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- PDB-8kem: PKS domains-fused AmpC EC2 -

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Basic information

Entry
Database: PDB / ID: 8kem
TitlePKS domains-fused AmpC EC2
ComponentsSDR family NAD(P)-dependent oxidoreductase,Beta-lactamase
KeywordsPROTEIN BINDING / trans-AT PKS docking domain / Macrolactin / fusion protein
Function / homology
Function and homology information


DIM/DIP cell wall layer assembly / secondary metabolite biosynthetic process / fatty acid synthase activity / phosphopantetheine binding / 3-oxoacyl-[acyl-carrier-protein] synthase activity / antibiotic catabolic process / fatty acid biosynthetic process / beta-lactamase activity / beta-lactamase / outer membrane-bounded periplasmic space ...DIM/DIP cell wall layer assembly / secondary metabolite biosynthetic process / fatty acid synthase activity / phosphopantetheine binding / 3-oxoacyl-[acyl-carrier-protein] synthase activity / antibiotic catabolic process / fatty acid biosynthetic process / beta-lactamase activity / beta-lactamase / outer membrane-bounded periplasmic space / response to antibiotic / plasma membrane / cytoplasm
Similarity search - Function
: / Beta-ketoacyl synthase-like, N-terminal / : / : / Polyketide synthase dehydratase domain / Thiolase, acyl-enzyme intermediate active site / Thiolases acyl-enzyme intermediate signature. / : / Polyketide and metazoan fatty acid synthase dehydratase (PKS/mFAS DH) domain profile. / PKS_PP_betabranch ...: / Beta-ketoacyl synthase-like, N-terminal / : / : / Polyketide synthase dehydratase domain / Thiolase, acyl-enzyme intermediate active site / Thiolases acyl-enzyme intermediate signature. / : / Polyketide and metazoan fatty acid synthase dehydratase (PKS/mFAS DH) domain profile. / PKS_PP_betabranch / Polyketide synthase dehydratase N-terminal domain / PKS_DH / Polyketide synthase, dehydratase domain / Polyketide synthase, dehydratase domain superfamily / Beta-lactamase, class-C active site / Beta-lactamase class-C active site. / Polyketide synthase, ketoreductase domain / KR domain / Polyketide synthase, C-terminal extension / Ketoacyl-synthetase C-terminal extension / Beta-lactamase-related / Beta-lactamase / PKS_KR / Ketosynthase family 3 (KS3) domain profile. / Polyketide synthase, phosphopantetheine-binding domain / Phosphopantetheine attachment site / Beta-ketoacyl synthase / Beta-ketoacyl synthase, active site / Ketosynthase family 3 (KS3) active site signature. / Polyketide synthase, beta-ketoacyl synthase domain / Beta-ketoacyl synthase, N-terminal / Beta-ketoacyl synthase, C-terminal / Beta-ketoacyl synthase, N-terminal domain / Beta-ketoacyl synthase, C-terminal domain / Thiolase-like / Phosphopantetheine attachment site / Phosphopantetheine attachment site. / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / Beta-lactamase/transpeptidase-like / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
SDR family NAD(P)-dependent oxidoreductase / SDR family NAD(P)-dependent oxidoreductase / Beta-lactamase
Similarity search - Component
Biological speciesBacillus amyloliquefaciens (bacteria)
Escherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.76998285856 Å
AuthorsSon, S.Y. / Bae, D.W. / Cha, S.S.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Structure / Year: 2024
Title: Structural investigation of the docking domain assembly from trans-AT polyketide synthases.
Authors: Son, S.Y. / Bae, D.W. / Kim, E. / Jeong, B.G. / Kim, M.Y. / Youn, S.Y. / Yi, S. / Kim, G. / Hahn, J.S. / Lee, N.K. / Yoon, Y.J. / Cha, S.S.
History
DepositionAug 12, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 5, 2024Provider: repository / Type: Initial release
Revision 1.1Jul 3, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SDR family NAD(P)-dependent oxidoreductase,Beta-lactamase
B: SDR family NAD(P)-dependent oxidoreductase,Beta-lactamase
C: SDR family NAD(P)-dependent oxidoreductase,Beta-lactamase


Theoretical massNumber of molelcules
Total (without water)142,1063
Polymers142,1063
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron density map
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2260 Å2
ΔGint-11 kcal/mol
Surface area50710 Å2
Unit cell
Length a, b, c (Å)108.470, 248.860, 153.700
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
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
11METMETPROPRO(chain A and (resseq 32:33 or (resid 34 and (name...AA32 - 3732 - 37
12GLNGLNVALVAL(chain A and (resseq 32:33 or (resid 34 and (name...AA39 - 4439 - 44
13ARGARGGLNGLN(chain A and (resseq 32:33 or (resid 34 and (name...AA46 - 5546 - 55
14ILEILEGLNGLN(chain A and (resseq 32:33 or (resid 34 and (name...AA57 - 6757 - 67
15PROPROTHRTHR(chain A and (resseq 32:33 or (resid 34 and (name...AA70 - 12970 - 129
16GLNGLNTRPTRP(chain A and (resseq 32:33 or (resid 34 and (name...AA132 - 170132 - 170
17PROPROASPASP(chain A and (resseq 32:33 or (resid 34 and (name...AA172 - 277172 - 277
18THRTHRASNASN(chain A and (resseq 32:33 or (resid 34 and (name...AA279 - 321279 - 321
19ILEILEGLYGLY(chain A and (resseq 32:33 or (resid 34 and (name...AA323 - 394323 - 394
210METMETPROPRO(chain B and (resseq 32:33 or (resid 34 and (name...BB32 - 3732 - 37
211GLNGLNVALVAL(chain B and (resseq 32:33 or (resid 34 and (name...BB39 - 4439 - 44
212ARGARGGLNGLN(chain B and (resseq 32:33 or (resid 34 and (name...BB46 - 5546 - 55
213ILEILEGLNGLN(chain B and (resseq 32:33 or (resid 34 and (name...BB57 - 6757 - 67
214PROPROTHRTHR(chain B and (resseq 32:33 or (resid 34 and (name...BB70 - 12970 - 129
215GLNGLNTRPTRP(chain B and (resseq 32:33 or (resid 34 and (name...BB132 - 170132 - 170
216PROPROASPASP(chain B and (resseq 32:33 or (resid 34 and (name...BB172 - 277172 - 277
217THRTHRASNASN(chain B and (resseq 32:33 or (resid 34 and (name...BB279 - 321279 - 321
218ILEILEGLYGLY(chain B and (resseq 32:33 or (resid 34 and (name...BB323 - 394323 - 394

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Components

#1: Protein SDR family NAD(P)-dependent oxidoreductase,Beta-lactamase


Mass: 47368.711 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus amyloliquefaciens (bacteria), (gene. exp.) Escherichia coli (E. coli)
Gene: RBAM_014350, ampC, RBAM_014340 / Production host: Escherichia coli (E. coli)
References: UniProt: A7Z472, UniProt: B7SNP8, UniProt: A7Z471, beta-lactamase

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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: 3.86 Å3/Da / Density % sol: 68.17 %
Crystal growTemperature: 295 K / Method: microbatch
Details: 20mM MgCl2, 100mM sodium citrate/citric acid, and 40% polyethylene glycol 400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Mar 16, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.76998285856→30 Å / Num. obs: 53091 / % possible obs: 99.8 % / Redundancy: 13.9 % / Biso Wilson estimate: 80.2579496529 Å2 / CC1/2: 0.999 / Net I/σ(I): 15.6
Reflection shellResolution: 2.77→2.84 Å / Num. unique obs: 3749 / CC1/2: 0.753

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Processing

Software
NameVersionClassification
phenix.refine1.10.1_2155refinement
PHENIX1.10.1_2155refinement
PHASERphasing
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.76998285856→29.3686176065 Å / SU ML: 0.471870143529 / Cross valid method: FREE R-VALUE / σ(F): 1.35607744589 / Phase error: 29.2528528513
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.265517589743 2655 5.00122440522 %
Rwork0.228881857788 50432 -
obs0.230729608144 53087 99.9472841947 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 78.9844387744 Å2
Refinement stepCycle: LAST / Resolution: 2.76998285856→29.3686176065 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9464 0 0 0 9464
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00248121986689712
X-RAY DIFFRACTIONf_angle_d0.60940824990913261
X-RAY DIFFRACTIONf_chiral_restr0.04285337126281452
X-RAY DIFFRACTIONf_plane_restr0.004894594325191723
X-RAY DIFFRACTIONf_dihedral_angle_d13.04042154685729
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.77-2.82030.4110180620441360.3757575339792583X-RAY DIFFRACTION99.8897869214
2.8203-2.87450.3692181876061380.3368213837992620X-RAY DIFFRACTION99.9637549837
2.8745-2.93310.3695628888151390.3175781584952645X-RAY DIFFRACTION99.9640933573
2.9331-2.99690.3914856642961380.3167997754772619X-RAY DIFFRACTION99.9637418419
2.9969-3.06650.3140809126331370.2959318938252610X-RAY DIFFRACTION99.9636098981
3.0665-3.14310.365338619851400.2846807447412642X-RAY DIFFRACTION99.964067553
3.1431-3.2280.3084750689221380.2669571491682633X-RAY DIFFRACTION100
3.228-3.32280.320124371571400.2775115062512650X-RAY DIFFRACTION99.9283667622
3.3228-3.42990.3387676785291380.267176730842634X-RAY DIFFRACTION100
3.4299-3.55230.3204873152371390.2511541189892634X-RAY DIFFRACTION100
3.5523-3.69430.2593878431231390.2351847562932652X-RAY DIFFRACTION100
3.6943-3.86210.2797477299471400.2320526040272655X-RAY DIFFRACTION100
3.8621-4.06520.3004372099661390.2331489892082629X-RAY DIFFRACTION100
4.0652-4.31920.2518432773751400.2086770648032661X-RAY DIFFRACTION99.9643112063
4.3192-4.65140.2212257798361410.1943904837782691X-RAY DIFFRACTION100
4.6514-5.11730.1964823330091400.1963075364312661X-RAY DIFFRACTION99.7507122507
5.1173-5.85270.2213079822811420.2118406264862686X-RAY DIFFRACTION99.9293286219
5.8527-7.35460.290585540371420.230398566452709X-RAY DIFFRACTION100
7.3546-29.37030.2185796195911490.1916306260142818X-RAY DIFFRACTION99.731092437

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