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- PDB-5loc: Crystal structure of the engineered D-Amino Acid Dehydrogenase (DAADH) -

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Basic information

Entry
Database: PDB / ID: 5loc
TitleCrystal structure of the engineered D-Amino Acid Dehydrogenase (DAADH)
ComponentsMeso-diaminopimelate D-dehydrogenase
KeywordsOXIDOREDUCTASE / DAADH / biocatalysis / amino acids / asymmetric synthesis / enzyme catalysis
Function / homology
Function and homology information


diaminopimelate dehydrogenase / diaminopimelate dehydrogenase activity / diaminopimelate biosynthetic process / L-lysine biosynthetic process via diaminopimelate
Similarity search - Function
Diaminopimelate dehydrogenase, Ddh / Meso-diaminopimelate D-dehydrogenase, C-terminal / Diaminopimelic acid dehydrogenase C-terminal domain / Dihydrodipicolinate Reductase; domain 2 / Dihydrodipicolinate Reductase; domain 2 / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Meso-diaminopimelate D-dehydrogenase
Similarity search - Component
Biological speciesCorynebacterium glutamicum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.04 Å
AuthorsDunstan, M.S. / Gahloth, D.
CitationJournal: To Be Published
Title: Single-biocatalyst synthesis of enantiopure D-arylalanines exploiting an engineered D-amino acid dehydrogenase
Authors: Parmeggiani, F. / Ahmed, S.T. / Thompson, M.P. / Weise, N.J. / Galman, J.L. / Gahloth, D. / Dunstan, M.S. / Leys, D. / Turner, N.J.
History
DepositionAug 9, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 16, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2019Group: Data collection / Category: reflns_shell
Revision 1.2May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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


Theoretical massNumber of molelcules
Total (without water)70,1142
Polymers70,1142
Non-polymers00
Water3,909217
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5270 Å2
ΔGint-39 kcal/mol
Surface area27440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.530, 120.530, 97.630
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

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


Mass: 35057.188 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Corynebacterium glutamicum (bacteria) / Gene: ddh, Cgl2617, cg2900 / Production host: Escherichia coli (E. coli) / References: UniProt: P04964, diaminopimelate dehydrogenase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 217 / 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: 2.92 Å3/Da / Density % sol: 57.87 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 0.12 M monosaccharides, 0.1 M Buffer System 3 pH 8.5, 30%, P500MME_P20K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9282 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jul 12, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9282 Å / Relative weight: 1
ReflectionResolution: 2.04→71.302 Å / Num. obs: 529247 / % possible obs: 99.6 % / Redundancy: 10.1 % / Net I/σ(I): 17.5

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Processing

Software
NameVersionClassification
xia2data scaling
PHENIX1.9_1692refinement
PDB_EXTRACT3.2data extraction
XDSdata reduction
PHASERphasing
RefinementResolution: 2.04→71.302 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 27.7
RfactorNum. reflection% reflection
Rfree0.2545 2549 4.86 %
Rwork0.2067 --
obs0.209 52409 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 152.09 Å2 / Biso mean: 66.1118 Å2 / Biso min: 31.38 Å2
Refinement stepCycle: final / Resolution: 2.04→71.302 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4909 0 0 217 5126
Biso mean---55.55 -
Num. residues----637
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.015013
X-RAY DIFFRACTIONf_angle_d1.3196806
X-RAY DIFFRACTIONf_chiral_restr0.05753
X-RAY DIFFRACTIONf_plane_restr0.006912
X-RAY DIFFRACTIONf_dihedral_angle_d14.7651812
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 18 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.04-2.07920.32281400.288427352875
2.0792-2.12170.29641190.27727592878
2.1217-2.16780.31441190.280227392858
2.1678-2.21830.33581360.271227782914
2.2183-2.27370.33971750.263826952870
2.2737-2.33520.30551520.257427102862
2.3352-2.40390.32371450.248127632908
2.4039-2.48150.3111590.248927292888
2.4815-2.57020.33591270.25127842911
2.5702-2.67310.29121300.239927762906
2.6731-2.79480.27161520.247327292881
2.7948-2.94220.32611690.253227412910
2.9422-3.12650.32051290.252927572886
3.1265-3.36790.28181450.230528102955
3.3679-3.70680.25811300.211727972927
3.7068-4.24310.2281150.180228182933
4.2431-5.34560.16381460.147628262972
5.3456-71.3460.22681610.171929143075
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.00410.04750.21981.2039-0.02921.16540.02660.33-0.2528-0.8185-0.39280.1020.0295-0.54370.16770.78310.17090.02120.5369-0.09180.471840.1052-14.7003101.9558
20.6217-0.2182-0.34470.19110.48570.72610.09740.20880.0491-0.2343-0.1192-0.0662-0.4083-0.36090.06750.68520.25610.05190.41670.04760.439349.86586.1724102.6734
30.762-0.13780.16670.3106-0.23990.50920.17870.12090.1088-0.269-0.12250.3005-0.2172-0.31690.27290.91650.9906-0.36961.0436-0.20570.693517.397329.9171110.6479
41.1092-0.1895-0.23140.8779-0.12890.22050.1439-0.09980.0178-0.0817-0.35840.6145-0.1373-0.71310.07530.47760.2654-0.07150.8861-0.22160.624822.073314.2854119.9728
51.0611-0.877-0.75632.03821.17510.95730.1998-0.0138-0.1592-0.2076-0.1899-0.15990.00080.05580.04830.45640.21550.01760.42290.05850.467543.18924.3899129.4501
60.56030.2640.01811.94090.0420.90660.2865-0.02870.0688-0.3512-0.2001-0.1267-0.0461-0.09310.04650.35410.12740.02670.3943-0.00520.442642.812331.761137.7838
70.298-0.1273-0.33761.20240.21230.35690.3290.25530.0539-0.4743-0.44140.1735-0.2651-0.37170.07410.63250.3812-0.0150.549-0.02460.41737.412419.7931115.7666
81.0129-0.7291-0.17681.12470.49192.36160.02580.2570.0292-0.644-0.15960.3732-0.0339-0.70730.12030.81660.4093-0.25670.8073-0.20740.577125.90978.0763103.7243
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 110 )A2 - 110
2X-RAY DIFFRACTION2chain 'A' and (resid 111 through 321 )A111 - 321
3X-RAY DIFFRACTION3chain 'B' and (resid 4 through 49 )B4 - 49
4X-RAY DIFFRACTION4chain 'B' and (resid 50 through 145 )B50 - 145
5X-RAY DIFFRACTION5chain 'B' and (resid 146 through 189 )B146 - 189
6X-RAY DIFFRACTION6chain 'B' and (resid 190 through 232 )B190 - 232
7X-RAY DIFFRACTION7chain 'B' and (resid 233 through 290 )B233 - 290
8X-RAY DIFFRACTION8chain 'B' and (resid 291 through 321 )B291 - 321

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