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- PDB-8hp3: Crystal structure of meso-diaminopimelate dehydrogenase from Prev... -

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Basic information

Entry
Database: PDB / ID: 8hp3
TitleCrystal structure of meso-diaminopimelate dehydrogenase from Prevotella timonensis
ComponentsMeso-diaminopimelate D-dehydrogenase
KeywordsOXIDOREDUCTASE / C2221 / fold
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
Chem-NDP / Meso-diaminopimelate D-dehydrogenase
Similarity search - Component
Biological speciesPrevotella timonensis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.07 Å
AuthorsTan, Y. / Song, W.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Appl.Environ.Microbiol. / Year: 2023
Title: Rational Design of Meso -Diaminopimelate Dehydrogenase with Enhanced Reductive Amination Activity for Efficient Production of d- p -Hydroxyphenylglycine.
Authors: Tan, Y. / Gao, C. / Song, W. / Wei, W. / Liu, J. / Gao, C. / Guo, L. / Chen, X. / Liu, L. / Wu, J.
History
DepositionDec 11, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 13, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 21, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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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)101,31723
Polymers97,7533
Non-polymers3,56320
Water54030
1
A: Meso-diaminopimelate D-dehydrogenase
B: Meso-diaminopimelate D-dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,63717
Polymers65,1692
Non-polymers2,46815
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9850 Å2
ΔGint-87 kcal/mol
Surface area25520 Å2
MethodPISA
2
C: Meso-diaminopimelate D-dehydrogenase
hetero molecules

C: Meso-diaminopimelate D-dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,36012
Polymers65,1692
Non-polymers2,19110
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Buried area8830 Å2
ΔGint-119 kcal/mol
Surface area25700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.730, 189.600, 101.820
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
22
33
/ NCS ensembles :
ID
1
2
3

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Components

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


Mass: 32584.482 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Prevotella timonensis (bacteria) / Gene: BFS16_11360 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A2K0XCZ3, diaminopimelate dehydrogenase
#2: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Nicotinamide adenine dinucleotide phosphate


Mass: 745.421 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C21H30N7O17P3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H6O2 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 30 / 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: 2.51 Å3/Da / Density % sol: 51.02 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: 0.1 M HEPES, pH 7.5, 0.1 M ammonium sulfate

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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: Nov 25, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 3.07→47.53 Å / Num. obs: 18754 / % possible obs: 99.8 % / Redundancy: 4.7 % / Rmerge(I) obs: 0.173 / Net I/σ(I): 7.8
Reflection shellResolution: 3.07→3.28 Å / Rmerge(I) obs: 0.66 / Num. unique obs: 3351

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Processing

Software
NameClassification
Aimlessdata scaling
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.07→47.53 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.869 / SU B: 24.307 / SU ML: 0.399 / Cross valid method: THROUGHOUT / ESU R Free: 0.511 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26051 870 4.6 %RANDOM
Rwork0.19786 ---
obs0.2007 17866 99.63 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 52.028 Å2
Baniso -1Baniso -2Baniso -3
1--2.66 Å2-0 Å2-0 Å2
2--0.04 Å20 Å2
3---2.62 Å2
Refinement stepCycle: 1 / Resolution: 3.07→47.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6804 0 220 30 7054
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0137148
X-RAY DIFFRACTIONr_bond_other_d0.0010.0156850
X-RAY DIFFRACTIONr_angle_refined_deg1.4851.6449686
X-RAY DIFFRACTIONr_angle_other_deg1.1571.5815825
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8275895
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.82122.795322
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.302151240
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.0021539
X-RAY DIFFRACTIONr_chiral_restr0.0530.2953
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.027919
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021444
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_it3.8855.3053577
X-RAY DIFFRACTIONr_mcbond_other3.8845.3053576
X-RAY DIFFRACTIONr_mcangle_it6.1347.9534467
X-RAY DIFFRACTIONr_mcangle_other6.1337.9534468
X-RAY DIFFRACTIONr_scbond_it4.1575.8953571
X-RAY DIFFRACTIONr_scbond_other4.1455.8933568
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.6778.7215212
X-RAY DIFFRACTIONr_long_range_B_refined9.71162.7527290
X-RAY DIFFRACTIONr_long_range_B_other9.7162.7547291
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)
11A90650.06
12B90650.06
21A90610.06
22C90610.06
31B90440.05
32C90440.05
LS refinement shellResolution: 3.07→3.149 Å
RfactorNum. reflection% reflection
Rfree0.401 67 -
Rwork0.327 1276 -
obs--99.33 %

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