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- PDB-5elp: Ketosynthase from module 1 of the bacillaene synthase from Bacill... -

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Basic information

Entry
Database: PDB / ID: 5elp
TitleKetosynthase from module 1 of the bacillaene synthase from Bacillus amyloliquefaciens FZB42
ComponentsNRPS/PKS protein
KeywordsHYDROLASE / trans-AT / 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
Alpha-Beta Plaits - #3290 / : / RhiE-like, KS-MAT linker domain / : / Polyketide synthase dehydratase N-terminal domain / Condensation domain / Condensation domain / Amino acid adenylation domain / Polyketide synthase, dehydratase domain / PKS_DH ...Alpha-Beta Plaits - #3290 / : / RhiE-like, KS-MAT linker domain / : / Polyketide synthase dehydratase N-terminal domain / Condensation domain / Condensation domain / Amino acid adenylation domain / Polyketide synthase, dehydratase domain / PKS_DH / PKS_PP_betabranch / : / Polyketide synthase dehydratase domain / : / Polyketide and metazoan fatty acid synthase dehydratase (PKS/mFAS DH) domain profile. / Polyketide synthase, dehydratase domain superfamily / Ketoacyl-synthetase C-terminal extension / Polyketide synthase, ketoreductase domain / KR domain / ANL, N-terminal domain / : / AMP-binding enzyme C-terminal domain / AMP-binding enzyme, C-terminal domain / AMP-binding, conserved site / Chloramphenicol acetyltransferase-like domain superfamily / Putative AMP-binding domain signature. / Thiolase/Chalcone synthase / Peroxisomal Thiolase; Chain A, domain 1 / AMP-dependent synthetase/ligase / AMP-binding enzyme / Polyketide synthase, phosphopantetheine-binding domain / Phosphopantetheine attachment site / PKS_KR / Beta-ketoacyl synthase / Beta-ketoacyl synthase, active site / Ketosynthase family 3 (KS3) active site signature. / AMP-binding enzyme, C-terminal domain superfamily / 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 / Alpha-Beta Plaits / NAD(P)-binding domain superfamily / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesBacillus amyloliquefaciens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.93 Å
AuthorsWagner, D.T. / Gay, D.C. / Keatinge-Clay, A.T. / Zogzas, C.E.
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 4, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 13, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 2, 2016Group: Database references
Revision 1.2Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_oper_list / struct_conn / struct_ncs_dom_lim
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _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
C: NRPS/PKS protein
A: NRPS/PKS protein
B: NRPS/PKS protein
D: NRPS/PKS protein


Theoretical massNumber of molelcules
Total (without water)273,4874
Polymers273,4874
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1820 Å2
ΔGint3 kcal/mol
Surface area97280 Å2
2
B: NRPS/PKS protein

C: NRPS/PKS protein


Theoretical massNumber of molelcules
Total (without water)136,7442
Polymers136,7442
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_545x,y-1,z1
Buried area4480 Å2
ΔGint-17 kcal/mol
Surface area46560 Å2
MethodPISA
3
A: NRPS/PKS protein

D: NRPS/PKS protein


Theoretical massNumber of molelcules
Total (without water)136,7442
Polymers136,7442
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_556x,y,z+11
Buried area4710 Å2
ΔGint-21 kcal/mol
Surface area43370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.620, 99.950, 100.840
Angle α, β, γ (deg.)91.93, 88.18, 96.04
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11C
21A
12C
22B
13C
23D
14A
24B
15A
25D
16B
26D

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLUGLUPROPROCA9 - 59926 - 616
21GLUGLUPROPROAB9 - 59826 - 616
12TYRTYRLYSLYSCA7 - 60024 - 617
22TYRTYRLYSLYSBC7 - 60024 - 617
13TYRTYRPROPROCA7 - 59924 - 616
23TYRTYRPROPRODD7 - 59924 - 616
14GLUGLULYSLYSAB9 - 59926 - 617
24GLUGLULYSLYSBC9 - 60026 - 617
15GLUGLULYSLYSAB9 - 59926 - 617
25GLUGLULYSLYSDD9 - 60026 - 617
16PROPROLYSLYSBC5 - 60022 - 617
26PROPROLYSLYSDD5 - 60022 - 617

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
NRPS/PKS protein


Mass: 68371.836 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus amyloliquefaciens (bacteria) / Gene: baeJ / Production host: Escherichia coli (E. coli) / References: UniProt: Q1RS73
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: 2.26 Å3/Da / Density % sol: 45.48 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 32% PEG 400 (v/v), 0.2 M MgCl2, 100 mM HEPES, pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jun 5, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.93→99.35 Å / Num. obs: 46279 / % possible obs: 98.7 % / Redundancy: 1.1 % / Net I/σ(I): 15.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0107refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementResolution: 2.93→99.35 Å / Cor.coef. Fo:Fc: 0.874 / Cor.coef. Fo:Fc free: 0.846 / Cross valid method: THROUGHOUT / ESU R Free: 0.552 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.30252 2426 5 %RANDOM
Rwork0.26971 ---
obs0.27139 46279 94.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 60.501 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å2-0 Å2-0.02 Å2
2---0.04 Å2-0.03 Å2
3---0.06 Å2
Refinement stepCycle: LAST / Resolution: 2.93→99.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16749 0 0 0 16749
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.01917144
X-RAY DIFFRACTIONr_bond_other_d00.0216133
X-RAY DIFFRACTIONr_angle_refined_deg2.0941.9623125
X-RAY DIFFRACTIONr_angle_other_deg3.618337368
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.59952135
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.10724.532737
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.93152897
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.5281558
X-RAY DIFFRACTIONr_chiral_restr0.1330.22466
X-RAY DIFFRACTIONr_gen_planes_refined0.010.02119250
X-RAY DIFFRACTIONr_gen_planes_other0.0030.023798
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_it5.4555.9218636
X-RAY DIFFRACTIONr_mcbond_other5.4555.9218635
X-RAY DIFFRACTIONr_mcangle_it8.5498.86410739
X-RAY DIFFRACTIONr_mcangle_other8.5498.86510740
X-RAY DIFFRACTIONr_scbond_it3.8116.2748508
X-RAY DIFFRACTIONr_scbond_other3.8116.2748509
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.279.28212387
X-RAY DIFFRACTIONr_long_range_B_refined11.22749.03520499
X-RAY DIFFRACTIONr_long_range_B_other11.22749.03820499
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)
11C515920.27
12A515920.27
21C512940.28
22B512940.28
31C487040.29
32D487040.29
41A512000.27
42B512000.27
51A493720.28
52D493720.28
61B494640.28
62D494640.28
LS refinement shellResolution: 2.93→3.006 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.377 164 -
Rwork0.359 3213 -
obs--89.72 %

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