
Solvent computation
*PLUS
Displacement parameters
*PLUS

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