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- PDB-5gz3: Structure of D-amino acid dehydrogenase in complex with NADP -

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Basic information

Entry
Database: PDB / ID: 5gz3
TitleStructure of D-amino acid dehydrogenase in complex with NADP
ComponentsMeso-diaminopimelate D-dehydrogenase
KeywordsOXIDOREDUCTASE / Rossmann fold
Function / homology
Function and homology information


diaminopimelate dehydrogenase / diaminopimelate dehydrogenase activity / 4-hydroxy-tetrahydrodipicolinate reductase / diaminopimelate biosynthetic process / 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, N-terminal / Dihydrodipicolinate reductase, N-terminus / Dihydrodipicolinate Reductase; domain 2 / Dihydrodipicolinate Reductase; domain 2 / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold ...Diaminopimelate dehydrogenase, Ddh / Meso-diaminopimelate D-dehydrogenase, C-terminal / Diaminopimelic acid dehydrogenase C-terminal domain / Dihydrodipicolinate reductase, N-terminal / Dihydrodipicolinate reductase, N-terminus / 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
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Meso-diaminopimelate D-dehydrogenase
Similarity search - Component
Biological speciesUreibacillus thermosphaericus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.59 Å
AuthorsSakuraba, H. / Seto, T. / Hayashi, J. / Akita, H. / Yoneda, K. / Ohshima, T.
CitationJournal: Appl. Environ. Microbiol. / Year: 2017
Title: Structure-Based Engineering of an Artificially Generated NADP+-Dependent d-Amino Acid Dehydrogenase
Authors: Hayashi, J. / Seto, T. / Akita, H. / Watanabe, M. / Hoshino, T. / Yoneda, K. / Ohshima, T. / Sakuraba, H.
History
DepositionSep 26, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 12, 2017Provider: repository / Type: Initial release
Revision 1.1May 31, 2017Group: Database references
Revision 1.2Dec 6, 2017Group: Database references / Category: citation / Item: _citation.title
Revision 1.3Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,4988
Polymers71,7632
Non-polymers1,7356
Water6,666370
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8710 Å2
ΔGint-26 kcal/mol
Surface area26780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.585, 78.232, 68.969
Angle α, β, γ (deg.)90.000, 107.250, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 35881.441 Da / Num. of mol.: 2
Mutation: Q154L, D158G, T173I, R199M, H249N, D94A, and Y224F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ureibacillus thermosphaericus (bacteria)
Gene: ddh / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosseta(DE3) / References: UniProt: G1UII1, diaminopimelate dehydrogenase
#2: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 370 / 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: 2.28 Å3/Da / Density % sol: 46.12 % / Mosaicity: 1.231 °
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: PEG 8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Dec 4, 2015 / Details: silicon single crystal
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.59→50 Å / Num. obs: 81038 / % possible obs: 93.7 % / Redundancy: 6.3 % / Rmerge(I) obs: 0.084 / Net I/av σ(I): 38.091 / Net I/σ(I): 16
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Diffraction-ID% possible all
1.59-1.625.60.4580.84183.1
1.62-1.656.10.4580.879194.4
1.65-1.686.10.4230.894193.9
1.68-1.716.10.3660.923193.6
1.71-1.756.10.3090.952193.5
1.75-1.796.10.2680.96193
1.79-1.8460.2420.968192.7
1.84-1.8960.2090.979192.8
1.89-1.946.10.1650.985193.7
1.94-26.20.1330.988195.3
2-2.076.30.1170.991196.8
2.07-2.166.40.1030.992197.3
2.16-2.266.40.0930.995197.9
2.26-2.386.50.0820.995198
2.38-2.526.70.0760.996198.6
2.52-2.726.90.0710.997198.8
2.72-2.996.90.0660.997198.5
2.99-3.436.90.0590.996196.5
3.43-4.326.40.0530.996187.7
4.32-506.10.0460.996178.5

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Processing

Software
NameVersionClassification
HKL-2000data collection
HKL-2000data scaling
REFMAC5.8.0135refinement
PDB_EXTRACT3.2data extraction
MOLREPphasing
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5GZ1

5gz1


Resolution: 1.59→50 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.926 / SU B: 3.759 / SU ML: 0.067 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.1 / ESU R Free: 0.101
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2293 4071 5 %RANDOM
Rwork0.1914 ---
obs0.1933 76871 93.56 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 68.6 Å2 / Biso mean: 20.81 Å2 / Biso min: 3.02 Å2
Baniso -1Baniso -2Baniso -3
1-1.69 Å20 Å21.36 Å2
2---1.68 Å2-0 Å2
3----0.72 Å2
Refinement stepCycle: final / Resolution: 1.59→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4983 0 112 370 5465
Biso mean--23.28 26.54 -
Num. residues----644
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.030.0195201
X-RAY DIFFRACTIONr_bond_other_d0.0020.024894
X-RAY DIFFRACTIONr_angle_refined_deg2.6211.9827053
X-RAY DIFFRACTIONr_angle_other_deg1.241311273
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7395641
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.01324.538238
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.33415853
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9951530
X-RAY DIFFRACTIONr_chiral_restr0.1740.2774
X-RAY DIFFRACTIONr_gen_planes_refined0.0160.0215894
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021182
X-RAY DIFFRACTIONr_mcbond_it1.4071.4332573
X-RAY DIFFRACTIONr_mcbond_other1.4071.4332572
X-RAY DIFFRACTIONr_mcangle_it1.9872.1463211
LS refinement shellResolution: 1.591→1.632 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.273 315 -
Rwork0.252 5174 -
all-5489 -
obs--85.73 %
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)
10.1214-0.0180.03080.14090.00270.01470.00930.0158-0.0239-0.0295-0.00120.0104-0.0034-0.0045-0.0080.02750.0019-0.02630.06690.00080.036518.4143-0.533513.5754
20.0793-0.0740.02760.39270.01170.0362-0.0075-0.01280.00980.02860.0346-0.04660.0131-0.0105-0.02710.01380.0108-0.02450.0636-0.01150.044636.38523.769939.4757
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 138
2X-RAY DIFFRACTION1A139 - 263
3X-RAY DIFFRACTION1A264 - 326
4X-RAY DIFFRACTION2B2 - 138
5X-RAY DIFFRACTION2B139 - 192
6X-RAY DIFFRACTION2B193 - 219
7X-RAY DIFFRACTION2B220 - 248
8X-RAY DIFFRACTION2B249 - 326

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