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- PDB-7btm: SDR protein/resistance protein NapW -

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Basic information

Entry
Database: PDB / ID: 7btm
TitleSDR protein/resistance protein NapW
ComponentsShort chain dehydrogenase
KeywordsOXIDOREDUCTASE / SDR / Rossmann / Resistance / NADPH / ANTIBIOTIC
Function / homologyShort-chain dehydrogenase/reductase SDR / NAD(P)-binding domain superfamily / Short chain dehydrogenase
Function and homology information
Biological speciesStreptomyces lusitanus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.08311646214 Å
AuthorsWen, W.H. / Tang, G.L.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31930002 China
CitationJournal: 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.
History
DepositionApr 2, 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


Theoretical massNumber of molelcules
Total (without water)290,0278
Polymers290,0278
Non-polymers00
Water24,8431379
1
A: Short chain dehydrogenase
D: Short chain dehydrogenase


Theoretical massNumber of molelcules
Total (without water)72,5072
Polymers72,5072
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3380 Å2
ΔGint-25 kcal/mol
Surface area22730 Å2
MethodPISA
2
B: Short chain dehydrogenase
C: Short chain dehydrogenase


Theoretical massNumber of molelcules
Total (without water)72,5072
Polymers72,5072
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3400 Å2
ΔGint-24 kcal/mol
Surface area22300 Å2
MethodPISA
3
E: Short chain dehydrogenase

H: Short chain dehydrogenase


Theoretical massNumber of molelcules
Total (without water)72,5072
Polymers72,5072
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_855-x+3,y,-z1
Buried area3340 Å2
ΔGint-27 kcal/mol
Surface area22720 Å2
MethodPISA
4
F: Short chain dehydrogenase

G: Short chain dehydrogenase


Theoretical massNumber of molelcules
Total (without water)72,5072
Polymers72,5072
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_855-x+3,y,-z1
Buried area3310 Å2
ΔGint-25 kcal/mol
Surface area22740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.149, 134.438, 117.216
Angle α, β, γ (deg.)90.000, 90.041, 90.000
Int Tables number3
Space group name H-MP121
Space group name HallP2y
Symmetry operation#1: x,y,z
#2: -x,y,-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
11ALAALAARGARG(chain 'A' and (resid 9 through 49 or resid 60 through 311))AA9 - 4929 - 69
12THRTHRASNASN(chain 'A' and (resid 9 through 49 or resid 60 through 311))AA60 - 10780 - 127
13ASPASPARGARG(chain 'A' and (resid 9 through 49 or resid 60 through 311))AA119 - 311139 - 331
24ALAALAARGARGchain 'B'BB9 - 4929 - 69
25THRTHRASNASNchain 'B'BB60 - 10780 - 127
26ASPASPARGARGchain 'B'BB119 - 311139 - 331
37ALAALAARGARG(chain 'C' and (resid 9 through 108 or resid 120 through 311))CC9 - 4929 - 69
38THRTHRASPASP(chain 'C' and (resid 9 through 108 or resid 120 through 311))CC60 - 10880 - 128
39LYSLYSARGARG(chain 'C' and (resid 9 through 108 or resid 120 through 311))CC120 - 311140 - 331
410ALAALAARGARG(chain 'D' and (resid 9 through 49 or resid 60 through 108 or resid 120 through 311))DD9 - 4929 - 69
411THRTHRASPASP(chain 'D' and (resid 9 through 49 or resid 60 through 108 or resid 120 through 311))DD60 - 10880 - 128
412LYSLYSARGARG(chain 'D' and (resid 9 through 49 or resid 60 through 108 or resid 120 through 311))DD120 - 311140 - 331
513ALAALAARGARG(chain 'E' and (resid 9 through 49 or resid 60 through 108 or resid 120 through 311))EE9 - 4929 - 69
514THRTHRASPASP(chain 'E' and (resid 9 through 49 or resid 60 through 108 or resid 120 through 311))EE60 - 10880 - 128
515LYSLYSARGARG(chain 'E' and (resid 9 through 49 or resid 60 through 108 or resid 120 through 311))EE120 - 311140 - 331
616ALAALAARGARG(chain 'F' and (resid 9 through 49 or resid 60 through 108 or resid 120 through 311))FF9 - 4929 - 69
617THRTHRASPASP(chain 'F' and (resid 9 through 49 or resid 60 through 108 or resid 120 through 311))FF60 - 10880 - 128
618LYSLYSARGARG(chain 'F' and (resid 9 through 49 or resid 60 through 108 or resid 120 through 311))FF120 - 311140 - 331
719ALAALAARGARG(chain 'G' and (resid 9 through 49 or resid 60 through 108 or resid 120 through 311))GG9 - 4929 - 69
720THRTHRASPASP(chain 'G' and (resid 9 through 49 or resid 60 through 108 or resid 120 through 311))GG60 - 10880 - 128
721LYSLYSARGARG(chain 'G' and (resid 9 through 49 or resid 60 through 108 or resid 120 through 311))GG120 - 311140 - 331
822ALAALAARGARG(chain 'H' and (resid 9 through 49 or resid 60 through 108 or resid 120 through 311))HH9 - 4929 - 69
823THRTHRASPASP(chain 'H' and (resid 9 through 49 or resid 60 through 108 or resid 120 through 311))HH60 - 10880 - 128
824LYSLYSARGARG(chain 'H' and (resid 9 through 49 or resid 60 through 108 or resid 120 through 311))HH120 - 311140 - 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1379 / 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: 3.21 Å3/Da / Density % sol: 61.74 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 1.2 M Ammonium sulfate, 0.1 M BIS-TRIS propane, 0.1 M Betaine hydrochloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 12, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 2.08→50 Å / Num. obs: 216044 / % possible obs: 100 % / Redundancy: 6.9 % / CC1/2: 0.99 / Net I/σ(I): 10.778
Reflection shellResolution: 2.08→2.12 Å / Num. unique obs: 10828 / CC1/2: 0.725

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Processing

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

2qq5


Resolution: 2.08311646214→41.3323979114 Å / Cross valid method: FREE R-VALUE / σ(F): 168.656879542 / Phase error: 28.5271919643
RfactorNum. reflection% reflection
Rfree0.249100877677 11084 5.19906938347 %
Rwork0.210211875541 --
obs0.215636045666 213192 98.5139181546 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 22.1661354539 Å2
Refinement stepCycle: LAST / Resolution: 2.08311646214→41.3323979114 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17583 0 0 1379 18962
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092273046059417930
X-RAY DIFFRACTIONf_angle_d0.93030039448324395
X-RAY DIFFRACTIONf_chiral_restr0.05076402301662741
X-RAY DIFFRACTIONf_plane_restr0.007008835743199
X-RAY DIFFRACTIONf_dihedral_angle_d15.407955021810540
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0839-2.11980.3962032018445390.3117500554159180X-RAY DIFFRACTION84.6316953996
2.1198-2.15840.3402225698124940.2820780956529849X-RAY DIFFRACTION91.8236061906
2.1584-2.19980.2833924919565300.28089781935610079X-RAY DIFFRACTION93.1171470806
2.1998-2.24470.3006294757625040.25642288957610087X-RAY DIFFRACTION94.0425135186
2.2447-2.29350.2712676551416410.25488839419310007X-RAY DIFFRACTION92.8465392466
2.2935-2.34680.3016050940735580.24818043656110189X-RAY DIFFRACTION94.1508039179
2.3468-2.40550.2859301159595110.25039202831510169X-RAY DIFFRACTION94.8954833893
2.4055-2.47050.2632418041685180.23514393177710202X-RAY DIFFRACTION94.9288173444
2.4705-2.54310.2399415207155790.22293979690710219X-RAY DIFFRACTION94.3582640813
2.5431-2.62510.2479941507035880.22143489814610123X-RAY DIFFRACTION94.0974158766
2.6251-2.71880.267321157145090.21159236424510214X-RAY DIFFRACTION94.9432980108
2.7188-2.82760.238476890675210.21063643974810188X-RAY DIFFRACTION94.6664188812
2.8276-2.95610.2692338131655970.20553535764610199X-RAY DIFFRACTION94.2693409742
2.9561-3.11170.2439042864265080.20708841361210242X-RAY DIFFRACTION95.0974930362
3.1117-3.30630.2173201359756190.19401464898910182X-RAY DIFFRACTION94.1122100009
3.3063-3.5610.2236704608895130.18937859291110299X-RAY DIFFRACTION94.9216589862
3.561-3.91830.2273824928965150.18010593474610241X-RAY DIFFRACTION94.8240740741
3.9183-4.48290.2146119104176030.17392334558210201X-RAY DIFFRACTION93.9491619083
4.4829-5.63870.2187090517946100.18083721458610117X-RAY DIFFRACTION93.2270549208
5.6387-26.18860.2951593870665220.25515599704610173X-RAY DIFFRACTION92.3558783477

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