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- PDB-7dl3: The structure of 3,5-DAHDHcca complex with NADPH -

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Basic information

Entry
Database: PDB / ID: 7dl3
TitleThe structure of 3,5-DAHDHcca complex with NADPH
Components3,5-diaminohexanoate dehydrogenase
KeywordsOXIDOREDUCTASE / Dehydrogenase / complex / NADPH
Function / homology
Function and homology information


L-erythro-3,5-diaminohexanoate dehydrogenase / L-erythro-3,5-diaminohexanoate dehydrogenase activity / quinone reductase (NADPH) activity / mRNA 3'-UTR AU-rich region binding / NADPH binding / cytosol
Similarity search - Function
Alcohol dehydrogenase-like, C-terminal / Zinc-binding dehydrogenase / GroES-like superfamily / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 3,5-diaminohexanoate dehydrogenase
Similarity search - Component
Biological speciesCloacimonas acidaminovorans
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.84606931637 Å
AuthorsLiu, N. / Wu, L. / Zhu, D.M. / Zhou, J.H.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)2177020792 China
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2021
Title: Crystal Structures and Catalytic Mechanism of l-erythro-3,5-Diaminohexanoate Dehydrogenase and Rational Engineering for Asymmetric Synthesis of beta-Amino Acids.
Authors: Liu, N. / Wu, L. / Feng, J. / Sheng, X. / Li, J. / Chen, X. / Li, J. / Liu, W. / Zhou, J. / Wu, Q. / Zhu, D.
History
DepositionNov 25, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 29, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 3,5-diaminohexanoate dehydrogenase
B: 3,5-diaminohexanoate dehydrogenase
C: 3,5-diaminohexanoate dehydrogenase
D: 3,5-diaminohexanoate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)158,1908
Polymers156,6324
Non-polymers1,5584
Water17,222956
1
A: 3,5-diaminohexanoate dehydrogenase
C: 3,5-diaminohexanoate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,8746
Polymers78,3162
Non-polymers1,5584
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6870 Å2
ΔGint-55 kcal/mol
Surface area27500 Å2
MethodPISA
2
B: 3,5-diaminohexanoate dehydrogenase
D: 3,5-diaminohexanoate dehydrogenase


Theoretical massNumber of molelcules
Total (without water)78,3162
Polymers78,3162
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4040 Å2
ΔGint-33 kcal/mol
Surface area27710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.594, 122.037, 114.645
Angle α, β, γ (deg.)90.000, 94.847, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11METMETILEILE(chain 'A' and (resid 1 through 121 or resid 123...AA1 - 1201 - 120
12LEULEUPROPRO(chain 'A' and (resid 1 through 121 or resid 123...AA123 - 182123 - 182
13VALVALSERSER(chain 'A' and (resid 1 through 121 or resid 123...AA185 - 329185 - 329
14ILEILETYRTYR(chain 'A' and (resid 1 through 121 or resid 123...AA331 - 350331 - 350
25METMETILEILE(chain 'B' and (resid 1 through 121 or resid 123...BB1 - 1201 - 120
26LEULEUPROPRO(chain 'B' and (resid 1 through 121 or resid 123...BB123 - 182123 - 182
27VALVALSERSER(chain 'B' and (resid 1 through 121 or resid 123...BB185 - 329185 - 329
28ILEILETYRTYR(chain 'B' and (resid 1 through 121 or resid 123...BB331 - 350331 - 350
39METMETILEILE(chain 'C' and (resid 1 through 121 or resid 123...CC1 - 1201 - 120
310LEULEUPROPRO(chain 'C' and (resid 1 through 121 or resid 123...CC123 - 182123 - 182
311VALVALSERSER(chain 'C' and (resid 1 through 121 or resid 123...CC185 - 329185 - 329
312ILEILETYRTYR(chain 'C' and (resid 1 through 121 or resid 123...CC331 - 350331 - 350
413METMETILEILE(chain 'D' and (resid 1 through 121 or resid 123...DD1 - 1201 - 120
414LEULEUPROPRO(chain 'D' and (resid 1 through 121 or resid 123...DD123 - 182123 - 182
415VALVALSERSER(chain 'D' and (resid 1 through 121 or resid 123...DD185 - 329185 - 329
416ILEILETYRTYR(chain 'D' and (resid 1 through 121 or resid 123...DD331 - 350331 - 350

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Components

#1: Protein
3,5-diaminohexanoate dehydrogenase / 3 / 5-DAHDHcca


Mass: 39158.012 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cloacimonas acidaminovorans (strain Evry) (bacteria)
Gene: kdd, CLOAM1348 / Production host: Escherichia coli DH1 (bacteria)
References: UniProt: B0VJ11, L-erythro-3,5-diaminohexanoate 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 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 956 / 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: 2.44 Å3/Da / Density % sol: 49.56 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 1.0M LiCl, 0.1M Tris-HCl buffer (pH 7.5), 12% w/v PEG 6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97917 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Dec 7, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97917 Å / Relative weight: 1
ReflectionResolution: 1.846→50 Å / Num. obs: 126514 / % possible obs: 99.2 % / Redundancy: 6.8 % / Biso Wilson estimate: 18.602839759 Å2 / Rmerge(I) obs: 0.121 / Net I/σ(I): 17.273
Reflection shellResolution: 1.86→1.89 Å / Redundancy: 5.6 % / Rmerge(I) obs: 1.116 / Mean I/σ(I) obs: 2 / Num. unique obs: 6293 / Rpim(I) all: 0.503 / % possible all: 99

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Processing

Software
NameVersionClassification
HKL-3000data processing
HKL-3000data scaling
PHENIXphasing
PHENIX1.11.1_2575refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7DL7

7dl7


Resolution: 1.84606931637→47.7191948296 Å / SU ML: 0.207285483618 / Cross valid method: NONE / σ(F): 1.35911005462 / Phase error: 23.6513829159
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.228935031744 6325 5.07298684633 %
Rwork0.200814889566 118355 -
obs0.202232064989 124680 96.9367127974 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 23.1006267445 Å2
Refinement stepCycle: LAST / Resolution: 1.84606931637→47.7191948296 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10701 0 98 956 11755
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081934499950310957
X-RAY DIFFRACTIONf_angle_d1.1471319291314787
X-RAY DIFFRACTIONf_chiral_restr0.06998704133591726
X-RAY DIFFRACTIONf_plane_restr0.006322728577961901
X-RAY DIFFRACTIONf_dihedral_angle_d18.1155429596737
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8461-1.8670.3225950133031230.270965084162506X-RAY DIFFRACTION61.025998143
1.867-1.8890.2961734291251860.2672827093643523X-RAY DIFFRACTION87.6210725254
1.889-1.91210.2994120269692170.2529300281533704X-RAY DIFFRACTION91.3347309574
1.9121-1.93630.2898743236632120.2526741560163809X-RAY DIFFRACTION94.6340315368
1.9363-1.96170.3023953759182160.2533666564433927X-RAY DIFFRACTION96.889616464
1.9617-1.98860.2965594322712330.2451737661543946X-RAY DIFFRACTION97.9376611202
1.9886-2.0170.2720011304482140.2378586583874010X-RAY DIFFRACTION98.5534297713
2.017-2.04710.2778130185062080.2380215271793985X-RAY DIFFRACTION97.4210037175
2.0471-2.07910.2820969034882240.2364758211353960X-RAY DIFFRACTION98.6327204149
2.0791-2.11320.2668947052222100.2286571869774036X-RAY DIFFRACTION99.0898483081
2.1132-2.14960.2433382480632240.2186483415894019X-RAY DIFFRACTION99.1355140187
2.1496-2.18870.2535340667582210.2180467875954021X-RAY DIFFRACTION99.4374120956
2.1887-2.23080.2477179833692440.2207275263594004X-RAY DIFFRACTION99.0671641791
2.2308-2.27640.24825227432180.2157743744584023X-RAY DIFFRACTION99.413970933
2.2764-2.32590.2773777908311890.2126661910284073X-RAY DIFFRACTION99.3473193473
2.3259-2.380.2509458235382140.2097407331184018X-RAY DIFFRACTION99.6233521657
2.38-2.43950.2233795925082130.2142812830994080X-RAY DIFFRACTION99.4440583739
2.4395-2.50540.2695747400551890.218194283314001X-RAY DIFFRACTION98.3106522759
2.5054-2.57910.2532989332192200.2138417950514057X-RAY DIFFRACTION99.6505125815
2.5791-2.66240.2437325953052120.2156135312444063X-RAY DIFFRACTION99.7200839748
2.6624-2.75750.2535828490332270.2204686383244018X-RAY DIFFRACTION99.6245012908
2.7575-2.86790.2383114625982210.2086349254174051X-RAY DIFFRACTION99.7897687456
2.8679-2.99840.2664029001492190.2205388937814063X-RAY DIFFRACTION99.790258681
2.9984-3.15650.2519068098132110.2136064213454111X-RAY DIFFRACTION99.7231195201
3.1565-3.35420.2402911574711770.206096426854012X-RAY DIFFRACTION98.0571161049
3.3542-3.61310.2180059545592060.1893435689064082X-RAY DIFFRACTION99.7905515476
3.6131-3.97650.1904111854382410.1698865378724048X-RAY DIFFRACTION99.7441860465
3.9765-4.55160.1661073568942030.1438964671374113X-RAY DIFFRACTION99.5157943279
4.5516-5.7330.139123557772260.1488605528754005X-RAY DIFFRACTION98.2126276695
5.733-47.70.1577967598062070.15784087X-RAY DIFFRACTION97.7019340159
Refinement TLS params.Method: refined / Origin x: 25.4671390348 Å / Origin y: -4.31560291275 Å / Origin z: 28.8593914039 Å
111213212223313233
T0.0423658918604 Å2-0.0241577098712 Å20.00108586758975 Å2-0.0455994039017 Å2-0.00624020738072 Å2--0.0476112810533 Å2
L-0.000197191546827 °20.0037176248189 °2-0.00951311948858 °2-0.00586401443485 °20.00177292948381 °2--0.00788985879712 °2
S-0.0232030574919 Å °-0.0146776049383 Å °0.019489810057 Å °0.0341568189178 Å °0.0236336784923 Å °-0.0164858893044 Å °0.0438777640993 Å °-0.0204509236959 Å °6.6E-14 Å °
Refinement TLS groupSelection details: all

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