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- PDB-5erb: Ketosynthase from module 5 of the bacillaene synthase from Bacill... -

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Basic information

Entry
Database: PDB / ID: 5erb
TitleKetosynthase from module 5 of the bacillaene synthase from Bacillus amyloliquefaciens FZB42
ComponentsPolyketide synthase
KeywordsTRANSFERASE / Ketosynthase / Polyketide / Bacillaene
Function / homology
Function and homology information


DIM/DIP cell wall layer assembly / fatty acid synthase activity / phosphopantetheine binding / 3-oxoacyl-[acyl-carrier-protein] synthase activity / fatty acid biosynthetic process / plasma membrane / cytoplasm
Similarity search - Function
: / RhiE-like, KS-MAT linker domain / : / Polyketide synthase dehydratase N-terminal domain / Polyketide synthase, dehydratase domain / PKS_DH / : / Polyketide synthase dehydratase domain / PKS_PP_betabranch / Polyketide synthase, dehydratase domain superfamily ...: / RhiE-like, KS-MAT linker domain / : / Polyketide synthase dehydratase N-terminal domain / Polyketide synthase, dehydratase domain / PKS_DH / : / Polyketide synthase dehydratase domain / PKS_PP_betabranch / Polyketide synthase, dehydratase domain superfamily / : / Polyketide and metazoan fatty acid synthase dehydratase (PKS/mFAS DH) domain profile. / Ketoacyl-synthetase C-terminal extension / Polyketide synthase, ketoreductase domain / KR domain / : / Polyketide synthase, phosphopantetheine-binding domain / Phosphopantetheine attachment site / PKS_KR / Beta-ketoacyl synthase, active site / Ketosynthase family 3 (KS3) active site signature. / Beta-ketoacyl synthase / Ketosynthase family 3 (KS3) domain profile. / Beta-ketoacyl synthase, N-terminal / Beta-ketoacyl synthase, C-terminal / Polyketide synthase, beta-ketoacyl synthase domain / 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 / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
Biological speciesBacillus amyloliquefaciens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 4.2 Å
AuthorsWagner, D.T. / Gay, D.C. / Keatinge-Clay, A.T. / Meinke, J.
CitationJournal: J.Struct.Biol. / Year: 2016
Title: The LINKS motif zippers trans-acyltransferase polyketide synthase assembly lines into a biosynthetic megacomplex.
Authors: Gay, D.C. / Wagner, D.T. / Meinke, J.L. / Zogzas, C.E. / Gay, G.R. / Keatinge-Clay, A.T.
History
DepositionNov 13, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 23, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 2, 2016Group: Database references
Revision 1.2Sep 27, 2017Group: Data collection / Database references / Derived calculations
Category: citation / diffrn_detector / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _diffrn_detector.detector / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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: Polyketide synthase
B: Polyketide synthase
C: Polyketide synthase
D: Polyketide synthase


Theoretical massNumber of molelcules
Total (without water)282,3694
Polymers282,3694
Non-polymers00
Water00
1
A: Polyketide synthase
B: Polyketide synthase


Theoretical massNumber of molelcules
Total (without water)141,1852
Polymers141,1852
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5180 Å2
ΔGint-27 kcal/mol
Surface area50140 Å2
MethodPISA
2
C: Polyketide synthase
D: Polyketide synthase


Theoretical massNumber of molelcules
Total (without water)141,1852
Polymers141,1852
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5340 Å2
ΔGint-24 kcal/mol
Surface area50180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.758, 319.132, 103.470
Angle α, β, γ (deg.)90.00, 110.26, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: ARG / Beg label comp-ID: ARG / Refine code: _

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ILEILEAA6 - 61526 - 635
21ILEILEBB6 - 61526 - 635
12ILEILEAA6 - 61526 - 635
22ILEILECC6 - 61526 - 635
13ILEILEAA6 - 61526 - 635
23ILEILEDD6 - 61526 - 635
14ASPASPBB6 - 61626 - 636
24ASPASPCC6 - 61626 - 636
15ASPASPBB6 - 61626 - 636
25ASPASPDD6 - 61626 - 636
16ASPASPCC6 - 61626 - 636
26ASPASPDD6 - 61626 - 636

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
Polyketide synthase


Mass: 70592.352 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus amyloliquefaciens (bacteria) / Gene: baeL / Production host: Escherichia coli (E. coli) / References: UniProt: Q1RS72
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.88 Å3/Da / Density % sol: 68.31 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop
Details: 1.75 uL protein solution (9.9 mg/mL BaeKS5, 150 mM NaCl, 15 mM HEPES, pH 7.5) with 0.5 uL crystallization buffer (1.1 M LiSO4, 0.1 M Tris, pH 8.0)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Jul 2, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 4.2→97.07 Å / Num. obs: 23712 / % possible obs: 79.88 % / Redundancy: 3.2 % / Net I/σ(I): 14.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0107refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementResolution: 4.2→97.07 Å / Cor.coef. Fo:Fc: 0.879 / Cor.coef. Fo:Fc free: 0.825 / Cross valid method: THROUGHOUT / ESU R Free: 1.38 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.34088 1279 5.1 %RANDOM
Rwork0.28843 ---
obs0.29112 23712 79.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 196.373 Å2
Baniso -1Baniso -2Baniso -3
1--0.27 Å2-0 Å20.02 Å2
2--0.21 Å2-0 Å2
3---0.04 Å2
Refinement stepCycle: LAST / Resolution: 4.2→97.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18315 0 0 0 18315
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.01918673
X-RAY DIFFRACTIONr_bond_other_d00.0217698
X-RAY DIFFRACTIONr_angle_refined_deg2.6511.96425180
X-RAY DIFFRACTIONr_angle_other_deg4.064340844
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.28952330
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.3324.655870
X-RAY DIFFRACTIONr_dihedral_angle_3_deg23.353153275
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.58715110
X-RAY DIFFRACTIONr_chiral_restr0.1480.22691
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02121289
X-RAY DIFFRACTIONr_gen_planes_other0.0050.024197
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it12.26619.149389
X-RAY DIFFRACTIONr_mcbond_other12.26619.149388
X-RAY DIFFRACTIONr_mcangle_it20.32428.67111696
X-RAY DIFFRACTIONr_mcangle_other20.32428.67111697
X-RAY DIFFRACTIONr_scbond_it10.64320.3439284
X-RAY DIFFRACTIONr_scbond_other10.64220.3429282
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other17.81130.113484
X-RAY DIFFRACTIONr_long_range_B_refined34.76321276
X-RAY DIFFRACTIONr_long_range_B_other34.76521272
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A564300.2
12B564300.2
21A565140.19
22C565140.19
31A572300.19
32D572300.19
41B570320.19
42C570320.19
51B573640.19
52D573640.19
61C568540.19
62D568540.19
LS refinement shellResolution: 4.2→4.309 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.403 60 -
Rwork0.385 1314 -
obs--59.3 %

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