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- PDB-2dap: C. GLUTAMICUM DAP DEHYDROGENASE IN COMPLEX WITH DAP -

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Basic information

Entry
Database: PDB / ID: 2dap
TitleC. GLUTAMICUM DAP DEHYDROGENASE IN COMPLEX WITH DAP
ComponentsDIAMINOPIMELIC ACID DEHYDROGENASE
KeywordsOXIDOREDUCTASE / DEHYDROGENASE / D-AMINO ACID DEHYDROGENASE / LYSINE BIOSYNTHESIS / DIAMINOPIMELATE
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
2,6-DIAMINOPIMELIC ACID / Meso-diaminopimelate D-dehydrogenase
Similarity search - Component
Biological speciesCorynebacterium glutamicum (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / 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 23, 1997Processing site: BNL
Revision 1.0Apr 8, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 2.0Aug 9, 2023Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Other / Refinement description
Category: atom_site / database_2 ...atom_site / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _atom_site.occupancy / _database_2.pdbx_DOI ..._atom_site.occupancy / _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
Revision 3.0Nov 15, 2023Group: Atomic model / Data collection / Database references
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / struct_ref
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id / _struct_ref.pdbx_seq_one_letter_code

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DIAMINOPIMELIC ACID DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,4332
Polymers35,2421
Non-polymers1901
Water2,702150
1
A: DIAMINOPIMELIC ACID DEHYDROGENASE
hetero molecules

A: DIAMINOPIMELIC ACID DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,8654
Polymers70,4852
Non-polymers3802
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_556-x,-x+y,-z+11
Buried area6120 Å2
ΔGint-28 kcal/mol
Surface area25060 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)121.640, 121.640, 52.360
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number150
Space group name H-MP321
Components on special symmetry positions
IDModelComponents
11A-933-

HOH

21A-1049-

HOH

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Components

#1: Protein DIAMINOPIMELIC ACID DEHYDROGENASE / DAPDH


Mass: 35242.328 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Corynebacterium glutamicum (bacteria) / Plasmid: PET23A / References: UniProt: P04964, diaminopimelate dehydrogenase
#2: Chemical ChemComp-API / 2,6-DIAMINOPIMELIC ACID


Type: L-peptide linking / Mass: 190.197 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H14N2O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 150 / 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: Jan 1, 1996
RadiationMonochromator: NI FILTERS / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→10 Å / Num. obs: 21456 / % possible obs: 94.8 % / Redundancy: 4 % / Biso Wilson estimate: 21.2 Å2 / Rsym value: 0.102 / Net I/σ(I): 10.7
Reflection shellResolution: 2.2→2.3 Å / Redundancy: 3.3 % / Mean I/σ(I) obs: 2.1 / Rsym value: 0.293 / % possible all: 82.3
Reflection
*PLUS
Num. measured all: 86282 / Rmerge(I) obs: 0.102
Reflection shell
*PLUS
% possible obs: 82.3 % / Num. unique obs: 2297 / Num. measured obs: 7642 / Rmerge(I) obs: 0.293

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
XENGENdata reduction
XENGENdata scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1DAP

1dap


Resolution: 2.2→10 Å / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.258 2069 10 %RANDOM
Rwork0.17 ---
obs0.17 21456 91.9 %-
Displacement parametersBiso mean: 23.4 Å2
Refinement stepCycle: LAST / Resolution: 2.2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2445 0 13 150 2608
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.011
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_deg1.701
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d26.6
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.27
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
Rfree0.342 211 11.2 %
Rwork0.273 1854 -
obs--75.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARAM19X.PROTOPH19X.PRO
X-RAY DIFFRACTION2DAP.PARDAP.PRO
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Rfactor all: 0.195 / Rfactor obs: 0.192 / Rfactor Rwork: 0.17 / Num. reflection obs: 20794
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg26.6
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.27

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