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- PDB-7bsx: SDR protein NapW-NADP -

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Basic information

Entry
Database: PDB / ID: 7bsx
TitleSDR protein NapW-NADP
ComponentsShort chain dehydrogenase
KeywordsOXIDOREDUCTASE / SDR / Rossmann / Resistance / NADPH / ANTIBIOTIC
Function / homologyShort-chain dehydrogenase/reductase SDR / NAD(P)-binding domain superfamily / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Short chain dehydrogenase
Function and homology information
Biological speciesStreptomyces lusitanus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsWen, W.H. / Tang, G.L.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31930002 China
Citation
Journal: Nat Commun / Year: 2021
Title: Reductive inactivation of the hemiaminal pharmacophore for resistance against tetrahydroisoquinoline antibiotics.
Authors: Wen, W.H. / Zhang, Y. / Zhang, Y.Y. / Yu, Q. / Jiang, C.C. / Tang, M.C. / Pu, J.Y. / Wu, L. / Zhao, Y.L. / Shi, T. / Zhou, J. / Tang, G.L.
#1: Journal: To Be Published
Title: Structure of NapW-NADP at 2.00 Angstroms resolution
Authors: Wen, W.H. / Tang, G.L.
History
DepositionMar 31, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 6, 2021Provider: repository / Type: Initial release
Revision 1.1Dec 22, 2021Group: Database references / Category: citation / citation_author
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
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._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: Short chain dehydrogenase
B: Short chain dehydrogenase
C: Short chain dehydrogenase
D: Short chain dehydrogenase
E: Short chain dehydrogenase
F: Short chain dehydrogenase
G: Short chain dehydrogenase
H: Short chain dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)295,97416
Polymers290,0278
Non-polymers5,9478
Water29,6891648
1
A: Short chain dehydrogenase
E: Short chain dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,9944
Polymers72,5072
Non-polymers1,4872
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3430 Å2
ΔGint-26 kcal/mol
Surface area23220 Å2
MethodPISA
2
B: Short chain dehydrogenase
hetero molecules

F: Short chain dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,9944
Polymers72,5072
Non-polymers1,4872
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y+1/2,-z1
Buried area3430 Å2
ΔGint-25 kcal/mol
Surface area23130 Å2
MethodPISA
3
C: Short chain dehydrogenase
G: Short chain dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,9944
Polymers72,5072
Non-polymers1,4872
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3430 Å2
ΔGint-25 kcal/mol
Surface area22960 Å2
MethodPISA
4
D: Short chain dehydrogenase
hetero molecules

H: Short chain dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,9944
Polymers72,5072
Non-polymers1,4872
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y+1/2,-z+11
Buried area3430 Å2
ΔGint-25 kcal/mol
Surface area23190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.420, 116.040, 134.760
Angle α, β, γ (deg.)90.000, 90.040, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41
51
61
71
81

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
11ALAALAGLUGLU(chain 'A' and (resid 9 through 228 or resid 230 through 311))AA9 - 22829 - 248
12TRPTRPARGARG(chain 'A' and (resid 9 through 228 or resid 230 through 311))AA230 - 311250 - 331
23ALAALAGLUGLU(chain 'B' and (resid 9 through 228 or resid 230 through 311))BB9 - 22829 - 248
24TRPTRPARGARG(chain 'B' and (resid 9 through 228 or resid 230 through 311))BB230 - 311250 - 331
35ALAALAGLUGLU(chain 'C' and (resid 9 through 228 or resid 230 through 311))CC9 - 22829 - 248
36TRPTRPARGARG(chain 'C' and (resid 9 through 228 or resid 230 through 311))CC230 - 311250 - 331
47ALAALAGLUGLU(chain 'D' and (resid 9 through 228 or resid 230 through 311))DD9 - 22829 - 248
48TRPTRPARGARG(chain 'D' and (resid 9 through 228 or resid 230 through 311))DD230 - 311250 - 331
59ALAALAGLUGLU(chain 'E' and (resid 9 through 228 or resid 230 through 311))EE9 - 22829 - 248
510TRPTRPARGARG(chain 'E' and (resid 9 through 228 or resid 230 through 311))EE230 - 311250 - 331
611ALAALAGLUGLU(chain 'F' and (resid 9 through 228 or resid 230 through 311))FF9 - 22829 - 248
612TRPTRPARGARG(chain 'F' and (resid 9 through 228 or resid 230 through 311))FF230 - 311250 - 331
713ALAALAGLUGLU(chain 'G' and (resid 9 through 228 or resid 230 through 311))GG9 - 22829 - 248
714TRPTRPARGARG(chain 'G' and (resid 9 through 228 or resid 230 through 311))GG230 - 311250 - 331
815ALAALAGLUGLU(chain 'H' and (resid 9 through 228 or resid 230 through 311))HH9 - 22829 - 248
816TRPTRPARGARG(chain 'H' and (resid 9 through 228 or resid 230 through 311))HH230 - 311250 - 331

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Components

#1: Protein
Short chain dehydrogenase


Mass: 36253.398 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces lusitanus (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: S4TKM8
#2: Chemical
ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE / Nicotinamide adenine dinucleotide phosphate


Mass: 743.405 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C21H28N7O17P3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1648 / 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: 3.17 Å3/Da / Density % sol: 61.2 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: Ammonium sulfate, BIS-TRIS propane

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jan 1, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2→58.27 Å / Num. obs: 238915 / % possible obs: 99 % / Redundancy: 6.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.082 / Net I/σ(I): 12.9
Reflection shellResolution: 2→2.05 Å / Rmerge(I) obs: 0.846 / Num. unique obs: 17659 / CC1/2: 0.836

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
xia2data reduction
HKL-3000data scaling
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2QQ5

2qq5


Resolution: 2→58.27 Å / SU ML: 0.216022089303 / Cross valid method: FREE R-VALUE / σ(F): 1.35749297834 / Phase error: 26.2141613512
RfactorNum. reflection% reflection
Rfree0.201680997825 11682 4.89259493485 %
Rwork0.177538099395 --
obs0.178754056467 238769 98.9297789121 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 35.8169175089 Å2
Refinement stepCycle: LAST / Resolution: 2→58.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18685 0 384 1648 20717
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0067733586393819912
X-RAY DIFFRACTIONf_angle_d1.160008749927231
X-RAY DIFFRACTIONf_chiral_restr0.05480716752172989
X-RAY DIFFRACTIONf_plane_restr0.005763182886373479
X-RAY DIFFRACTIONf_dihedral_angle_d19.864150902411614
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.02270.3285499543884100.2726931445657539X-RAY DIFFRACTION99.2136794808
2.0227-2.04650.3052518368453860.257456966447614X-RAY DIFFRACTION99.4282873478
2.0465-2.07150.3095317890573640.2409276285757567X-RAY DIFFRACTION99.4981809058
2.0715-2.09770.2609325581014490.2258141966297479X-RAY DIFFRACTION99.4106583072
2.0977-2.12530.2798211667313540.2241319835577616X-RAY DIFFRACTION99.4013469693
2.1253-2.15440.272362317663960.2209771841037590X-RAY DIFFRACTION99.4025392084
2.1544-2.18520.2539773188153580.2172374218057582X-RAY DIFFRACTION99.2748187047
2.1852-2.21780.253105313544160.2081468535827550X-RAY DIFFRACTION99.1289198606
2.2178-2.25250.2391034113473860.204544547677551X-RAY DIFFRACTION98.9897730107
2.2525-2.28940.2433205527554030.1950895061267552X-RAY DIFFRACTION99.0536670402
2.2894-2.32890.2013516635884030.1931321364227528X-RAY DIFFRACTION98.9519650655
2.3289-2.37120.2267832704092920.2016095141547650X-RAY DIFFRACTION98.7442496581
2.3712-2.41680.2576323557943860.1988947580117557X-RAY DIFFRACTION98.4995039683
2.4168-2.46620.2110541873893460.1877612155447524X-RAY DIFFRACTION98.3872984123
2.4662-2.51980.2144967589383220.1840453447657450X-RAY DIFFRACTION97.2350806956
2.5198-2.57840.206732536663720.1753786518777648X-RAY DIFFRACTION99.5902148268
2.5784-2.64290.2218509919013410.1807611313687657X-RAY DIFFRACTION99.8252621068
2.6429-2.71440.2316741549573700.1772251230767646X-RAY DIFFRACTION99.7511199602
2.7144-2.79420.2206018802244750.1778399521987550X-RAY DIFFRACTION99.6894409938
2.7942-2.88440.2251082442144800.1817723437157506X-RAY DIFFRACTION99.625748503
2.8844-2.98750.2061290499624400.1783223750517632X-RAY DIFFRACTION99.6420195038
2.9875-3.10710.2131231822863410.1872884936227571X-RAY DIFFRACTION99.2224730374
3.1071-3.24850.2038341514824160.1784949651037524X-RAY DIFFRACTION98.4256848891
3.2485-3.41980.1759876129774420.167678338787488X-RAY DIFFRACTION98.022249691
3.4198-3.6340.1655629705063830.1697116571577435X-RAY DIFFRACTION96.8173374613
3.634-3.91450.218939264093640.1617950842727559X-RAY DIFFRACTION98.8151658768
3.9145-4.30830.1696854142334330.1450935047237630X-RAY DIFFRACTION99.4695287441
4.3083-4.93150.1487891575943680.1463865083717662X-RAY DIFFRACTION99.2828882295
4.9315-6.2120.1835509339554030.1676783662287645X-RAY DIFFRACTION98.7605841208
6.212-58.270.1700772297943830.1773921939987585X-RAY DIFFRACTION96.511627907

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