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- PDB-7w5k: The C296A mutant of L-sorbosone dehydrogenase (SNDH) from Glucono... -

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Basic information

Entry
Database: PDB / ID: 7w5k
TitleThe C296A mutant of L-sorbosone dehydrogenase (SNDH) from Gluconobacter Oxydans WSH-004
ComponentsL-sorbosone dehydrogenase, NAD(P) dependent
KeywordsOXIDOREDUCTASE / L-sorbosone dehydrogenase / NAD(P)+ / C296A
Function / homologyNADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
Function and homology information
Biological speciesGluconobacter oxydans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.22 Å
AuthorsLi, D. / Hou, X.D. / Rao, Y.J. / Zhou, J.W. / Chen, J.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31830068 China
CitationJournal: Adv Sci / Year: 2023
Title: Structural Insight into the Catalytic Mechanisms of an L-Sorbosone Dehydrogenase.
Authors: Li, D. / Deng, Z. / Hou, X. / Qin, Z. / Wang, X. / Yin, D. / Chen, Y. / Rao, Y. / Chen, J. / Zhou, J.
History
DepositionNov 30, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 1, 2023Provider: repository / Type: Initial release
Revision 1.1Dec 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author / struct_ncs_dom_lim
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _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 / _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: L-sorbosone dehydrogenase, NAD(P) dependent
B: L-sorbosone dehydrogenase, NAD(P) dependent
C: L-sorbosone dehydrogenase, NAD(P) dependent
D: L-sorbosone dehydrogenase, NAD(P) dependent
hetero molecules


Theoretical massNumber of molelcules
Total (without water)220,6618
Polymers217,6884
Non-polymers2,9744
Water14,340796
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area25230 Å2
ΔGint-104 kcal/mol
Surface area52730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.305, 117.928, 108.179
Angle α, β, γ (deg.)90.000, 95.140, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 9 through 20 or (resid 21...
21(chain B and (resid 9 through 62 or (resid 63...
31(chain C and (resid 9 through 20 or (resid 21...
41(chain D and (resid 9 through 20 or (resid 21...

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
11SERSERPHEPHE(chain A and (resid 9 through 20 or (resid 21...AA9 - 209 - 20
12ILEILEILEILE(chain A and (resid 9 through 20 or (resid 21...AA2121
13VALVALSERSER(chain A and (resid 9 through 20 or (resid 21...AA8 - 4988 - 498
14VALVALSERSER(chain A and (resid 9 through 20 or (resid 21...AA8 - 4988 - 498
15VALVALSERSER(chain A and (resid 9 through 20 or (resid 21...AA8 - 4988 - 498
16VALVALSERSER(chain A and (resid 9 through 20 or (resid 21...AA8 - 4988 - 498
17VALVALSERSER(chain A and (resid 9 through 20 or (resid 21...AA8 - 4988 - 498
21SERSERARGARG(chain B and (resid 9 through 62 or (resid 63...BB9 - 629 - 62
22ARGARGARGARG(chain B and (resid 9 through 62 or (resid 63...BB6363
23SERSERSERSER(chain B and (resid 9 through 62 or (resid 63...BB9 - 4989 - 498
24SERSERSERSER(chain B and (resid 9 through 62 or (resid 63...BB9 - 4989 - 498
25SERSERSERSER(chain B and (resid 9 through 62 or (resid 63...BB9 - 4989 - 498
26SERSERSERSER(chain B and (resid 9 through 62 or (resid 63...BB9 - 4989 - 498
27SERSERSERSER(chain B and (resid 9 through 62 or (resid 63...BB9 - 4989 - 498
28SERSERSERSER(chain B and (resid 9 through 62 or (resid 63...BB9 - 4989 - 498
29SERSERSERSER(chain B and (resid 9 through 62 or (resid 63...BB9 - 4989 - 498
31SERSERPHEPHE(chain C and (resid 9 through 20 or (resid 21...CC9 - 209 - 20
32ILEILEILEILE(chain C and (resid 9 through 20 or (resid 21...CC2121
33VALVALGLUGLU(chain C and (resid 9 through 20 or (resid 21...CC8 - 4898 - 489
34VALVALGLUGLU(chain C and (resid 9 through 20 or (resid 21...CC8 - 4898 - 489
35VALVALGLUGLU(chain C and (resid 9 through 20 or (resid 21...CC8 - 4898 - 489
36VALVALGLUGLU(chain C and (resid 9 through 20 or (resid 21...CC8 - 4898 - 489
37VALVALGLUGLU(chain C and (resid 9 through 20 or (resid 21...CC8 - 4898 - 489
38VALVALGLUGLU(chain C and (resid 9 through 20 or (resid 21...CC8 - 4898 - 489
41SERSERPHEPHE(chain D and (resid 9 through 20 or (resid 21...DD9 - 209 - 20
42ILEILEILEILE(chain D and (resid 9 through 20 or (resid 21...DD2121
43SERSERGLUGLU(chain D and (resid 9 through 20 or (resid 21...DD9 - 4899 - 489
44SERSERGLUGLU(chain D and (resid 9 through 20 or (resid 21...DD9 - 4899 - 489
45SERSERGLUGLU(chain D and (resid 9 through 20 or (resid 21...DD9 - 4899 - 489
46SERSERGLUGLU(chain D and (resid 9 through 20 or (resid 21...DD9 - 4899 - 489
47SERSERGLUGLU(chain D and (resid 9 through 20 or (resid 21...DD9 - 4899 - 489

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Components

#1: Protein
L-sorbosone dehydrogenase, NAD(P) dependent


Mass: 54421.938 Da / Num. of mol.: 4 / Mutation: C296A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gluconobacter oxydans (bacteria) / Strain: WSH-004 / Production host: Escherichia coli (E. coli)
#2: Chemical
ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE / Nicotinamide adenine dinucleotide phosphate


Mass: 743.405 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H28N7O17P3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 796 / 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: 2.34 Å3/Da / Density % sol: 47.52 %
Crystal growTemperature: 290.15 K / Method: vapor diffusion, sitting drop / Details: cholride hexahydrate, Tris, Polyvinyplyrrolidone

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NFPSS / Beamline: BL17B / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 X 1M / Detector: PIXEL / Date: Jul 3, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.21→50 Å / Num. obs: 96495 / % possible obs: 97.7 % / Redundancy: 6.6 % / Biso Wilson estimate: 32.08 Å2 / Rmerge(I) obs: 0.132 / Rpim(I) all: 0.055 / Rrim(I) all: 0.143 / Χ2: 0.976 / Net I/σ(I): 4.6 / Num. measured all: 634227
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.21-2.255.40.51442580.8540.2250.5620.96485.9
2.25-2.295.70.48543480.880.2070.5290.98489
2.29-2.335.80.44345120.9020.1880.4830.97491.7
2.33-2.385.90.42346380.910.180.4610.97494.9
2.38-2.436.20.448130.9160.1690.4350.97697.8
2.43-2.496.50.39248930.9320.1630.4260.97499.2
2.49-2.556.70.35148730.9480.1450.380.99299.8
2.55-2.626.80.34149290.9510.1390.3680.98599.8
2.62-2.76.80.29949470.9620.1230.3240.98699.8
2.7-2.786.40.27448950.9620.1170.2990.97999.8
2.78-2.886.30.21948690.9770.0940.2380.9999
2.88-37.20.18349560.9860.0730.1971.02299.9
3-3.147.20.15549060.9880.0610.1661.02399.8
3.14-3.37.20.12749330.9910.0510.1371.0299.8
3.3-3.517.10.10349030.9940.0410.1111.00799.8
3.51-3.7870.08449720.9960.0340.0911.01199.8
3.78-4.166.20.07249020.9960.0310.0791.00699.3
4.16-4.767.10.06249450.9970.0250.0670.94799.9
4.76-67.10.06549650.9970.0260.070.84199.8
6-506.60.05250380.9980.0210.0560.85599.4

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
PDB_EXTRACTdata extraction
HKL-3000data reduction
HKL-3000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.22→33.58 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 21.78 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2043 4712 5.12 %
Rwork0.1648 87294 -
obs0.1668 92006 92.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 87.81 Å2 / Biso mean: 35.2413 Å2 / Biso min: 18.1 Å2
Refinement stepCycle: final / Resolution: 2.22→33.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14669 0 192 796 15657
Biso mean--38.29 35.48 -
Num. residues----1943
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A5860X-RAY DIFFRACTION6.758TORSIONAL
12B5860X-RAY DIFFRACTION6.758TORSIONAL
13C5860X-RAY DIFFRACTION6.758TORSIONAL
14D5860X-RAY DIFFRACTION6.758TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.22-2.240.2503900.21221627171752
2.24-2.270.28321280.21292285241373
2.27-2.30.27891090.21112340244974
2.3-2.330.25341220.20972371249376
2.33-2.360.25551340.20922490262479
2.36-2.390.26361440.20892515265981
2.39-2.420.27991620.20012644280685
2.42-2.460.25121460.20162814296089
2.46-2.50.27151300.19842874300492
2.5-2.540.24081670.19222928309594
2.54-2.580.22921610.18543008316996
2.58-2.630.27161570.18963082323999
2.63-2.680.21331710.19093107327899
2.68-2.730.251570.18563115327299
2.73-2.790.21981640.194431043268100
2.79-2.860.23471800.18833123330399
2.86-2.930.21781560.181431073263100
2.93-3.010.23662020.179131123314100
3.01-3.10.2261540.168931293283100
3.1-3.20.22191700.163231353305100
3.2-3.310.21161660.163831283294100
3.31-3.440.21461800.163331113291100
3.45-3.60.19441540.155231613315100
3.6-3.790.18451640.151531553319100
3.79-4.030.18891600.140831443304100
4.03-4.340.14331760.13033109328599
4.34-4.770.14861940.124631343328100
4.77-5.460.18121540.151231703324100
5.46-6.870.20731990.174131353334100
6.87-33.580.16741610.15073137329897

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