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- PDB-7dl7: The wild-type structure of 3,5-DAHDHcca -

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Basic information

Entry
Database: PDB / ID: 7dl7
TitleThe wild-type structure of 3,5-DAHDHcca
Components3,5-diaminohexanoate dehydrogenase
KeywordsOXIDOREDUCTASE / Dehydrogenase / 3S / 5S-DAH
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
DI(HYDROXYETHYL)ETHER / 3,5-diaminohexanoate dehydrogenase
Similarity search - Component
Biological speciesCloacimonas acidaminovorans
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.30065812844 Å
AuthorsLiu, N. / Wu, L. / Zhu, D.M. / Zhou, J.H.
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 26, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 29, 2021Provider: repository / Type: Initial release
Revision 1.1May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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
E: 3,5-diaminohexanoate dehydrogenase
F: 3,5-diaminohexanoate dehydrogenase
G: 3,5-diaminohexanoate dehydrogenase
H: 3,5-diaminohexanoate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)316,13553
Polymers313,2648
Non-polymers2,87045
Water8,179454
1
A: 3,5-diaminohexanoate dehydrogenase
F: 3,5-diaminohexanoate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,08413
Polymers78,3162
Non-polymers76811
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5700 Å2
ΔGint-40 kcal/mol
Surface area27950 Å2
MethodPISA
2
B: 3,5-diaminohexanoate dehydrogenase
G: 3,5-diaminohexanoate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,21416
Polymers78,3162
Non-polymers89814
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5480 Å2
ΔGint-44 kcal/mol
Surface area28000 Å2
MethodPISA
3
C: 3,5-diaminohexanoate dehydrogenase
H: 3,5-diaminohexanoate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,13115
Polymers78,3162
Non-polymers81513
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6530 Å2
ΔGint-28 kcal/mol
Surface area28470 Å2
MethodPISA
4
D: 3,5-diaminohexanoate dehydrogenase
E: 3,5-diaminohexanoate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,7059
Polymers78,3162
Non-polymers3897
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4940 Å2
ΔGint-48 kcal/mol
Surface area27820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.604, 89.889, 123.693
Angle α, β, γ (deg.)87.328, 70.970, 80.562
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

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Protein , 1 types, 8 molecules ABCDEFGH

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


Mass: 39158.012 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cloacimonas acidaminovorans (strain Evry) (bacteria)
Strain: Evry / Gene: kdd, CLOAM1348 / Production host: Escherichia coli DH1 (bacteria)
References: UniProt: B0VJ11, L-erythro-3,5-diaminohexanoate dehydrogenase

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Non-polymers , 8 types, 499 molecules

#2: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 27 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: Cl
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#8: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Feature type: SUBJECT OF INVESTIGATION / Comment: pH buffer*YM
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 454 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.04 Å3/Da / Density % sol: 59.58 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 0.2M Li2SO4, 0.1M Tris-HCl buffer (pH 7.5), 24% w/v PEG 3000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97852 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Apr 19, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97852 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 155611 / % possible obs: 97.67 % / Redundancy: 5.2 % / Biso Wilson estimate: 39.4401440588 Å2 / Rmerge(I) obs: 0.103 / Net I/σ(I): 13.455
Reflection shellResolution: 2.3→2.34 Å / Rmerge(I) obs: 0.512 / Num. unique obs: 7443

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.30065812844→48.9754126335 Å / SU ML: 0.348231159542 / Cross valid method: NONE / σ(F): 1.95281299978 / Phase error: 30.3839184422
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.257135458701 7602 4.88912327639 %
Rwork0.225633498439 147886 -
obs0.227174200437 155488 97.3320813772 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 47.2471034037 Å2
Refinement stepCycle: LAST / Resolution: 2.30065812844→48.9754126335 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21158 0 170 454 21782
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.001694031441821611
X-RAY DIFFRACTIONf_angle_d0.45470438940729073
X-RAY DIFFRACTIONf_chiral_restr0.04347271515023397
X-RAY DIFFRACTIONf_plane_restr0.003065763316653756
X-RAY DIFFRACTIONf_dihedral_angle_d3.133887615317022
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3007-2.32680.3357110270212490.303022624994426X-RAY DIFFRACTION88.5416666667
2.3268-2.35420.3498501716722240.2992099077294950X-RAY DIFFRACTION96.6922070641
2.3542-2.38290.3260042350862450.3085423570274897X-RAY DIFFRACTION97.3126419379
2.3829-2.4130.3565098103252760.3029600698134943X-RAY DIFFRACTION97.6792064383
2.413-2.44480.3283267309712480.2901566553374950X-RAY DIFFRACTION97.5234521576
2.4448-2.47830.3270826504552380.2928410124754977X-RAY DIFFRACTION97.6408912189
2.4783-2.51370.3309497155342610.2936184239744912X-RAY DIFFRACTION97.5669558657
2.5137-2.55120.3300359866642150.2831661070995010X-RAY DIFFRACTION98.0300187617
2.5512-2.59110.3332969324962390.2814706690355025X-RAY DIFFRACTION97.9713381723
2.5911-2.63350.2923626252172220.2665842753145060X-RAY DIFFRACTION98.1966908347
2.6335-2.6790.3355249521262510.2776330774524864X-RAY DIFFRACTION97.8198508319
2.679-2.72770.3444241947582780.2702110080124936X-RAY DIFFRACTION97.3669467787
2.7277-2.78010.309850715292660.2739314886894866X-RAY DIFFRACTION97.0132325142
2.7801-2.83690.324138590112450.2734733735584804X-RAY DIFFRACTION94.0398584466
2.8369-2.89850.3124559402522620.2715689999774977X-RAY DIFFRACTION98.4034560481
2.8985-2.9660.3473145704192690.2666061055394962X-RAY DIFFRACTION98.3270676692
2.966-3.04010.3065441684822920.2694795178144903X-RAY DIFFRACTION98.1299584435
3.0401-3.12230.3071006897282570.2615998511494984X-RAY DIFFRACTION97.8894284647
3.1223-3.21420.3073039082782680.2573527450314945X-RAY DIFFRACTION98.1362951807
3.2142-3.31790.2969627324822620.2529933650265039X-RAY DIFFRACTION98.807082945
3.3179-3.43640.2936443647382520.241520587114979X-RAY DIFFRACTION98.4751506024
3.4364-3.5740.2661957605442420.2339052440634920X-RAY DIFFRACTION97.506611258
3.574-3.73660.2370042530262530.2152948298624911X-RAY DIFFRACTION95.7005189029
3.7366-3.93350.2155974054672370.1948906128034960X-RAY DIFFRACTION98.9527798934
3.9335-4.17980.2152436375352580.1861622213145023X-RAY DIFFRACTION99.1178678679
4.1798-4.50240.2168221405962290.1746728416975035X-RAY DIFFRACTION98.7802589604
4.5024-4.95510.1754866008462600.1688378582624967X-RAY DIFFRACTION98.0491465016
4.9551-5.67120.2106997169742410.1899053872884884X-RAY DIFFRACTION96.1899399399
5.6712-7.14150.2115115423752890.1965480834134914X-RAY DIFFRACTION97.8743416102
7.1415-48.9750.1805083721912740.1755238081654863X-RAY DIFFRACTION96.2706146927

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