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- PDB-6gvs: Engineered glycolyl-CoA reductase comprising 8 mutations with bou... -

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Basic information

Entry
Database: PDB / ID: 6gvs
TitleEngineered glycolyl-CoA reductase comprising 8 mutations with bound NADP+
ComponentsAldehyde dehydrogenase
KeywordsOXIDOREDUCTASE / glycolyl-CoA reductase / enzyme engineering / NADPH
Function / homology
Function and homology information


acetaldehyde dehydrogenase (acetylating) activity / nucleotide binding
Similarity search - Function
Acetaldehyde/propionaldehyde dehydrogenase, EutE/PduP-related / 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 domain / Aldehyde dehydrogenase family / Aldehyde dehydrogenase, C-terminal / Aldehyde dehydrogenase, N-terminal / Aldehyde/histidinol dehydrogenase ...Acetaldehyde/propionaldehyde dehydrogenase, EutE/PduP-related / 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 domain / Aldehyde dehydrogenase family / Aldehyde dehydrogenase, C-terminal / Aldehyde dehydrogenase, N-terminal / Aldehyde/histidinol dehydrogenase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
: / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Aldehyde dehydrogenase
Similarity search - Component
Biological speciesRhodopseudomonas palustris BisB18 (phototrophic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.579 Å
AuthorsZarzycki, J. / Trudeau, D. / Scheffen, M. / Erb, T.J. / Tawfik, D.S.
Funding support Germany, 1items
OrganizationGrant numberCountry
European Research CouncilFET-OPEN 686330 Germany
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2018
Title: Design and in vitro realization of carbon-conserving photorespiration.
Authors: Trudeau, D.L. / Edlich-Muth, C. / Zarzycki, J. / Scheffen, M. / Goldsmith, M. / Khersonsky, O. / Avizemer, Z. / Fleishman, S.J. / Cotton, C.A.R. / Erb, T.J. / Tawfik, D.S. / Bar-Even, A.
History
DepositionJun 21, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 28, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 5, 2018Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed ..._citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Dec 19, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Jan 17, 2024Group: 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
B: Aldehyde dehydrogenase
C: Aldehyde dehydrogenase
D: Aldehyde dehydrogenase
E: Aldehyde dehydrogenase
F: Aldehyde dehydrogenase
G: Aldehyde dehydrogenase
H: Aldehyde dehydrogenase
I: Aldehyde dehydrogenase
J: Aldehyde dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)560,57630
Polymers552,75110
Non-polymers7,82520
Water9,080504
1
A: Aldehyde dehydrogenase
B: Aldehyde dehydrogenase
C: Aldehyde dehydrogenase
D: Aldehyde dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)224,23112
Polymers221,1014
Non-polymers3,1308
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20340 Å2
ΔGint-55 kcal/mol
Surface area55860 Å2
MethodPISA
2
E: Aldehyde dehydrogenase
F: Aldehyde dehydrogenase
G: Aldehyde dehydrogenase
H: Aldehyde dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)224,23112
Polymers221,1014
Non-polymers3,1308
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20630 Å2
ΔGint-53 kcal/mol
Surface area56090 Å2
MethodPISA
3
I: Aldehyde dehydrogenase
J: Aldehyde dehydrogenase
hetero molecules

I: Aldehyde dehydrogenase
J: Aldehyde dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)224,23112
Polymers221,1014
Non-polymers3,1308
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area20840 Å2
ΔGint-56 kcal/mol
Surface area55830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)362.202, 123.183, 165.096
Angle α, β, γ (deg.)90.000, 109.250, 90.000
Int Tables number5
Space group name H-MC121
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

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Components

#1: Protein
Aldehyde dehydrogenase


Mass: 55275.141 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodopseudomonas palustris BisB18 (phototrophic)
Gene: RPC_1174 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q21A49
#2: Chemical
ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Formula: C21H28N7O17P3
Source: (gene. exp.) Rhodopseudomonas palustris BisB18 (phototrophic)
Production host: Escherichia coli BL21(DE3) (bacteria)
#3: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: K
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 504 / 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: 3.69 Å3/Da / Density % sol: 66.63 % / Description: needle
Crystal growTemperature: 288 K / Method: vapor diffusion, sitting drop / pH: 8.4
Details: Enzyme (6.5 mg/mL) was mixed with 0.2 M potassium citrate/KOH pH 8.4, 20% (w/v) PEG 3350, and supplemented with NADP+ from a 30 mM stock in a ratio of 2:2:1 (enzyme: crystallization buffer: ...Details: Enzyme (6.5 mg/mL) was mixed with 0.2 M potassium citrate/KOH pH 8.4, 20% (w/v) PEG 3350, and supplemented with NADP+ from a 30 mM stock in a ratio of 2:2:1 (enzyme: crystallization buffer: substrate). The final drop volume was 5 micro liters.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.976251 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 3, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976251 Å / Relative weight: 1
ReflectionResolution: 2.579→39.133 Å / Num. all: 212592 / Num. obs: 212592 / % possible obs: 98.8 % / Redundancy: 4 % / Biso Wilson estimate: 50.94 Å2 / Rpim(I) all: 0.074 / Rrim(I) all: 0.15 / Rsym value: 0.13 / Net I/av σ(I): 5.2 / Net I/σ(I): 7.6 / Num. measured all: 853804
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique obsRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
2.58-2.724.10.9690.8123635304720.5481.1160.9691.597.4
2.72-2.8840.6461.2116525292910.3710.7470.6462.198.7
2.88-3.0840.4361.8111223275820.250.5040.4363.198.9
3.08-3.334.20.2682.9107183256980.150.3080.268599
3.33-3.6540.151594677236600.0870.1750.1517.799.1
3.65-4.0840.0967.586258215150.0550.1110.09611.399.3
4.08-4.714.10.0699.778760190540.0380.080.0691599.5
4.71-5.773.90.0679.862412159910.0380.0780.06714.998.8
5.77-8.163.90.0679.148678125240.0380.0770.06715.799.5
8.16-39.1333.60.0599.62445368050.0350.0690.05921.196.9

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Processing

Software
NameVersionClassification
PHENIXrefinement
XDSdata reduction
SCALAdata scaling
PHENIX1.13_2998phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5JFL

5jfl


Resolution: 2.579→39.133 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2098 3860 0.94 %
Rwork0.1915 406816 -
obs0.1916 410676 96.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 159.68 Å2 / Biso mean: 58.0242 Å2 / Biso min: 26.12 Å2
Refinement stepCycle: final / Resolution: 2.579→39.133 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms32970 0 470 504 33944
Biso mean--86.62 55.06 -
Num. residues----4406
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 28

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.579-2.61050.37541280.3499134521358090
2.6105-2.64350.38641370.3347146141475198
2.6435-2.67830.35081380.3265147391487797
2.6783-2.7150.31021420.3188146191476198
2.715-2.75370.2961360.3157147161485297
2.7537-2.79480.31131390.3036143451448496
2.7948-2.83850.30811360.2962140611419794
2.8385-2.8850.29331420.2873147611490398
2.885-2.93470.27011400.2837148571499798
2.9347-2.98810.29671410.2799146191476098
2.9881-3.04550.3531390.2707142761441595
3.0455-3.10770.32241390.2738146851482498
3.1077-3.17520.28571410.26148761501799
3.1752-3.2490.27131420.2444148051494798
3.249-3.33030.25561420.2313147171485998
3.3303-3.42020.23681400.2244148201496099
3.4202-3.52080.23091370.2075147341487198
3.5208-3.63440.21421330.1926142111434495
3.6344-3.76420.22861390.1826146811482098
3.7642-3.91480.19241340.1654147171485198
3.9148-4.09280.16471390.1542144541459396
4.0928-4.30830.16731410.14149101505199
4.3083-4.57780.13011410.1307148491499099
4.5778-4.93070.14571400.123146801482098
4.9307-5.42570.16851360.139141481428494
5.4257-6.20810.16281350.1662143681450396
6.2081-7.81130.161340.1475145091464396
7.8113-39.13720.12711290.1199135931372291
Refinement TLS params.Method: refined / Origin x: 33.6594 Å / Origin y: 53.1937 Å / Origin z: 39.9715 Å
111213212223313233
T0.3064 Å2-0.0561 Å2-0.0033 Å2-0.3637 Å20.0233 Å2--0.3124 Å2
L0.1133 °2-0.0451 °2-0.013 °2-0.0963 °20.0367 °2--0.0807 °2
S0.0147 Å °-0.006 Å °-0.0118 Å °0.0043 Å °-0.0169 Å °0.0074 Å °0.0088 Å °-0.0394 Å °0.0033 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA82 - 522
2X-RAY DIFFRACTION1allB83 - 522
3X-RAY DIFFRACTION1allC82 - 522
4X-RAY DIFFRACTION1allD83 - 522
5X-RAY DIFFRACTION1allE82 - 522
6X-RAY DIFFRACTION1allF82 - 522
7X-RAY DIFFRACTION1allG83 - 522
8X-RAY DIFFRACTION1allH82 - 522
9X-RAY DIFFRACTION1allI82 - 522
10X-RAY DIFFRACTION1allJ83 - 522
11X-RAY DIFFRACTION1allA570
12X-RAY DIFFRACTION1allB570
13X-RAY DIFFRACTION1allC570
14X-RAY DIFFRACTION1allD570
15X-RAY DIFFRACTION1allE570
16X-RAY DIFFRACTION1allF570
17X-RAY DIFFRACTION1allG570
18X-RAY DIFFRACTION1allH570
19X-RAY DIFFRACTION1allI570
20X-RAY DIFFRACTION1allJ570
21X-RAY DIFFRACTION1allK1 - 10
22X-RAY DIFFRACTION1allS1 - 504

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