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- PDB-4imp: The missing linker: a dimerization motif located within polyketid... -

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Basic information

Entry
Database: PDB / ID: 4imp
TitleThe missing linker: a dimerization motif located within polyketide synthase modules
ComponentsPolyketide synthase extender modules 3-4
KeywordsTRANSFERASE / dimerization element
Function / homology
Function and homology information


phosphopantetheine binding / antibiotic biosynthetic process / transferase activity / nucleotide binding
Similarity search - Function
Helix Hairpins - #1830 / Rossmann fold - #11460 / Polyketide synthase dimerisation element domain / Polyketide synthase dimerisation element domain / : / Polyketide synthase, docking domain superfmaily / Polyketide synthase, docking domain / Erythronolide synthase docking domain / Polyketide synthase, ketoreductase domain / KR domain ...Helix Hairpins - #1830 / Rossmann fold - #11460 / Polyketide synthase dimerisation element domain / Polyketide synthase dimerisation element domain / : / Polyketide synthase, docking domain superfmaily / Polyketide synthase, docking domain / Erythronolide synthase docking domain / Polyketide synthase, ketoreductase domain / KR domain / Polyketide synthase, C-terminal extension / Ketoacyl-synthetase C-terminal extension / Malonyl-CoA ACP transacylase, ACP-binding / Acyl transferase domain superfamily / Acyl transferase / Acyl transferase domain / Acyl transferase domain in polyketide synthase (PKS) enzymes. / Acyl transferase/acyl hydrolase/lysophospholipase / Polyketide synthase, phosphopantetheine-binding domain / Phosphopantetheine attachment site / Helix Hairpins / 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 / Phosphopantetheine attachment site / Phosphopantetheine attachment site. / Thiolase-like / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / Helix non-globular / Special / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-NDP / Acyl transferase domain-containing protein
Similarity search - Component
Biological speciesSaccharopolyspora spinosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.57 Å
AuthorsZheng, J. / Keatinge-Clay, A.T.
CitationJournal: Acs Chem.Biol. / Year: 2013
Title: The missing linker: a dimerization motif located within polyketide synthase modules.
Authors: Zheng, J. / Fage, C.D. / Demeler, B. / Hoffman, D.W. / Keatinge-Clay, A.T.
History
DepositionJan 3, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 27, 2013Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2013Group: Structure summary
Revision 1.2Nov 20, 2013Group: Database references
Revision 1.3Feb 26, 2014Group: Database references
Revision 1.4Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Polyketide synthase extender modules 3-4
B: Polyketide synthase extender modules 3-4
C: Polyketide synthase extender modules 3-4
D: Polyketide synthase extender modules 3-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)249,3808
Polymers246,3984
Non-polymers2,9824
Water66737
1
A: Polyketide synthase extender modules 3-4
B: Polyketide synthase extender modules 3-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,6904
Polymers123,1992
Non-polymers1,4912
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4460 Å2
ΔGint-27 kcal/mol
Surface area41300 Å2
MethodPISA
2
C: Polyketide synthase extender modules 3-4
D: Polyketide synthase extender modules 3-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,6904
Polymers123,1992
Non-polymers1,4912
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4470 Å2
ΔGint-27 kcal/mol
Surface area42130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.815, 211.690, 101.742
Angle α, β, γ (deg.)90.00, 95.26, 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:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010A924 - 1440
2010B924 - 1440
1020A923 - 1440
2020C923 - 1440
1030A925 - 1440
2030D925 - 1440
1040B924 - 1440
2040C924 - 1440
1050B925 - 1441
2050D925 - 1441
1060C925 - 1441
2060D925 - 1441

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
Polyketide synthase extender modules 3-4


Mass: 61599.574 Da / Num. of mol.: 4 / Fragment: dimerization element
Source method: isolated from a genetically manipulated source
Details: SpnC residues 913-1471 / Source: (gene. exp.) Saccharopolyspora spinosa (bacteria) / Strain: NRRL 18395 / Gene: spnC / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9ALM4
#2: Chemical
ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Nicotinamide adenine dinucleotide phosphate


Mass: 745.421 Da / Num. of mol.: 4 / Fragment: ketoreductase / Source method: obtained synthetically / Formula: C21H30N7O17P3 / References: 3-oxoacyl-[acyl-carrier-protein] reductase
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 37 / 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: 2.47 Å3/Da / Density % sol: 50.26 %
Crystal growTemperature: 293 K / pH: 6
Details: 15 % (w/v) polyethylene glycol 3350, 0.2 M magnesium acetate, 30% glycerol (v/v), pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 25, 2012
RadiationMonochromator: DOUBLE-CRYSTAL, SI(111) LIQUID N2 COOLED / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.57→50 Å / Num. obs: 73458 / % possible obs: 98.2 % / Observed criterion σ(I): 2 / Redundancy: 3.5 % / Biso Wilson estimate: 60.9 Å2 / Rmerge(I) obs: 0.056 / Net I/σ(I): 20.3
Reflection shellResolution: 2.6→2.64 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.555 / Mean I/σ(I) obs: 2.7 / % possible all: 97.5

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASESphasing
REFMAC5.6.0117refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3MJS

3mjs


Resolution: 2.57→50 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.933 / SU B: 9.991 / SU ML: 0.219 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R: 0.844 / ESU R Free: 0.309 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.245 3670 5 %RANDOM
Rwork0.204 ---
obs0.206 69297 96.2 %-
all-74822 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 64.65 Å2
Baniso -1Baniso -2Baniso -3
1--0.35 Å20 Å2-2.56 Å2
2---2.43 Å2-0 Å2
3---2.31 Å2
Refinement stepCycle: LAST / Resolution: 2.57→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15481 0 192 37 15710
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01915981
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1491.9821812
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.35752067
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.33222.582674
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.656152449
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.52815188
X-RAY DIFFRACTIONr_chiral_restr0.090.22486
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.02112216
X-RAY DIFFRACTIONr_gen_planes_other
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
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)
11A5470.26
12B5470.26
21A5730.3
22C5730.3
31A5590.27
32D5590.27
41B5490.31
42C5490.31
51B5450.3
52D5450.3
61C5600.3
62D5600.3
LS refinement shellResolution: 2.57→2.64 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.295 233 -
Rwork0.27 4099 -
obs--78.28 %

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