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- PDB-6smz: Crystal structure of SLA Reductase YihU from E. Coli in complex w... -

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Basic information

Entry
Database: PDB / ID: 6smz
TitleCrystal structure of SLA Reductase YihU from E. Coli in complex with NADH
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 to glycerone phosphate and 3-sulfolactaldehyde / 6-sulfoquinovose(1-) catabolic process / 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 to glycerone phosphate and 3-sulfolactaldehyde / 6-sulfoquinovose(1-) catabolic process / 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 / N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 / N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 ...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 / N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 / N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 / 6-phosphogluconate dehydrogenase, domain 2 / 6-phosphogluconate dehydrogenase-like, C-terminal domain superfamily / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / 3-sulfolactaldehyde reductase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 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
C: 3-sulfolactaldehyde reductase
B: 3-sulfolactaldehyde reductase
D: 3-sulfolactaldehyde reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)131,6838
Polymers129,0294
Non-polymers2,6544
Water14,484804
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, SEC-MALS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area24550 Å2
ΔGint-215 kcal/mol
Surface area38310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.512, 113.743, 142.708
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
21C
12A
22B
13A
23D
14C
24B
15C
25D
16B
26D

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / Refine code: _

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ALAALAAA2 - 2942 - 294
21ALAALACB2 - 2942 - 294
12LYSLYSAA2 - 2952 - 295
22LYSLYSBC2 - 2952 - 295
13ALAALAAA2 - 2942 - 294
23ALAALADD2 - 2942 - 294
14ALAALACB2 - 2942 - 294
24ALAALABC2 - 2942 - 294
15VALVALCB2 - 2962 - 296
25VALVALDD2 - 2962 - 296
16ALAALABC2 - 2942 - 294
26ALAALADD2 - 2942 - 294

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-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


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


Mass: 18.015 Da / Num. of mol.: 804 / 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: 2.28 Å3/Da / Density % sol: 46.07 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: YihU was co-crystallized with 5 mM NADH using 0.2 M Ammonium acetate, 0.1 M Bis-Tris pH 6.5, 25% w/v PEG 3,350 as precipitant.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 1, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.75→88.95 Å / Num. obs: 119505 / % possible obs: 100 % / Redundancy: 8.2 % / CC1/2: 0.998 / Rmerge(I) obs: 0.057 / Rpim(I) all: 0.021 / Rrim(I) all: 0.061 / Net I/σ(I): 18.8 / Num. measured all: 976872 / Scaling rejects: 165
Reflection shellResolution: 1.75→1.78 Å / Redundancy: 8.3 % / Rmerge(I) obs: 0.473 / Num. unique obs: 5864 / CC1/2: 0.954 / Rpim(I) all: 0.172 / Rrim(I) all: 0.504 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0253refinement
Aimless5.8.0253data scaling
PDB_EXTRACT3.25data extraction
xia2data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6SM7

6sm7


Resolution: 1.75→88.95 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.961 / SU B: 2.375 / SU ML: 0.075 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.111 / ESU R Free: 0.103 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2001 5879 4.9 %RANDOM
Rwork0.1766 ---
obs0.1778 113534 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 82.25 Å2 / Biso mean: 27.35 Å2 / Biso min: 15.58 Å2
Baniso -1Baniso -2Baniso -3
1--1.52 Å2-0 Å2-0 Å2
2---1.2 Å20 Å2
3---2.72 Å2
Refinement stepCycle: final / Resolution: 1.75→88.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8403 0 176 804 9383
Biso mean--32.96 37.17 -
Num. residues----1178
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0138757
X-RAY DIFFRACTIONr_bond_other_d0.0010.0178247
X-RAY DIFFRACTIONr_angle_refined_deg1.5921.62611943
X-RAY DIFFRACTIONr_angle_other_deg1.4891.56619066
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.83651190
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.84923.168322
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.173151356
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.1241537
X-RAY DIFFRACTIONr_chiral_restr0.0860.21233
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.029928
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021627
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A87770.06
12C87770.06
21A87670.05
22B87670.05
31A87910.06
32D87910.06
41C87000.06
42B87000.06
51C88110.07
52D88110.07
61B86830.06
62D86830.06
LS refinement shellResolution: 1.75→1.795 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.261 410 -
Rwork0.239 8333 -
all-8743 -
obs--100 %

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