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- PDB-8i7h: Meso-Diaminopimelate dehydrogenase -

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Basic information

Entry
Database: PDB / ID: 8i7h
TitleMeso-Diaminopimelate dehydrogenase
ComponentsMeso-diaminopimelate D-dehydrogenase
KeywordsOXIDOREDUCTASE / Meso-Diaminopimelate dehydrogenase / oxidordeuctase / D-Amino acid / Reductive amination
Function / homology2,6-DIAMINOPIMELIC ACID / :
Function and homology information
Biological speciesProteus vulgaris (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.02 Å
AuthorsWu, T.F. / Song, W.
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. / Song, W.
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)132,06227
Polymers129,1004
Non-polymers2,96323
Water32418
1
A: Meso-diaminopimelate D-dehydrogenase
B: Meso-diaminopimelate D-dehydrogenase
C: Meso-diaminopimelate D-dehydrogenase
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)197,85338
Polymers193,6496
Non-polymers4,20432
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z1
Buried area34260 Å2
ΔGint-344 kcal/mol
Surface area67460 Å2
MethodPISA
2
D: Meso-diaminopimelate D-dehydrogenase
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)198,81448
Polymers193,6496
Non-polymers5,16442
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 area36640 Å2
ΔGint-535 kcal/mol
Surface area67270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)213.300, 213.300, 245.840
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
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: Chemical
ChemComp-API / 2,6-DIAMINOPIMELIC ACID


Type: L-peptide linking / Mass: 190.197 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C7H14N2O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 18 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 4.17 Å3/Da / Density % sol: 70.49 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion
Details: 0.1M Sodium acetate trihydrate,2M ammonium sulfate, 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: 1.541 Å
DetectorType: Bruker PHOTON II / Detector: PIXEL / Date: Feb 20, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.541 Å / Relative weight: 1
ReflectionResolution: 3.02→47.29 Å / Num. obs: 40836 / % possible obs: 97 % / Redundancy: 5.7 % / CC1/2: 0.98 / Net I/σ(I): 8
Reflection shellResolution: 3.02→3.14 Å / Redundancy: 4.4 % / Num. unique obs: 4541 / CC1/2: 0.701 / % possible all: 96.4

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Processing

SoftwareName: PHENIX / Version: V1.0 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.02→47 Å / Cor.coef. Fo:Fc: 0.919 / Cor.coef. Fo:Fc free: 0.879 / SU B: 15.904 / SU ML: 0.273 / Cross valid method: THROUGHOUT / ESU R: 1.2 / ESU R Free: 0.367 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24335 1981 4.9 %RANDOM
Rwork0.20735 ---
obs0.20905 38848 96.63 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.564 Å2
Baniso -1Baniso -2Baniso -3
1--1.39 Å2-0.69 Å20 Å2
2---1.39 Å2-0 Å2
3---4.49 Å2
Refinement stepCycle: 1 / Resolution: 3.02→47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8980 0 179 18 9177
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0139272
X-RAY DIFFRACTIONr_bond_other_d0.0010.0178976
X-RAY DIFFRACTIONr_angle_refined_deg1.441.64212562
X-RAY DIFFRACTIONr_angle_other_deg1.1891.59520652
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.21351184
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.72323.301412
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.394151596
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.8991544
X-RAY DIFFRACTIONr_chiral_restr0.0550.21268
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0210444
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021948
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_it2.2153.6344748
X-RAY DIFFRACTIONr_mcbond_other2.2153.6344747
X-RAY DIFFRACTIONr_mcangle_it3.5515.4515928
X-RAY DIFFRACTIONr_mcangle_other3.5515.455929
X-RAY DIFFRACTIONr_scbond_it2.713.9914521
X-RAY DIFFRACTIONr_scbond_other2.673.9734500
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.3885.856600
X-RAY DIFFRACTIONr_long_range_B_refined6.46742.8619251
X-RAY DIFFRACTIONr_long_range_B_other6.46642.8669252
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)
11A89800.05
12B89800.05
21A89390.05
22C89390.05
31A89790.04
32D89790.04
41B89680.05
42C89680.05
51B89860.04
52D89860.04
61C89970.04
62D89970.04
LS refinement shellResolution: 3.02→3.098 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.331 144 -
Rwork0.319 2806 -
obs--95.75 %

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