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- PDB-5gz6: Structure of D-amino acid dehydrogenase in complex with NADPH and... -

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Basic information

Entry
Database: PDB / ID: 5gz6
TitleStructure of D-amino acid dehydrogenase in complex with NADPH and 2-keto-6-aminocapronic acid
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
6-azanyl-2-oxidanylidene-hexanoic acid / ACETATE ION / Chem-NDP / Meso-diaminopimelate D-dehydrogenase
Similarity search - Component
Biological speciesUreibacillus thermosphaericus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.74 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

Downloads & links

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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)72,9057
Polymers71,7632
Non-polymers1,1425
Water7,152397
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6740 Å2
ΔGint-63 kcal/mol
Surface area28360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.838, 94.773, 138.791
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 35881.441 Da / Num. of mol.: 2 / Mutation: Q154L, D158G, T173I, R199M, H249N, D94A, 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

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Non-polymers , 5 types, 402 molecules

#2: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#3: Chemical ChemComp-7C3 / 6-azanyl-2-oxidanylidene-hexanoic acid


Mass: 145.156 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H11NO3
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 397 / 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: 2.51 Å3/Da / Density % sol: 51.05 % / Mosaicity: 0.32 °
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: PEG 4000

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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: 1.74→50 Å / Num. obs: 74999 / % possible obs: 99.8 % / Redundancy: 7 % / Rmerge(I) obs: 0.116 / Net I/av σ(I): 34.576 / Net I/σ(I): 9.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Diffraction-ID% possible all
1.74-1.7771.6170.4111100
1.77-1.871.2940.5391100
1.8-1.8471.1350.6121100
1.84-1.8770.9960.7141100
1.87-1.927.10.8160.8011100
1.92-1.967.10.6070.8751100
1.96-2.017.20.4580.9121100
2.01-2.067.20.4060.9371100
2.06-2.127.20.330.9531100
2.12-2.197.20.2790.9681100
2.19-2.277.20.2490.9751100
2.27-2.367.20.2150.9811100
2.36-2.477.10.1790.9841100
2.47-2.67.10.1550.9891100
2.6-2.7670.1280.9911100
2.76-2.986.90.1070.9931100
2.98-3.276.80.0870.9951100
3.27-3.756.70.0730.9951100
3.75-4.726.50.0670.994199.7
4.72-506.20.0610.994195.9

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Processing

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

5gz1


Resolution: 1.74→50 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.938 / SU B: 6.517 / SU ML: 0.103 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.121 / ESU R Free: 0.122
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2502 3780 5 %RANDOM
Rwork0.2075 ---
obs0.2097 71112 99.64 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 104.43 Å2 / Biso mean: 35.261 Å2 / Biso min: 15.23 Å2
Baniso -1Baniso -2Baniso -3
1--0.07 Å20 Å20 Å2
2--0.8 Å2-0 Å2
3----0.74 Å2
Refinement stepCycle: final / Resolution: 1.74→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4920 0 72 397 5389
Biso mean--41.29 39.35 -
Num. residues----634
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0280.0195100
X-RAY DIFFRACTIONr_bond_other_d0.0030.024841
X-RAY DIFFRACTIONr_angle_refined_deg2.3571.9756906
X-RAY DIFFRACTIONr_angle_other_deg1.2153.00111142
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7845629
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.37724.468235
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.15215848
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.7751531
X-RAY DIFFRACTIONr_chiral_restr0.1560.2761
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0215775
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021154
X-RAY DIFFRACTIONr_mcbond_it2.5782.5252537
X-RAY DIFFRACTIONr_mcbond_other2.5782.5252536
X-RAY DIFFRACTIONr_mcangle_it3.8923.7583158
LS refinement shellResolution: 1.739→1.784 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.371 291 -
Rwork0.344 5130 -
all-5421 -
obs--98.94 %
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)
10.37050.1284-0.0410.0749-0.14340.59550.0338-0.079-0.0117-0.0155-0.0335-0.01250.09810.0256-0.00030.03570.0050.0150.02430.0070.042414.318695.183415.4279
20.56530.0378-0.69270.0169-0.01610.9555-0.11620.1852-0.01910.01520.02540.02360.1587-0.19710.09070.0953-0.03150.03820.07130.01120.051514.42896.1934-16.2408
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 48
2X-RAY DIFFRACTION1A49 - 149
3X-RAY DIFFRACTION1A150 - 256
4X-RAY DIFFRACTION1A257 - 326
5X-RAY DIFFRACTION2B2 - 74
6X-RAY DIFFRACTION2B75 - 138
7X-RAY DIFFRACTION2B139 - 256
8X-RAY DIFFRACTION2B257 - 326

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