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- PDB-7dl1: The mutant E310G/G323S structure of 3,5-DAHDHcca complex with NADPH -

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Basic information

Entry
Database: PDB / ID: 7dl1
TitleThe mutant E310G/G323S structure of 3,5-DAHDHcca complex with NADPH
Components3,5-diaminohexanoate dehydrogenase
KeywordsOXIDOREDUCTASE / Dehydrogenase / complex / NADPH
Function / homologyL-erythro-3,5-diaminohexanoate dehydrogenase / L-erythro-3,5-diaminohexanoate dehydrogenase activity / Alcohol dehydrogenase-like, C-terminal / Zinc-binding dehydrogenase / GroES-like superfamily / NAD(P)-binding domain superfamily / nucleotide binding / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 3,5-diaminohexanoate dehydrogenase
Function and homology information
Biological speciesCloacimonas acidaminovorans
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.72 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 1.1May 29, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / 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)157,9516
Polymers156,4644
Non-polymers1,4872
Water3,387188
1
A: 3,5-diaminohexanoate dehydrogenase
C: 3,5-diaminohexanoate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,7194
Polymers78,2322
Non-polymers1,4872
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6340 Å2
ΔGint-35 kcal/mol
Surface area27730 Å2
MethodPISA
2
B: 3,5-diaminohexanoate dehydrogenase
D: 3,5-diaminohexanoate dehydrogenase


Theoretical massNumber of molelcules
Total (without water)78,2322
Polymers78,2322
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3860 Å2
ΔGint-32 kcal/mol
Surface area28560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.241, 127.874, 116.994
Angle α, β, γ (deg.)90.000, 96.295, 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
11METMETHISHIS(chain 'A' and (resid 1 through 11 or resid 13 through 351))AA1 - 111 - 11
12VALVALTYRTYR(chain 'A' and (resid 1 through 11 or resid 13 through 351))AA13 - 35013 - 350
23METMETHISHIS(chain 'B' and (resid 1 through 11 or resid 13 through 351))BB1 - 111 - 11
24VALVALTYRTYR(chain 'B' and (resid 1 through 11 or resid 13 through 351))BB13 - 35013 - 350
35METMETHISHIS(chain 'C' and (resid 1 through 11 or resid 13 through 351))CC1 - 111 - 11
36VALVALTYRTYR(chain 'C' and (resid 1 through 11 or resid 13 through 351))CC13 - 35013 - 350
47METMETHISHIS(chain 'D' and (resid 1 through 11 or resid 13 through 351))DD1 - 111 - 11
48VALVALTYRTYR(chain 'D' and (resid 1 through 11 or resid 13 through 351))DD13 - 35013 - 350

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Components

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


Mass: 39115.977 Da / Num. of mol.: 4 / Mutation: E310G/G323S
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 188 / 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: 2.52 Å3/Da / Density % sol: 51.27 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 1.0 M LiCl, 0.1 M Tris-HCl buffer (pH 7.0), 11% w/v PEG 6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9793 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Oct 20, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.715→50 Å / Num. obs: 41956 / % possible obs: 100 % / Redundancy: 6.7 % / Biso Wilson estimate: 45.971547396 Å2 / Rmerge(I) obs: 0.165 / Net I/σ(I): 14.182
Reflection shellResolution: 2.72→2.77 Å / Rmerge(I) obs: 1.121 / Num. unique obs: 2097

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Processing

Software
NameVersionClassification
HKL-3000data processing
HKL-3000data scaling
PHASERphasing
PHENIX1.11.1_2575refinement
RefinementMethod to determine structure: SAD / Resolution: 2.72→26.7356531244 Å / SU ML: 0.337034135776 / Cross valid method: NONE / σ(F): 1.35917437456 / Phase error: 25.587312232
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.238780821475 1937 4.94966014208 %
Rwork0.192255300579 37197 -
obs0.194548456194 39134 93.2605690863 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 49.6587355884 Å2
Refinement stepCycle: LAST / Resolution: 2.72→26.7356531244 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10654 0 96 188 10938
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0044649352881510890
X-RAY DIFFRACTIONf_angle_d0.93944424603214693
X-RAY DIFFRACTIONf_chiral_restr0.05660451408731720
X-RAY DIFFRACTIONf_plane_restr0.00456322758931885
X-RAY DIFFRACTIONf_dihedral_angle_d16.26652549086689
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.72-2.78280.3173992841431030.2510702639591924X-RAY DIFFRACTION67.4766977364
2.7828-2.8580.3063368422581340.2497248905272163X-RAY DIFFRACTION77.2620248907
2.858-2.9420.3040582219361020.2590031948552375X-RAY DIFFRACTION83.5977050287
2.942-3.03680.2990408342871240.257423884442565X-RAY DIFFRACTION89.6632210737
3.0368-3.14520.3086469115071460.2553279670862635X-RAY DIFFRACTION93.1034482759
3.1452-3.27090.2824918300491340.2546039359042731X-RAY DIFFRACTION96.4321777179
3.2709-3.41950.278498188731550.2179616853692822X-RAY DIFFRACTION99.7654155496
3.4195-3.59940.242289312831530.2084430004452853X-RAY DIFFRACTION100
3.5994-3.82430.2470330716231400.1878440902652848X-RAY DIFFRACTION99.9665439946
3.8243-4.11860.2224286487081580.1844634701412851X-RAY DIFFRACTION100
4.1186-4.53130.1912191142591380.1501573446272846X-RAY DIFFRACTION99.9664991625
4.5313-5.18280.2147171989071390.1497241912182877X-RAY DIFFRACTION100
5.1828-6.51420.2093728519671570.1834482414842856X-RAY DIFFRACTION100
6.5142-26.735650.2051142076271540.1578904411232851X-RAY DIFFRACTION98.2026143791
Refinement TLS params.Method: refined / Origin x: 23.5268881533 Å / Origin y: -5.00697541575 Å / Origin z: 29.3976773243 Å
111213212223313233
T0.25309344526 Å2-0.0436217010029 Å2-0.0365258277524 Å2-0.217151052631 Å2-0.0146548817823 Å2--0.246063005673 Å2
L0.640338734085 °2-0.0108185949815 °2-0.451427990197 °2-0.296264210194 °2-0.145923676764 °2--0.708857795935 °2
S0.0386451705774 Å °0.042109396942 Å °0.00359787041614 Å °0.00469228881901 Å °-0.0206514052329 Å °-0.0581939638183 Å °-0.118660617042 Å °0.0584609187078 Å °-0.00937726490875 Å °
Refinement TLS groupSelection details: all

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