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- PDB-6ixj: The crystal structure of sulfoacetaldehyde reductase from Klebsie... -

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Basic information

Entry
Database: PDB / ID: 6ixj
TitleThe crystal structure of sulfoacetaldehyde reductase from Klebsiella oxytoca
ComponentsSulfoacetaldehyde reductase
KeywordsCYTOSOLIC PROTEIN / Sulfoacetaldehyde Reductase / SDR / NADPH
Function / homology
Function and homology information


sulfoacetaldehyde reductase (NADPH) / oxidoreductase activity
Similarity search - Function
short chain dehydrogenase / Short-chain dehydrogenase/reductase, conserved site / Short-chain dehydrogenases/reductases family signature. / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
2-hydroxyethylsulfonic acid / Chem-NDP / Sulfoacetaldehyde reductase
Similarity search - Component
Biological speciesKlebsiella oxytoca (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsZhou, Y. / Xu, T. / Lin, L. / Zhang, Y. / Yuchi, Z.
Funding support China, 1items
OrganizationGrant numberCountry
National Science Foundation (China)31570060 China
CitationJournal: Biochem. J. / Year: 2019
Title: Biochemical and structural investigation of sulfoacetaldehyde reductase fromKlebsiella oxytoca.
Authors: Zhou, Y. / Wei, Y. / Lin, L. / Xu, T. / Ang, E.L. / Zhao, H. / Yuchi, Z. / Zhang, Y.
History
DepositionDec 10, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 13, 2019Provider: repository / Type: Initial release
Revision 1.1Feb 20, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_DOI ..._citation.journal_abbrev / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Mar 13, 2019Group: 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 1.3Nov 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 / 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: Sulfoacetaldehyde reductase
B: Sulfoacetaldehyde reductase
C: Sulfoacetaldehyde reductase
D: Sulfoacetaldehyde reductase
E: Sulfoacetaldehyde reductase
F: Sulfoacetaldehyde reductase
G: Sulfoacetaldehyde reductase
H: Sulfoacetaldehyde reductase
I: Sulfoacetaldehyde reductase
J: Sulfoacetaldehyde reductase
K: Sulfoacetaldehyde reductase
L: Sulfoacetaldehyde reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)340,72436
Polymers330,26612
Non-polymers10,45924
Water4,810267
1
A: Sulfoacetaldehyde reductase
B: Sulfoacetaldehyde reductase
H: Sulfoacetaldehyde reductase
I: Sulfoacetaldehyde reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,57512
Polymers110,0894
Non-polymers3,4868
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22950 Å2
ΔGint-128 kcal/mol
Surface area28890 Å2
MethodPISA
2
F: Sulfoacetaldehyde reductase
J: Sulfoacetaldehyde reductase
K: Sulfoacetaldehyde reductase
hetero molecules

C: Sulfoacetaldehyde reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,57512
Polymers110,0894
Non-polymers3,4868
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_554-y,x-y,z-1/31
Buried area22880 Å2
ΔGint-137 kcal/mol
Surface area28850 Å2
MethodPISA
3
D: Sulfoacetaldehyde reductase
E: Sulfoacetaldehyde reductase
L: Sulfoacetaldehyde reductase
hetero molecules

G: Sulfoacetaldehyde reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,57512
Polymers110,0894
Non-polymers3,4868
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_654-y+1,x-y,z-1/31
Buried area22650 Å2
ΔGint-136 kcal/mol
Surface area29080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)125.856, 125.856, 173.919
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number145
Space group name H-MP32
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 4 through 9 or (resid 10...
21(chain B and (resid 4 through 9 or (resid 10...
31(chain C and (resid 4 through 9 or (resid 10...
41(chain D and (resid 4 through 9 or (resid 10...
51(chain E and (resid 4 through 9 or (resid 10...
61(chain F and (resid 4 through 9 or (resid 10...
71(chain G and (resid 4 through 9 or (resid 10...
81(chain H and (resid 4 through 9 or (resid 10...
91(chain I and (resid 4 through 9 or (resid 10...
101(chain J and (resid 4 through 9 or (resid 10...
111(chain K and (resid 4 through 9 or (resid 10...
121(chain L and (resid 4 through 13 or (resid 14...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11SERSERILEILE(chain A and (resid 4 through 9 or (resid 10...AA4 - 96 - 11
12THRTHRTHRTHR(chain A and (resid 4 through 9 or (resid 10...AA1012
13SERSERASPASP(chain A and (resid 4 through 9 or (resid 10...AA4 - 2546 - 256
21SERSERILEILE(chain B and (resid 4 through 9 or (resid 10...BB4 - 96 - 11
22THRTHRTHRTHR(chain B and (resid 4 through 9 or (resid 10...BB1012
23SERSERASPASP(chain B and (resid 4 through 9 or (resid 10...BB4 - 2546 - 256
24SERSERASPASP(chain B and (resid 4 through 9 or (resid 10...BB4 - 2546 - 256
25SERSERASPASP(chain B and (resid 4 through 9 or (resid 10...BB4 - 2546 - 256
26SERSERASPASP(chain B and (resid 4 through 9 or (resid 10...BB4 - 2546 - 256
31SERSERILEILE(chain C and (resid 4 through 9 or (resid 10...CC4 - 96 - 11
32THRTHRTHRTHR(chain C and (resid 4 through 9 or (resid 10...CC1012
33SERSERARGARG(chain C and (resid 4 through 9 or (resid 10...CC4 - 2536 - 255
41SERSERILEILE(chain D and (resid 4 through 9 or (resid 10...DD4 - 96 - 11
42THRTHRTHRTHR(chain D and (resid 4 through 9 or (resid 10...DD1012
43SERSERASPASP(chain D and (resid 4 through 9 or (resid 10...DD4 - 2546 - 256
44SERSERASPASP(chain D and (resid 4 through 9 or (resid 10...DD4 - 2546 - 256
45SERSERASPASP(chain D and (resid 4 through 9 or (resid 10...DD4 - 2546 - 256
46SERSERASPASP(chain D and (resid 4 through 9 or (resid 10...DD4 - 2546 - 256
51SERSERILEILE(chain E and (resid 4 through 9 or (resid 10...EE4 - 96 - 11
52THRTHRTHRTHR(chain E and (resid 4 through 9 or (resid 10...EE1012
53SERSERASPASP(chain E and (resid 4 through 9 or (resid 10...EE4 - 2546 - 256
54SERSERASPASP(chain E and (resid 4 through 9 or (resid 10...EE4 - 2546 - 256
55SERSERASPASP(chain E and (resid 4 through 9 or (resid 10...EE4 - 2546 - 256
56SERSERASPASP(chain E and (resid 4 through 9 or (resid 10...EE4 - 2546 - 256
61SERSERILEILE(chain F and (resid 4 through 9 or (resid 10...FF4 - 96 - 11
62THRTHRTHRTHR(chain F and (resid 4 through 9 or (resid 10...FF1012
63SERSERASPASP(chain F and (resid 4 through 9 or (resid 10...FF4 - 2546 - 256
64SERSERASPASP(chain F and (resid 4 through 9 or (resid 10...FF4 - 2546 - 256
65SERSERASPASP(chain F and (resid 4 through 9 or (resid 10...FF4 - 2546 - 256
66SERSERASPASP(chain F and (resid 4 through 9 or (resid 10...FF4 - 2546 - 256
71SERSERILEILE(chain G and (resid 4 through 9 or (resid 10...GG4 - 96 - 11
72THRTHRTHRTHR(chain G and (resid 4 through 9 or (resid 10...GG1012
73SERSERASPASP(chain G and (resid 4 through 9 or (resid 10...GG4 - 2546 - 256
74SERSERASPASP(chain G and (resid 4 through 9 or (resid 10...GG4 - 2546 - 256
75SERSERASPASP(chain G and (resid 4 through 9 or (resid 10...GG4 - 2546 - 256
76SERSERASPASP(chain G and (resid 4 through 9 or (resid 10...GG4 - 2546 - 256
81SERSERILEILE(chain H and (resid 4 through 9 or (resid 10...HH4 - 96 - 11
82THRTHRTHRTHR(chain H and (resid 4 through 9 or (resid 10...HH1012
83SERSERASPASP(chain H and (resid 4 through 9 or (resid 10...HH4 - 2546 - 256
91SERSERILEILE(chain I and (resid 4 through 9 or (resid 10...II4 - 96 - 11
92THRTHRTHRTHR(chain I and (resid 4 through 9 or (resid 10...II1012
93SERSERASPASP(chain I and (resid 4 through 9 or (resid 10...II4 - 2546 - 256
94SERSERASPASP(chain I and (resid 4 through 9 or (resid 10...II4 - 2546 - 256
95SERSERASPASP(chain I and (resid 4 through 9 or (resid 10...II4 - 2546 - 256
101SERSERILEILE(chain J and (resid 4 through 9 or (resid 10...JJ4 - 96 - 11
102THRTHRTHRTHR(chain J and (resid 4 through 9 or (resid 10...JJ1012
103SERSERASPASP(chain J and (resid 4 through 9 or (resid 10...JJ4 - 2546 - 256
104SERSERASPASP(chain J and (resid 4 through 9 or (resid 10...JJ4 - 2546 - 256
105SERSERASPASP(chain J and (resid 4 through 9 or (resid 10...JJ4 - 2546 - 256
106SERSERASPASP(chain J and (resid 4 through 9 or (resid 10...JJ4 - 2546 - 256
111SERSERILEILE(chain K and (resid 4 through 9 or (resid 10...KK4 - 96 - 11
112THRTHRTHRTHR(chain K and (resid 4 through 9 or (resid 10...KK1012
113SERSERASPASP(chain K and (resid 4 through 9 or (resid 10...KK4 - 2546 - 256
121SERSERTHRTHR(chain L and (resid 4 through 13 or (resid 14...LL4 - 136 - 15
122SERSERSERSER(chain L and (resid 4 through 13 or (resid 14...LL1416
123SERSERASPASP(chain L and (resid 4 through 13 or (resid 14...LL4 - 2546 - 256

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Components

#1: Protein
Sulfoacetaldehyde reductase / Isethionate formation reductase


Mass: 27522.127 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella oxytoca (bacteria) / Gene: isfD / Production host: Escherichia coli (E. coli)
References: UniProt: D3U1D9, sulfoacetaldehyde reductase (NADPH)
#2: Chemical
ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Nicotinamide adenine dinucleotide phosphate


Mass: 745.421 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C21H30N7O17P3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-8X3 / 2-hydroxyethylsulfonic acid / 2-oxidanylethanesulfonic acid / Isethionic acid


Mass: 126.132 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C2H6O4S / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 267 / 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: 2.4 Å3/Da / Density % sol: 48.79 %
Crystal growTemperature: 298.15 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.2M Ammonium acetate, 0.1M Sodium citrate pH 5.5, 30%(W/V) PEG 4000, 5mM NADPH, 0.4M Isethionate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 29, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 75984 / % possible obs: 100 % / Redundancy: 5.2 % / Rmerge(I) obs: 0.15 / Rpim(I) all: 0.073 / Rrim(I) all: 0.167 / Χ2: 0.547 / Net I/σ(I): 3.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.8-2.855.30.70837850.8150.3410.7870.445100
2.85-2.95.30.65638060.8430.3170.730.443100
2.9-2.965.20.56637780.8770.2740.630.457100
2.96-3.025.20.51637900.8890.2510.5740.464100
3.02-3.085.10.4338190.9210.2120.480.474100
3.08-3.154.80.40838270.910.2090.4590.46100
3.15-3.234.90.36138090.9420.1840.4050.479100
3.23-3.324.90.2937390.9530.1460.3250.499100
3.32-3.425.30.23838550.9750.1140.2640.516100
3.42-3.535.50.21637770.9780.1020.2390.533100
3.53-3.655.40.16937610.9850.080.1870.573100
3.65-3.85.40.14238420.9880.0680.1570.592100
3.8-3.975.30.13438100.9880.0640.1490.599100
3.97-4.185.30.11337960.990.0550.1250.604100
4.18-4.445.10.08837770.9930.0430.0980.60899.9
4.44-4.794.70.07638100.9940.0390.0860.597100
4.79-5.275.10.07538030.9950.0370.0840.575100
5.27-6.035.50.08538080.9950.040.0940.522100
6.03-7.595.30.07437840.9950.0360.0820.525100
7.59-5050.07538080.9880.0380.0850.9899.5

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.14_3247refinement
PDB_EXTRACT3.24data extraction
HKL-3000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2NWQ

2nwq


Resolution: 2.8→37.23 Å / SU ML: 0.41 / Cross valid method: THROUGHOUT / σ(F): 2 / Phase error: 27.15
RfactorNum. reflection% reflection
Rfree0.2397 2006 2.64 %
Rwork0.1937 --
obs0.1949 75913 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 116.1 Å2 / Biso mean: 43.4982 Å2 / Biso min: 10.39 Å2
Refinement stepCycle: final / Resolution: 2.8→37.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22404 0 660 267 23331
Biso mean--44.48 33.17 -
Num. residues----3011
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A9228X-RAY DIFFRACTION13.887TORSIONAL
12B9228X-RAY DIFFRACTION13.887TORSIONAL
13C9228X-RAY DIFFRACTION13.887TORSIONAL
14D9228X-RAY DIFFRACTION13.887TORSIONAL
15E9228X-RAY DIFFRACTION13.887TORSIONAL
16F9228X-RAY DIFFRACTION13.887TORSIONAL
17G9228X-RAY DIFFRACTION13.887TORSIONAL
18H9228X-RAY DIFFRACTION13.887TORSIONAL
19I9228X-RAY DIFFRACTION13.887TORSIONAL
110J9228X-RAY DIFFRACTION13.887TORSIONAL
111K9228X-RAY DIFFRACTION13.887TORSIONAL
112L9228X-RAY DIFFRACTION13.887TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.7979-2.86780.37231500.28965284543499
2.8678-2.94530.32041400.263752185358100
2.9453-3.0320.33131440.248753075451100
3.032-3.12980.32861440.245752745418100
3.1298-3.24160.29261330.232352835416100
3.2416-3.37130.27571460.213852585404100
3.3713-3.52460.25951440.211753175461100
3.5246-3.71030.24691500.195752955445100
3.7103-3.94250.24291400.188852815421100
3.9425-4.24650.23521500.17952455395100
4.2465-4.67310.20081440.156153435487100
4.6731-5.34760.18971440.155852335377100
5.3476-6.73090.20841400.193653045444100
6.7309-37.23290.16861370.154352655402100

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