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- PDB-6smy: Crystal structure of SLA Reductase YihU from E. Coli with NADH an... -

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Basic information

Entry
Database: PDB / ID: 6smy
TitleCrystal structure of SLA Reductase YihU from E. Coli with NADH and product DHPS
Components3-sulfolactaldehyde reductase
KeywordsOXIDOREDUCTASE / apo / reductase / sulfoquinovose / dihydroxypropanesulfonate
Function / homology
Function and homology information


sulfolactaldehyde 3-reductase / 4-hydroxybutyrate dehydrogenase / 4-hydroxybutyrate dehydrogenase activity / 3-sulfolactaldehyde reductase activity / 6-sulfoquinovose(1-) catabolic process / 6-sulfoquinovose(1-) catabolic process to glycerone phosphate and 3-sulfolactaldehyde / toxin catabolic process / oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor / NAD binding / NADP binding ...sulfolactaldehyde 3-reductase / 4-hydroxybutyrate dehydrogenase / 4-hydroxybutyrate dehydrogenase activity / 3-sulfolactaldehyde reductase activity / 6-sulfoquinovose(1-) catabolic process / 6-sulfoquinovose(1-) catabolic process to glycerone phosphate and 3-sulfolactaldehyde / toxin catabolic process / oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor / NAD binding / NADP binding / protein homotetramerization / protein-containing complex / identical protein binding
Similarity search - Function
3-sulfolactaldehyde reductase / 3-hydroxyisobutyrate dehydrogenase-related, conserved site / 3-hydroxyisobutyrate dehydrogenase signature. / 3-hydroxyisobutyrate dehydrogenase-like, NAD-binding domain / NAD-binding of NADP-dependent 3-hydroxyisobutyrate dehydrogenase / 3-hydroxyisobutyrate dehydrogenase-related / 6-phosphogluconate dehydrogenase, NADP-binding / NAD binding domain of 6-phosphogluconate dehydrogenase / 6-phosphogluconate dehydrogenase, domain 2 / 6-phosphogluconate dehydrogenase-like, C-terminal domain superfamily / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
(2~{S})-2,3-bis(oxidanyl)propane-1-sulfonic acid / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / 3-sulfolactaldehyde reductase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsSharma, M. / Davies, G.J.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Leverhulme TrustRPG-2017-190 United Kingdom
CitationJournal: Acs Catalysis / Year: 2020
Title: Dynamic Structural Changes Accompany the Production of Dihydroxypropanesulfonate by Sulfolactaldehyde Reductase
Authors: Sharma, M. / Abayakoon, P. / Lingford, J.P. / Epa, R. / John, A. / Jin, Y. / Goddard-Borger, E.D. / Davies, G.J. / Williams, S.J.
History
DepositionAug 23, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 12, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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-sulfolactaldehyde reductase
B: 3-sulfolactaldehyde reductase
C: 3-sulfolactaldehyde reductase
D: 3-sulfolactaldehyde reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,0057
Polymers129,0294
Non-polymers9763
Water1,72996
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, SEC-MALS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21530 Å2
ΔGint-191 kcal/mol
Surface area38450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.121, 113.168, 132.393
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11PHEPHEALAALAAA6 - 2946 - 294
21PHEPHEALAALABB6 - 2946 - 294
12ALAALALYSLYSAA2 - 2952 - 295
22ALAALALYSLYSCC2 - 2952 - 295
13ALAALALYSLYSAA2 - 2952 - 295
23ALAALALYSLYSDD2 - 2952 - 295
14PHEPHEALAALABB6 - 2946 - 294
24PHEPHEALAALACC6 - 2946 - 294
15PHEPHEALAALABB6 - 2946 - 294
25PHEPHEALAALADD6 - 2946 - 294
16ALAALALYSLYSCC2 - 2952 - 295
26ALAALALYSLYSDD2 - 2952 - 295

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
3-sulfolactaldehyde reductase / SLA reductase


Mass: 32257.246 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: yihU, b3882, JW3853 / Plasmid: pET28a(+) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0A9V8, sulfolactaldehyde 3-reductase
#2: Chemical ChemComp-LLQ / (2~{S})-2,3-bis(oxidanyl)propane-1-sulfonic acid


Mass: 156.158 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O5S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 96 / 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: 2.04 Å3/Da / Density % sol: 39.58 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: YihU was co-crystallized with 5mM NADH using 0.2 M Ammonium acetate, 0.1 M Bis-Tris pH 6.5, 32% PEG 3,350 as precipitant. The crystal was then soaked with solid DHPS in the mother liquor for ...Details: YihU was co-crystallized with 5mM NADH using 0.2 M Ammonium acetate, 0.1 M Bis-Tris pH 6.5, 32% PEG 3,350 as precipitant. The crystal was then soaked with solid DHPS in the mother liquor for 2 min prior to harvesting into liquid nitrogen without any cryoprotectant.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9159 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jul 14, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9159 Å / Relative weight: 1
ReflectionResolution: 2.45→86.02 Å / Num. obs: 39554 / % possible obs: 100 % / Redundancy: 8.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.067 / Rpim(I) all: 0.025 / Rrim(I) all: 0.071 / Net I/σ(I): 18.2 / Num. measured all: 320728 / Scaling rejects: 416
Reflection shellResolution: 2.45→2.55 Å / Redundancy: 8.2 % / Rmerge(I) obs: 0.207 / Num. unique obs: 4387 / CC1/2: 0.986 / Rpim(I) all: 0.076 / Rrim(I) all: 0.221 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0253refinement
Aimless0.7.4data scaling
PDB_EXTRACT3.25data extraction
xia2data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6SM7

6sm7


Resolution: 2.45→86.02 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.892 / SU B: 9.945 / SU ML: 0.229 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.689 / ESU R Free: 0.311 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2701 1937 4.9 %RANDOM
Rwork0.2302 ---
obs0.2322 37556 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 122.97 Å2 / Biso mean: 42.027 Å2 / Biso min: 15.42 Å2
Baniso -1Baniso -2Baniso -3
1--1.49 Å2-0 Å2-0 Å2
2---2.62 Å20 Å2
3---4.12 Å2
Refinement stepCycle: final / Resolution: 2.45→86.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7846 0 62 96 8004
Biso mean--52.9 33.25 -
Num. residues----1151
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0138022
X-RAY DIFFRACTIONr_bond_other_d0.0010.0177326
X-RAY DIFFRACTIONr_angle_refined_deg1.4231.62310939
X-RAY DIFFRACTIONr_angle_other_deg1.3211.56716828
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.05751142
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.88223.284268
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.606151105
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.7461529
X-RAY DIFFRACTIONr_chiral_restr0.0660.21151
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.029295
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021499
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A67630.08
12B67630.08
21A83040.06
22C83040.06
31A79040.07
32D79040.07
41B68420.08
42C68420.08
51B66890.1
52D66890.1
61C80560.07
62D80560.07
LS refinement shellResolution: 2.45→2.514 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.319 125 -
Rwork0.238 2778 -
all-2903 -
obs--100 %

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