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- PDB-8zmx: Crystal Structures of meso-diaminopimelate dehydrogenase from Bac... -

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Basic information

Entry
Database: PDB / ID: 8zmx
TitleCrystal Structures of meso-diaminopimelate dehydrogenase from Bacillus thermozeamaize
ComponentsMeso-diaminopimelate D-dehydrogenase
KeywordsOXIDOREDUCTASE / Complex
Function / homology
Function and homology information


diaminopimelate dehydrogenase / diaminopimelate dehydrogenase activity / diaminopimelate biosynthetic process / 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
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Meso-diaminopimelate D-dehydrogenase
Similarity search - Component
Biological speciesBacillus thermozeamaize (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.46 Å
AuthorsGeng, Q. / Wei, Y. / Zhang, Z.J.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32071475 China
CitationJournal: Acs Catalysis / Year: 2024
Title: Hierarchical Engineering of meso-Diaminopimelate Dehydrogenase for Efficient Synthesis of Bulky d-Amino Acids
Authors: Wei, Y. / Geng, Q. / Liu, H.P. / Wang, Y.Q. / Zhang, G.F. / Qian, X.L. / Yu, H.L. / Xu, J.H. / Zhang, Z.J.
History
DepositionMay 24, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Nov 13, 2024Provider: 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)106,3486
Polymers104,1173
Non-polymers2,2303
Water46826
1
A: Meso-diaminopimelate D-dehydrogenase
hetero molecules

B: Meso-diaminopimelate D-dehydrogenase
hetero molecules

C: Meso-diaminopimelate D-dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,3486
Polymers104,1173
Non-polymers2,2303
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_444-y-1/2,x-1/2,z-1/41
crystal symmetry operation7_555y,x,-z1
Buried area7540 Å2
ΔGint-17 kcal/mol
Surface area43490 Å2
MethodPISA
2
A: Meso-diaminopimelate D-dehydrogenase
C: Meso-diaminopimelate D-dehydrogenase
hetero molecules

A: Meso-diaminopimelate D-dehydrogenase
C: Meso-diaminopimelate D-dehydrogenase
hetero molecules

B: Meso-diaminopimelate D-dehydrogenase
hetero molecules

B: Meso-diaminopimelate D-dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)212,69512
Polymers208,2356
Non-polymers4,4606
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
crystal symmetry operation3_444-y-1/2,x-1/2,z-1/41
crystal symmetry operation6_445x-1/2,-y-1/2,-z+1/41
Buried area33340 Å2
ΔGint-127 kcal/mol
Surface area68730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)157.090, 157.090, 111.450
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
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

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Components

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


Mass: 34705.805 Da / Num. of mol.: 3 / Mutation: W129T,D134C,F154V,S177A,H235I
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
#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
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 26 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 3.3 Å3/Da / Density % sol: 66.91 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1 M Carboxylic acids; 0.1 M Imidazole-MES monohydrate (acid) pH 6.5; 20% v/v Ethylene glycol; 10% w/v PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Oct 14, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.46→49.81 Å / Num. obs: 51060 / % possible obs: 99.91 % / Redundancy: 26.8 % / Biso Wilson estimate: 64.57 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.2187 / Net I/σ(I): 16.38
Reflection shellResolution: 2.46→2.548 Å / Rmerge(I) obs: 5.182 / Num. unique obs: 5017 / CC1/2: 0.39 / CC star: 0.749

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3WBB

3wbb


Resolution: 2.46→49.81 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 30.73 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2748 2560 5.02 %
Rwork0.2251 --
obs0.2275 51032 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.46→49.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6606 0 144 26 6776
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0096888
X-RAY DIFFRACTIONf_angle_d1.0899360
X-RAY DIFFRACTIONf_dihedral_angle_d10.1011064
X-RAY DIFFRACTIONf_chiral_restr0.0581105
X-RAY DIFFRACTIONf_plane_restr0.0111206
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.46-2.510.4131430.38942627X-RAY DIFFRACTION100
2.51-2.560.42761410.35532653X-RAY DIFFRACTION100
2.56-2.610.34421460.33312638X-RAY DIFFRACTION100
2.61-2.670.38241500.30952653X-RAY DIFFRACTION100
2.67-2.740.35721360.28922640X-RAY DIFFRACTION100
2.74-2.820.38751330.27452687X-RAY DIFFRACTION100
2.82-2.90.34771530.27312643X-RAY DIFFRACTION100
2.9-2.990.30681390.27482677X-RAY DIFFRACTION100
2.99-3.10.34051460.27652666X-RAY DIFFRACTION100
3.1-3.220.32231430.2612671X-RAY DIFFRACTION100
3.22-3.370.27871450.24442680X-RAY DIFFRACTION100
3.37-3.550.2891240.22012701X-RAY DIFFRACTION100
3.55-3.770.25021310.22232696X-RAY DIFFRACTION100
3.77-4.060.28071550.20382690X-RAY DIFFRACTION100
4.06-4.470.21061290.18142749X-RAY DIFFRACTION100
4.47-5.120.23151640.18132704X-RAY DIFFRACTION100
5.12-6.440.27251500.2242765X-RAY DIFFRACTION100
6.44-49.810.24111320.20632932X-RAY DIFFRACTION99

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