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- PDB-6j75: Structure of 3,6-anhydro-L-galactose Dehydrogenase -

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Basic information

Entry
Database: PDB / ID: 6j75
TitleStructure of 3,6-anhydro-L-galactose Dehydrogenase
ComponentsAldehyde dehydrogenase A
KeywordsOXIDOREDUCTASE / Dehydrogenase
Function / homology
Function and homology information


lactaldehyde dehydrogenase / lactaldehyde dehydrogenase activity
Similarity search - Function
Aldehyde Dehydrogenase; Chain A, domain 2 / Aldehyde Dehydrogenase; Chain A, domain 2 / Aldehyde Dehydrogenase; Chain A, domain 1 / Aldehyde Dehydrogenase; Chain A, domain 1 / Aldehyde dehydrogenase, glutamic acid active site / Aldehyde dehydrogenases glutamic acid active site. / Aldehyde dehydrogenase, cysteine active site / Aldehyde dehydrogenases cysteine active site. / Aldehyde dehydrogenase domain / Aldehyde dehydrogenase family ...Aldehyde Dehydrogenase; Chain A, domain 2 / Aldehyde Dehydrogenase; Chain A, domain 2 / Aldehyde Dehydrogenase; Chain A, domain 1 / Aldehyde Dehydrogenase; Chain A, domain 1 / Aldehyde dehydrogenase, glutamic acid active site / Aldehyde dehydrogenases glutamic acid active site. / Aldehyde dehydrogenase, cysteine active site / Aldehyde dehydrogenases cysteine active site. / Aldehyde dehydrogenase domain / Aldehyde dehydrogenase family / Aldehyde dehydrogenase, N-terminal / Aldehyde dehydrogenase, C-terminal / Aldehyde/histidinol dehydrogenase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Aldehyde dehydrogenase A
Similarity search - Component
Biological speciesVibrio variabilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.695 Å
AuthorsLi, P.Y. / Wang, Y. / Chen, X.L. / Zhang, Y.Z.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China41676180 China
National Natural Science Foundation of China91751101 China
CitationJournal: J.Mol.Biol. / Year: 2020
Title: 3,6-Anhydro-L-Galactose Dehydrogenase VvAHGD is a Member of a New Aldehyde Dehydrogenase Family and Catalyzes by a Novel Mechanism with Conformational Switch of Two Catalytic Residues Cysteine ...Title: 3,6-Anhydro-L-Galactose Dehydrogenase VvAHGD is a Member of a New Aldehyde Dehydrogenase Family and Catalyzes by a Novel Mechanism with Conformational Switch of Two Catalytic Residues Cysteine 282 and Glutamate 248.
Authors: Wang, Y. / Li, P.Y. / Zhang, Y. / Cao, H.Y. / Wang, Y.J. / Li, C.Y. / Wang, P. / Su, H.N. / Chen, Y. / Chen, X.L. / Zhang, Y.Z.
History
DepositionJan 17, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 22, 2020Provider: repository / Type: Initial release
Revision 1.1Aug 5, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 22, 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: Aldehyde dehydrogenase A
B: Aldehyde dehydrogenase A
C: Aldehyde dehydrogenase A
D: Aldehyde dehydrogenase A


Theoretical massNumber of molelcules
Total (without water)215,0664
Polymers215,0664
Non-polymers00
Water7,332407
1
A: Aldehyde dehydrogenase A
B: Aldehyde dehydrogenase A


Theoretical massNumber of molelcules
Total (without water)107,5332
Polymers107,5332
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5060 Å2
ΔGint-20 kcal/mol
Surface area33200 Å2
MethodPISA
2
C: Aldehyde dehydrogenase A
D: Aldehyde dehydrogenase A


Theoretical massNumber of molelcules
Total (without water)107,5332
Polymers107,5332
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4900 Å2
ΔGint-21 kcal/mol
Surface area33140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.390, 132.355, 159.337
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Aldehyde dehydrogenase A


Mass: 53766.527 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio variabilis (bacteria) / Gene: JCM19239_2055 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A090SK43, lactaldehyde dehydrogenase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 407 / 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: 2.53 Å3/Da / Density % sol: 51.47 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: NaAC, sodium cacodylate trihydrate, PEG 8,000

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Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 27, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.695→50 Å / Num. obs: 60262 / % possible obs: 99 % / Redundancy: 12.2 % / Rmerge(I) obs: 0.174 / Net I/σ(I): 27.46
Reflection shellResolution: 2.695→2.792 Å / Rmerge(I) obs: 0.431 / Num. unique obs: 5280

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3K2W

3k2w


Resolution: 2.695→47.243 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 21.27
RfactorNum. reflection% reflection
Rfree0.2136 2936 4.88 %
Rwork0.1577 --
obs0.1604 60214 98.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.695→47.243 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14684 0 0 407 15091
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00914972
X-RAY DIFFRACTIONf_angle_d1.0620284
X-RAY DIFFRACTIONf_dihedral_angle_d14.8515472
X-RAY DIFFRACTIONf_chiral_restr0.0472232
X-RAY DIFFRACTIONf_plane_restr0.0052684
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6952-2.73940.32431060.20271984X-RAY DIFFRACTION73
2.7394-2.78660.22861350.19882758X-RAY DIFFRACTION100
2.7866-2.83730.26681440.19612720X-RAY DIFFRACTION100
2.8373-2.89180.25421410.18742723X-RAY DIFFRACTION100
2.8918-2.95090.28241380.19542745X-RAY DIFFRACTION100
2.9509-3.0150.26521560.19552704X-RAY DIFFRACTION100
3.015-3.08510.28941320.19712729X-RAY DIFFRACTION100
3.0851-3.16230.23581550.18372732X-RAY DIFFRACTION100
3.1623-3.24770.26711420.18712728X-RAY DIFFRACTION100
3.2477-3.34330.24391340.17542754X-RAY DIFFRACTION100
3.3433-3.45120.21631420.16842765X-RAY DIFFRACTION100
3.4512-3.57450.22671480.15922735X-RAY DIFFRACTION100
3.5745-3.71750.19421460.14582741X-RAY DIFFRACTION100
3.7175-3.88670.18881500.13232734X-RAY DIFFRACTION100
3.8867-4.09150.1841360.13112783X-RAY DIFFRACTION100
4.0915-4.34760.16951360.12832756X-RAY DIFFRACTION100
4.3476-4.6830.16261310.1212807X-RAY DIFFRACTION100
4.683-5.15380.17281370.12442805X-RAY DIFFRACTION100
5.1538-5.89840.21821460.15122786X-RAY DIFFRACTION100
5.8984-7.42670.20031410.16252862X-RAY DIFFRACTION100
7.4267-47.25050.19641400.16322927X-RAY DIFFRACTION99

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