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- PDB-8i78: Meso-Diaminopimelate dehydrogenase -

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Basic information

Entry
Database: PDB / ID: 8i78
TitleMeso-Diaminopimelate dehydrogenase
ComponentsMeso-diaminopimelate D-dehydrogenase
KeywordsOXIDOREDUCTASE / oxidordeuctase / Meso-Diaminopimelate dehydrogenase / D-Amino acid / Reductive amination
Function / homology:
Function and homology information
Biological speciesProteus vulgaris (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.64 Å
AuthorsWei, S. / Wu, T.F.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Analysis of the catalytic mechanism of meso-DAPDH and extension of D-aromatic amino acid substrate scope
Authors: wu, T.F. / wei, S.
History
DepositionJan 31, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 7, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Meso-diaminopimelate D-dehydrogenase
B: Meso-diaminopimelate D-dehydrogenase
C: Meso-diaminopimelate D-dehydrogenase
D: Meso-diaminopimelate D-dehydrogenase


Theoretical massNumber of molelcules
Total (without water)129,1004
Polymers129,1004
Non-polymers00
Water8,233457
1
A: Meso-diaminopimelate D-dehydrogenase
x 6


Theoretical massNumber of molelcules
Total (without water)193,6496
Polymers193,6496
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-y,x-y-1,z1
crystal symmetry operation3_655-x+y+1,-x,z1
crystal symmetry operation10_545y+2/3,x-2/3,-z+1/31
crystal symmetry operation11_445x-y-1/3,-y-2/3,-z+1/31
crystal symmetry operation12_555-x+2/3,-x+y+1/3,-z+1/31
Buried area24190 Å2
ΔGint-143 kcal/mol
Surface area69380 Å2
MethodPISA
2
B: Meso-diaminopimelate D-dehydrogenase
C: Meso-diaminopimelate D-dehydrogenase
D: Meso-diaminopimelate D-dehydrogenase

B: Meso-diaminopimelate D-dehydrogenase
C: Meso-diaminopimelate D-dehydrogenase
D: Meso-diaminopimelate D-dehydrogenase


Theoretical massNumber of molelcules
Total (without water)193,6496
Polymers193,6496
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z1
Buried area24050 Å2
ΔGint-145 kcal/mol
Surface area69090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)211.910, 211.910, 245.760
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-434-

HOH

21A-435-

HOH

31B-392-

HOH

41B-412-

HOH

51B-418-

HOH

61C-399-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
22
33
44
55
66
/ NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
Meso-diaminopimelate D-dehydrogenase


Mass: 32274.896 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Proteus vulgaris (bacteria) / Gene: EKQ45_05540 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A857SCE6
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 457 / 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: 4.11 Å3/Da / Density % sol: 70.09 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion
Details: 2M ammonium sulfate, 0.1M Sodium acetate trihydrate, pH 4.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SEALED TUBE / Type: BRUKER D8 QUEST / Wavelength: 1.54178 Å
DetectorType: Bruker PHOTON II / Detector: PIXEL / Date: Jun 25, 2021 / Details: multilayer
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.64→47.48 Å / Num. obs: 58941 / % possible obs: 99.97 % / Redundancy: 5.13 % / CC1/2: 0.995 / Net I/σ(I): 14.9
Reflection shellResolution: 2.64→2.71 Å / Num. unique obs: 4572 / CC1/2: 0.689

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Processing

Software
NameVersionClassification
PHENIXV1.0refinement
PDB_EXTRACTdata extraction
HKL-3000data scaling
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.64→47.52 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.927 / SU B: 9.086 / SU ML: 0.176 / Cross valid method: THROUGHOUT / ESU R: 0.329 / ESU R Free: 0.23 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21409 3204 5.2 %RANDOM
Rwork0.18332 ---
obs0.18491 58941 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.672 Å2
Baniso -1Baniso -2Baniso -3
1--0.73 Å2-0.36 Å20 Å2
2---0.73 Å2-0 Å2
3---2.35 Å2
Refinement stepCycle: 1 / Resolution: 2.64→47.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8980 0 0 457 9437
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0139125
X-RAY DIFFRACTIONr_bond_other_d0.0010.0178892
X-RAY DIFFRACTIONr_angle_refined_deg1.4351.6312365
X-RAY DIFFRACTIONr_angle_other_deg1.2481.58120463
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.99251186
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.00723.237414
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.692151599
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.0291545
X-RAY DIFFRACTIONr_chiral_restr0.0610.21253
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0210360
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021922
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.8453.8244750
X-RAY DIFFRACTIONr_mcbond_other2.8453.8244749
X-RAY DIFFRACTIONr_mcangle_it4.4925.7355931
X-RAY DIFFRACTIONr_mcangle_other4.4925.7345932
X-RAY DIFFRACTIONr_scbond_it3.7374.2574373
X-RAY DIFFRACTIONr_scbond_other3.7374.2574373
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.9246.2076431
X-RAY DIFFRACTIONr_long_range_B_refined8.07944.9469419
X-RAY DIFFRACTIONr_long_range_B_other8.07844.9469414
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A90670.04
12B90670.04
21A90540.05
22C90540.05
31A90390.05
32D90390.05
41B91160.04
42C91160.04
51B90630.05
52D90630.05
61C90420.06
62D90420.06
LS refinement shellResolution: 2.64→2.709 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.328 257 -
Rwork0.292 4315 -
obs--100 %

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