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- PDB-9ksn: Crystal structure of meso-diaminopimelate dehydrogenase from Baci... -

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Basic information

Entry
Database: PDB / ID: 9ksn
TitleCrystal structure of meso-diaminopimelate dehydrogenase from Bacillus thermozeamaize mutant M9 complexed with NADP+
ComponentsMeso-diaminopimelate D-dehydrogenase
KeywordsOXIDOREDUCTASE / Amino acid dehydrogenase / Complex / NADP+
Function / homology
Function and homology information


diaminopimelate dehydrogenase / diaminopimelate dehydrogenase activity / diaminopimelate biosynthetic process / L-lysine biosynthetic process via diaminopimelate / nucleotide binding
Similarity search - Function
Diaminopimelate dehydrogenase, Ddh / Meso-diaminopimelate D-dehydrogenase, C-terminal / Diaminopimelic acid dehydrogenase C-terminal domain / Gfo/Idh/MocA-like oxidoreductase, N-terminal / Oxidoreductase family, NAD-binding Rossmann fold / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
ACETIC ACID / IMIDAZOLE / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / OXAMIC ACID / Meso-diaminopimelate D-dehydrogenase
Similarity search - Component
Biological speciesBacillus thermozeamaize (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsWei, Y. / Geng, Q. / Zheng, Y.-C. / Zhang, Z.-J.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Acs Catalysis / Year: 2025
Title: An Engineered meso-Diaminopimelate Dehydrogenase Enables the Biocatalytic Synthesis of Bulky beta-Substituted d-Amino Acids
Authors: Wei, Y. / Zheng, Y.C. / Liu, H.P. / Geng, Q. / Wang, Z. / Wang, Y.Q. / Yu, H.L. / Xu, J.H. / Zhang, Z.J.
History
DepositionNov 30, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0May 21, 2025Provider: repository / Type: Initial release

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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
C: Meso-diaminopimelate D-dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,68518
Polymers114,5643
Non-polymers3,12115
Water81145
1
A: Meso-diaminopimelate D-dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,1505
Polymers38,1881
Non-polymers9624
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Meso-diaminopimelate D-dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,3578
Polymers38,1881
Non-polymers1,1697
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Meso-diaminopimelate D-dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,1795
Polymers38,1881
Non-polymers9914
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)156.070, 156.070, 112.310
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+3/4
#3: y+1/2,-x+1/2,z+1/4
#4: x+1/2,-y+1/2,-z+1/4
#5: -x+1/2,y+1/2,-z+3/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 5 through 196 or resid 198...
d_2ens_1(chain "B" and (resid 5 through 196 or resid 198...
d_3ens_1(chain "C" and (resid 5 through 232 or resid 234 through 307 or resid 401 through 402))

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11ARGARGGLUGLUAA5 - 19645 - 236
d_12GLYGLYASPASPAA198 - 232238 - 272
d_13GLYGLYVALVALAA234 - 307274 - 347
d_14NAPNAPNAPNAPAD401
d_15OXMOXMOXMOXMAE402
d_21ARGARGGLUGLUBB5 - 19645 - 236
d_22GLYGLYASPASPBB198 - 232238 - 272
d_23GLYGLYVALVALBB234 - 307274 - 347
d_24NAPNAPNAPNAPBH401
d_25OXMOXMOXMOXMBI402
d_31ARGARGASPASPCC5 - 23245 - 272
d_32GLYGLYVALVALCC234 - 307274 - 347
d_33NAPNAPNAPNAPCO401
d_34OXMOXMOXMOXMCP402

NCS oper:
IDCodeMatrixVector
1given(-0.99945029039, 0.0244032899938, 0.0224409553558), (0.0225582189782, 0.00454057921008, 0.999735219894), (0.0242949335527, 0.999691883821, -0.00508857796952)29.704409553, -53.1579518732, 52.771517536
2given(0.0205271783373, 0.00492790039801, 0.999777150543), (-0.0103850878443, -0.999932853195, 0.00514189192329), (0.999735357432, -0.0104883220657, -0.0204746233244)-23.9025249209, -48.879460525, 24.3576956426

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Components

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Protein , 1 types, 3 molecules ABC

#1: Protein Meso-diaminopimelate D-dehydrogenase / DAPDH / Meso-DAP dehydrogenase


Mass: 38187.918 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus thermozeamaize (bacteria) / Gene: BAA01_00405 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A0A1Y3PXT7, diaminopimelate dehydrogenase

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Non-polymers , 5 types, 60 molecules

#2: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C21H28N7O17P3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-OXM / OXAMIC ACID


Mass: 89.050 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3NO3
#4: Chemical
ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H5N2
#5: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H4O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 45 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: 2.98 Å3/Da / Density % sol: 58.79 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.75
Details: 20 mM sodium formate; 20 mM ammonium acetate; 20 mM sodium citrate tribasic dihydrate; 20 mM potassium sodium tartrate tetrahydrate; 20 mM sodium oxamate; 100 mM MES/imidazole, pH 6.75; 20% ...Details: 20 mM sodium formate; 20 mM ammonium acetate; 20 mM sodium citrate tribasic dihydrate; 20 mM potassium sodium tartrate tetrahydrate; 20 mM sodium oxamate; 100 mM MES/imidazole, pH 6.75; 20% (v/v) ethylene glycol and 10% (w/v) PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-1 / Wavelength: 0.987 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Mar 24, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.65→50.05 Å / Num. obs: 40873 / % possible obs: 100 % / Redundancy: 26.6 % / Biso Wilson estimate: 55.66 Å2 / CC1/2: 0.999 / Net I/σ(I): 17
Reflection shellResolution: 2.65→2.76 Å / Num. unique obs: 4548 / CC1/2: 0.848

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PHENIX1.20.1_4487refinement
autoPROCdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8ZMX

8zmx


Resolution: 2.65→50.05 Å / SU ML: 0.3443 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.3839
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2375 1976 4.84 %
Rwork0.2011 38816 -
obs0.2028 40792 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 66.67 Å2
Refinement stepCycle: LAST / Resolution: 2.65→50.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7051 0 206 45 7302
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00277382
X-RAY DIFFRACTIONf_angle_d0.718210024
X-RAY DIFFRACTIONf_chiral_restr0.05021175
X-RAY DIFFRACTIONf_plane_restr0.00421293
X-RAY DIFFRACTIONf_dihedral_angle_d18.89852796
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AAX-RAY DIFFRACTIONTorsion NCS1.24249591717
ens_1d_3AAX-RAY DIFFRACTIONTorsion NCS1.72169322996
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.65-2.720.35881700.29632707X-RAY DIFFRACTION99.93
2.72-2.790.28971250.27262750X-RAY DIFFRACTION99.93
2.79-2.870.30441400.25052716X-RAY DIFFRACTION99.96
2.87-2.960.3181540.25762710X-RAY DIFFRACTION99.97
2.96-3.070.30291240.24692743X-RAY DIFFRACTION99.93
3.07-3.190.30561340.2592752X-RAY DIFFRACTION100
3.19-3.340.31851300.23642750X-RAY DIFFRACTION100
3.34-3.510.22281560.20822744X-RAY DIFFRACTION100
3.51-3.730.25251320.19952774X-RAY DIFFRACTION99.97
3.73-4.020.24011480.20042762X-RAY DIFFRACTION99.97
4.02-4.430.18641340.17572781X-RAY DIFFRACTION100
4.43-5.070.17831480.16172810X-RAY DIFFRACTION100
5.07-6.380.20951400.19792836X-RAY DIFFRACTION100
6.39-50.050.21781410.16842981X-RAY DIFFRACTION99.4

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