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- PDB-1f06: THREE DIMENSIONAL STRUCTURE OF THE TERNARY COMPLEX OF CORYNEBACTE... -

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Basic information

Entry
Database: PDB / ID: 1f06
TitleTHREE DIMENSIONAL STRUCTURE OF THE TERNARY COMPLEX OF CORYNEBACTERIUM GLUTAMICUM DIAMINOPIMELATE DEHYDROGENASE NADPH-L-2-AMINO-6-METHYLENE-PIMELATE
ComponentsMESO-DIAMINOPIMELATE D-DEHYDROGENASE
KeywordsOXIDOREDUCTASE / Enzyme-NADPH-inhibitor ternary complex
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
L-2-AMINO-6-METHYLENE-PIMELIC ACID / Chem-NDP / Meso-diaminopimelate D-dehydrogenase
Similarity search - Component
Biological speciesCorynebacterium glutamicum (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2.1 Å
AuthorsCirilli, M. / Scapin, G. / Sutherland, A. / Caplan, J.F. / Vederas, J.C. / Blanchard, J.S.
CitationJournal: Protein Sci. / Year: 2000
Title: The three-dimensional structure of the ternary complex of Corynebacterium glutamicum diaminopimelate dehydrogenase-NADPH-L-2-amino-6-methylene-pimelate.
Authors: Cirilli, M. / Scapin, G. / Sutherland, A. / Vederas, J.C. / Blanchard, J.S.
History
DepositionMay 14, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 14, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Feb 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

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Assembly

Deposited unit
A: MESO-DIAMINOPIMELATE D-DEHYDROGENASE
B: MESO-DIAMINOPIMELATE D-DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,1635
Polymers70,4852
Non-polymers1,6783
Water2,090116
1
A: MESO-DIAMINOPIMELATE D-DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,9882
Polymers35,2421
Non-polymers7451
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: MESO-DIAMINOPIMELATE D-DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,1753
Polymers35,2421
Non-polymers9332
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7990 Å2
ΔGint-37 kcal/mol
Surface area25340 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)75.547, 65.591, 84.281
Angle α, β, γ (deg.)90.00, 106.52, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein MESO-DIAMINOPIMELATE D-DEHYDROGENASE


Mass: 35242.328 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Corynebacterium glutamicum (bacteria) / Plasmid: PET23B / Production host: Escherichia coli (E. coli) / 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-2NP / L-2-AMINO-6-METHYLENE-PIMELIC ACID


Mass: 187.193 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H13NO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 116 / 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: 2.84 Å3/Da / Density % sol: 56.68 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: PEG 8000, magnesium acetate, cacodylate, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal grow
*PLUS
pH: 7.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
114 %PEG80001reservoir
2200 mMmagnesium acetate1reservoir
3100 mMsodium acetate1reservoir
424 mg/mlprotein1drop
520 mMHEPES1drop
65 mMNADPH1drop
720 mML-2-amino-6-methylene-pimelate1drop

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418
DetectorType: XENTRONICS / Detector: AREA DETECTOR / Date: Jul 28, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→48.6 Å / Num. all: 111792 / Num. obs: 111416 / % possible obs: 86.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 2.82 % / Biso Wilson estimate: 32.7 Å2 / Rmerge(I) obs: 0.076 / Net I/σ(I): 8.615
Reflection shellResolution: 2.11→2.25 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.224 / % possible all: 47.3
Reflection
*PLUS
Num. obs: 39441
Reflection shell
*PLUS
% possible obs: 67 %

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Processing

Software
NameVersionClassification
X-PLORmodel building
X-PLOR3.851refinement
X-GENdata reduction
X-GENdata scaling
X-PLORphasing
RefinementResolution: 2.1→48.6 Å / σ(F): 2 / σ(I): 4 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.209 1027 RANDOM
Rwork0.179 --
all0.197 39428 -
obs0.185 39428 -
Refinement stepCycle: LAST / Resolution: 2.1→48.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4950 0 109 116 5175
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_angle_deg1.398
X-RAY DIFFRACTIONx_torsion_deg26.412
X-RAY DIFFRACTIONx_torsion_impr_deg1.332
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.1 Å / Lowest resolution: 48.6 Å / σ(F): 2 / Rfactor obs: 0.178
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg26.4
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.33

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