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- PDB-3f5h: Crystal structure of fused docking domains from PikAIII and PikAI... -

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Basic information

Entry
Database: PDB / ID: 3f5h
TitleCrystal structure of fused docking domains from PikAIII and PikAIV of the pikromycin polyketide synthase
ComponentsType I polyketide synthase PikAIII, Type I polyketide synthase PikAIV fusion protein
KeywordsPROTEIN BINDING / docking domain / polyketide synthase / pikromycin / H2-T2
Function / homology
Function and homology information


10-deoxymethynolide synthase / narbonolide synthase / macrolide biosynthetic process / DIM/DIP cell wall layer assembly / fatty acid synthase activity / acyltransferase activity, transferring groups other than amino-acyl groups / phosphopantetheine binding / 3-oxoacyl-[acyl-carrier-protein] synthase activity / fatty acid biosynthetic process / identical protein binding ...10-deoxymethynolide synthase / narbonolide synthase / macrolide biosynthetic process / DIM/DIP cell wall layer assembly / fatty acid synthase activity / acyltransferase activity, transferring groups other than amino-acyl groups / phosphopantetheine binding / 3-oxoacyl-[acyl-carrier-protein] synthase activity / fatty acid biosynthetic process / identical protein binding / plasma membrane / cytoplasm
Similarity search - Function
Polyketide synthase, docking domain superfmaily / Polyketide synthase, thioesterase domain / Thioesterase / Polyketide synthase, docking domain / Erythronolide synthase docking domain / PKS_PP_betabranch / Thioesterase / Thioesterase domain / Polyketide synthase, ketoreductase domain / KR domain ...Polyketide synthase, docking domain superfmaily / Polyketide synthase, thioesterase domain / Thioesterase / Polyketide synthase, docking domain / Erythronolide synthase docking domain / PKS_PP_betabranch / Thioesterase / Thioesterase domain / Polyketide synthase, ketoreductase domain / KR domain / Malonyl-CoA ACP transacylase, ACP-binding / Polyketide synthase, C-terminal extension / Ketoacyl-synthetase C-terminal extension / PKS_KR / Acyl transferase domain superfamily / Acyl transferase / Acyl transferase domain / Acyl transferase domain in polyketide synthase (PKS) enzymes. / Acyl transferase/acyl hydrolase/lysophospholipase / 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 / Alpha/Beta hydrolase fold / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
Narbonolide/10-deoxymethynolide synthase PikA4, module 6 / Narbonolide/10-deoxymethynolide synthase PikA3, module 5
Similarity search - Component
Biological speciesStreptomyces venezuelae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.75 Å
AuthorsBuchholz, T.J. / Geders, T.W. / Bartley, F.E. / Reynolds, K.A. / Smith, J.L. / Sherman, D.H.
CitationJournal: Acs Chem.Biol. / Year: 2009
Title: Structural basis for binding specificity between subclasses of modular polyketide synthase docking domains.
Authors: Buchholz, T.J. / Geders, T.W. / Bartley, F.E. / Reynolds, K.A. / Smith, J.L. / Sherman, D.H.
History
DepositionNov 3, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 27, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 2, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.3Oct 25, 2017Group: Refinement description / Category: software
Revision 1.4Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Type I polyketide synthase PikAIII, Type I polyketide synthase PikAIV fusion protein
B: Type I polyketide synthase PikAIII, Type I polyketide synthase PikAIV fusion protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,2923
Polymers15,2692
Non-polymers231
Water2,720151
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1830 Å2
ΔGint-20 kcal/mol
Surface area9320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.016, 117.944, 41.773
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
DetailsTHE CONTENTS OF THE ASYMMETRIC UNIT IS AN UNNATURAL FUSION OF THE C-TERMINUS OF ONE PROTEIN TO THE N-TERMINUS OF A SECOND PROTEIN. THE BIOLOGICAL ASSEMBLY IS FORMED PARTIALLY THROUGH CRYSTALLOGRAPHIC SYMMETRY. THE RELEVANT BIOLOGICAL ASSEMBLY IS FORMED BY APPLYING THE FOLLOWING TRANSFORMATIONS: RESIDUES 1-34 OF CHAIN A AND RESIDUES 1-37 OF CHAIN B:[X, Y, Z]. RESIDUES 1543-1562 OF CHAIN A:[-X+3/2, -Y+1/2, Z-1/2]. RESIDUES 1543-1562 OF CHAIN B:[-X+3/2, -Y+1/2, Z+1/2].

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Components

#1: Protein Type I polyketide synthase PikAIII, Type I polyketide synthase PikAIV fusion protein


Mass: 7634.411 Da / Num. of mol.: 2
Fragment: C-terminal domain of PikAIII fused to N-terminal domain of PikAIV
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces venezuelae (bacteria) / Strain: ATCC15439 / Gene: pIKAIII, pIKAIV / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9ZGI3, UniProt: Q9ZGI2
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 151 / 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: 2.38 Å3/Da / Density % sol: 48.33 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 20 mM HEPES pH 7.8, 150 mM NaCl, 55% 2-methyl-2,4-pentanediol, 200 mM sodium acetate pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 23-ID-D10.97934
SYNCHROTRONAPS 23-ID-B20.9794
Detector
TypeIDDetectorDateDetails
MARMOSAIC 300 mm CCD1CCDFeb 10, 2008K-B PAIR OF BIOMORPH MIRRORS FOR VERTICAL AND HORIZONTAL FOCUSING
MARMOSAIC 300 mm CCD2CCDApr 21, 2008K-B PAIR OF BIOMORPH MIRRORS FOR VERTICAL AND HORIZONTAL FOCUSING
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1DOUBLE CRYSTAL MONOCHROMATORSINGLE WAVELENGTHMx-ray1
2DOUBLE CRYSTAL MONOCHROMATORSINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.979341
20.97941
ReflectionRedundancy: 5.1 % / Av σ(I) over netI: 15.59 / Number: 36536 / Rmerge(I) obs: 0.123 / Χ2: 0.98 / D res high: 2.8 Å / D res low: 50 Å / Num. obs: 7102 / % possible obs: 100
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
6.035099.910.0910.9485.1
4.796.0310010.0880.9695.1
4.184.7910010.0971.0195.2
3.84.1810010.0970.9765.2
3.533.810010.1111.0475.2
3.323.5310010.1320.9475.1
3.153.3210010.1531.0365.2
3.023.1510010.2051.0025.2
2.93.0210010.2250.9235.1
2.82.910010.2970.9345.1
ReflectionResolution: 1.75→50 Å / Num. all: 15084 / Num. obs: 14954 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 20.3 Å2 / Rmerge(I) obs: 0.069 / Rsym value: 0.069 / Χ2: 0.996 / Net I/σ(I): 15.586
Reflection shellResolution: 1.75→1.81 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.507 / Mean I/σ(I) obs: 2.1 / Num. unique all: 1471 / Rsym value: 0.507 / Χ2: 0.993 / % possible all: 98

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Phasing

PhasingMethod: SAD
Phasing dmFOM : 0.36 / FOM acentric: 0.37 / FOM centric: 0.33 / Reflection: 3089 / Reflection acentric: 2531 / Reflection centric: 558
Phasing dm shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
8.6-34.1970.490.550.421538865
5.4-8.60.340.350.29423316107
4.3-5.40.430.450.37528427101
3.8-4.30.460.470.453043496
3.2-3.80.330.340.26904783121
3-3.20.240.230.355148368

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SOLVE2.13phasing
RESOLVE2.13phasing
REFMACrefinement
PDB_EXTRACT3.006data extraction
HKL-2000data collection
RefinementMethod to determine structure: SAD / Resolution: 1.75→32.76 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.932 / WRfactor Rfree: 0.25 / WRfactor Rwork: 0.206 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.801 / SU B: 2.945 / SU ML: 0.091 / SU R Cruickshank DPI: 0.118 / SU Rfree: 0.123 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.118 / ESU R Free: 0.123 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25 750 5 %RANDOM
Rwork0.201 ---
all0.203 15079 --
obs0.203 14942 99.09 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 63.09 Å2 / Biso mean: 26.546 Å2 / Biso min: 12.69 Å2
Baniso -1Baniso -2Baniso -3
1-3.52 Å20 Å20 Å2
2---1.88 Å20 Å2
3----1.65 Å2
Refinement stepCycle: LAST / Resolution: 1.75→32.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms919 0 1 151 1071
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.021926
X-RAY DIFFRACTIONr_angle_refined_deg1.2162.0011244
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.9585120
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.24122.8353
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.76515198
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8771519
X-RAY DIFFRACTIONr_chiral_restr0.0710.2139
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021707
X-RAY DIFFRACTIONr_mcbond_it0.8021.5573
X-RAY DIFFRACTIONr_mcangle_it1.6522921
X-RAY DIFFRACTIONr_scbond_it3.2113353
X-RAY DIFFRACTIONr_scangle_it5.7594.5317
LS refinement shellResolution: 1.752→1.797 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.258 59 -
Rwork0.281 982 -
all-1041 -
obs--96.39 %

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