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- PDB-3dap: C. GLUTAMICUM DAP DEHYDROGENASE IN COMPLEX WITH NADP+ AND THE INH... -

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Basic information

Entry
Database: PDB / ID: 3dap
TitleC. GLUTAMICUM DAP DEHYDROGENASE IN COMPLEX WITH NADP+ AND THE INHIBITOR 5S-ISOXAZOLINE
ComponentsDIAMINOPIMELIC ACID DEHYDROGENASE
KeywordsOXIDOREDUCTASE / NADP / DEHYDROGENASE / D-AMINO ACID DEHYDROGENASE / LYSINE BIOSYNTHESIS / ASYMMETRIC DIMER / INHIBITOR
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
Chem-DA3 / Chem-NDP / Meso-diaminopimelate D-dehydrogenase
Similarity search - Component
Biological speciesCorynebacterium glutamicum (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2.2 Å
AuthorsScapin, G. / Cirilli, M. / Reddy, S.G. / Gao, Y. / Vederas, J.C. / Blanchard, J.S.
Citation
Journal: Biochemistry / Year: 1998
Title: Substrate and inhibitor binding sites in Corynebacterium glutamicum diaminopimelate dehydrogenase.
Authors: Scapin, G. / Cirilli, M. / Reddy, S.G. / Gao, Y. / Vederas, J.C. / Blanchard, J.S.
#1: 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.
#2: 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
DepositionDec 29, 1997Processing site: BNL
Revision 1.0Apr 8, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 21, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _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)72,1785
Polymers70,4852
Non-polymers1,6933
Water2,396133
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8000 Å2
ΔGint-42 kcal/mol
Surface area25150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.600, 65.600, 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(0.492347, 0.099919, -0.864645), (0.103664, -0.99305, -0.05573), (-0.864204, -0.062194, -0.499283)19.8113, 82.9747, 43.9029
2given(0.496887, 0.098737, -0.86218), (0.101916, -0.993271, -0.055014), (-0.86181, -0.060534, -0.503606)19.6869, 83.0343, 43.9464

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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) / 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-DA3 / (2S,5',S)-2-AMINO-3-(3-CARBOXY-2-ISOXAZOLIN-5-YL)PROPANOIC ACID


Mass: 202.165 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H10N2O5
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 133 / 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
*PLUS
Density % sol: 60 %
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
112-14 %PEG80001reservoir
2150-300 mMmagnesium acetate1reservoir
3100 mMsodium cacodylate1reservoir
46-7 %PEG80001drop
575-150 mMmagnesium acetate1drop
650 mMsodium cacodylate1drop
710 mg/mlprotein1drop
81 mMNADP+1drop
915 mMDAP1drop

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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: Jun 1, 1997
RadiationMonochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→19 Å / Num. obs: 46303 / % possible obs: 88.9 % / Redundancy: 2 % / Biso Wilson estimate: 19.9 Å2 / Rsym value: 0.074 / Net I/σ(I): 10
Reflection shellResolution: 2→2.1 Å / Redundancy: 1.5 % / Mean I/σ(I) obs: 2.5 / Rsym value: 0.209 / % possible all: 77.7
Reflection
*PLUS
Num. measured all: 70458 / Rmerge(I) obs: 0.074
Reflection shell
*PLUS
% possible obs: 77.7 % / Num. unique obs: 4342 / Num. measured obs: 5440 / Rmerge(I) obs: 0.209

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Processing

Software
NameVersionClassification
X-PLOR3.851model building
X-PLOR3.851refinement
XENGENdata reduction
XENGENdata scaling
X-PLOR3.851phasing
RefinementResolution: 2.2→19 Å / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.001 / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.233 3475 10 %RANDOM
Rwork0.175 ---
obs0.175 34783 86.1 %-
Displacement parametersBiso mean: 24.5 Å2
Refinement stepCycle: LAST / Resolution: 2.2→19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4928 0 110 133 5171
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.009
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.5
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d25.2
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.4
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 2.2→2.3 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.303 376 10.9 %
Rwork0.268 3204 -
obs--71.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMTOPHCSDX.PRO
X-RAY DIFFRACTION2NADP.PARNADP.TOP
X-RAY DIFFRACTION3INH.PARIHN.TOP
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Rfactor all: 0.179
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg25.2
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.4

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