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- PDB-4f32: Crystal structure of 3-oxoacyl-[acyl-carrier-protein] synthase II... -

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Basic information

Entry
Database: PDB / ID: 4f32
TitleCrystal structure of 3-oxoacyl-[acyl-carrier-protein] synthase II from Burkholderia vietnamiensis in complex with platencin
Components
  • 3-oxoacyl-[acyl-carrier-protein] synthase 2
  • Unknown peptide
KeywordsTransferase/Antibiotic / SSGCID / 3-oxoacyl-[acyl-carrier-protein] synthase II / platencin / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / Transferase-Antibiotic complex
Function / homology
Function and homology information


beta-ketoacyl-[acyl-carrier-protein] synthase II / 3-oxoacyl-[acyl-carrier-protein] synthase activity / fatty acid biosynthetic process / cytosol
Similarity search - Function
3-oxoacyl-[acyl-carrier-protein] synthase 2 / Beta-ketoacyl synthase / Thiolase/Chalcone synthase / Peroxisomal Thiolase; Chain A, domain 1 / Beta-ketoacyl synthase / Beta-ketoacyl synthase, active site / Ketosynthase family 3 (KS3) active site signature. / Ketosynthase family 3 (KS3) domain profile. / Beta-ketoacyl synthase, N-terminal / Beta-ketoacyl synthase, C-terminal ...3-oxoacyl-[acyl-carrier-protein] synthase 2 / Beta-ketoacyl synthase / Thiolase/Chalcone synthase / Peroxisomal Thiolase; Chain A, domain 1 / Beta-ketoacyl synthase / Beta-ketoacyl synthase, active site / Ketosynthase family 3 (KS3) active site signature. / 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 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-N32 / 3-oxoacyl-[acyl-carrier-protein] synthase 2
Similarity search - Component
Biological speciesBurkholderia vietnamiensis (bacteria)
Streptomyces platensis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: Plos One / Year: 2013
Title: Combining functional and structural genomics to sample the essential Burkholderia structome.
Authors: Baugh, L. / Gallagher, L.A. / Patrapuvich, R. / Clifton, M.C. / Gardberg, A.S. / Edwards, T.E. / Armour, B. / Begley, D.W. / Dieterich, S.H. / Dranow, D.M. / Abendroth, J. / Fairman, J.W. / ...Authors: Baugh, L. / Gallagher, L.A. / Patrapuvich, R. / Clifton, M.C. / Gardberg, A.S. / Edwards, T.E. / Armour, B. / Begley, D.W. / Dieterich, S.H. / Dranow, D.M. / Abendroth, J. / Fairman, J.W. / Fox, D. / Staker, B.L. / Phan, I. / Gillespie, A. / Choi, R. / Nakazawa-Hewitt, S. / Nguyen, M.T. / Napuli, A. / Barrett, L. / Buchko, G.W. / Stacy, R. / Myler, P.J. / Stewart, L.J. / Manoil, C. / Van Voorhis, W.C.
History
DepositionMay 8, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 23, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2013Group: Database references
Revision 1.2Feb 12, 2014Group: Structure summary
Revision 1.3Mar 26, 2025Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / 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_conn.pdbx_leaving_atom_flag / _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: 3-oxoacyl-[acyl-carrier-protein] synthase 2
B: 3-oxoacyl-[acyl-carrier-protein] synthase 2
C: Unknown peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,8567
Polymers93,8813
Non-polymers9754
Water14,700816
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6750 Å2
ΔGint-45 kcal/mol
Surface area24670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.490, 100.840, 143.420
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Detailsbiological unit is a dimer, same as the asymmetric unit

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Components

#1: Protein 3-oxoacyl-[acyl-carrier-protein] synthase 2


Mass: 46803.812 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia vietnamiensis (bacteria) / Strain: G4/LMG 22486 / Gene: Bcep1808_4002 / Plasmid: AVA0421 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: A4JL30, beta-ketoacyl-[acyl-carrier-protein] synthase II
#2: Protein/peptide Unknown peptide


Mass: 273.330 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: from a strain of S. platensis, MA7339, recovered from a soil sample collected in Minut II (Mallorca) in Spain, Proc Natl Acad Sci U S A. 2007 May 1;104(18):7612-6
Source: (synth.) Streptomyces platensis (bacteria)
#3: Chemical ChemComp-N32 / 2,4-dihydroxy-3-({3-[(2S,4aS,8S,8aR)-8-methyl-3-methylidene-7-oxo-1,3,4,7,8,8a-hexahydro-2H-2,4a-ethanonaphthalen-8-yl]propanoyl}amino)benzoic acid / Platencin


Mass: 425.474 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H27NO6
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 816 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.14 Å3/Da / Density % sol: 42.61 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop
Details: MD Morpheus a2: 10% PEG 8000, 20% Ethylene glycol, 30mM MgCl2, 30mM CaCl2, 100mM MES/Imidazole 6.5, BuviA.00113.b.A1 PS01317 at 20mg/ml with 1mM Platencin, VAPOR DIFFUSION, SITTING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Apr 3, 2012 / Details: RIGAKU VARIMAX HF
RadiationMonochromator: RIGAKU VARIMAX HF / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. all: 64282 / Num. obs: 63570 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 17.4 % / Biso Wilson estimate: 16.926 Å2 / Rmerge(I) obs: 0.095 / Net I/σ(I): 27.11
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.9-1.956.30.3345.6927540437392.8
1.95-29.80.2699.1542449434595.7
2-2.0612.30.22312.5353460435297.2
2.06-2.1213.60.18915.3458080426799.2
2.12-2.1915.10.17118.1963459419599.8
2.19-2.2716.40.15820.55663484053100
2.27-2.3617.60.14222.97694333940100
2.36-2.4520.10.13825.21760273783100
2.45-2.5621.60.12927.31785993635100
2.56-2.6921.70.11828.83752023469100
2.69-2.8321.70.10630.61720653322100
2.83-321.80.09732.99684033141100
3-3.2121.80.08735.75646962975100
3.21-3.4721.70.07541.55603522780100
3.47-3.821.40.06549.95542742534100
3.8-4.2521.30.05955.61500722350100
4.25-4.9121.30.05655.96438142057100
4.91-6.0121.30.06246.57379201777100
6.01-8.520.90.05746.0829241140099.9
8.518.80.04556.991547382298.9

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3.5 Å19.97 Å
Translation3.5 Å19.97 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER2.3.0phasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
StructureStudiodata collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→50 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.944 / WRfactor Rfree: 0.1538 / WRfactor Rwork: 0.1238 / Occupancy max: 1 / Occupancy min: 0.25 / FOM work R set: 0.9207 / SU B: 4.133 / SU ML: 0.065 / SU R Cruickshank DPI: 0.1249 / SU Rfree: 0.1126 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.125 / ESU R Free: 0.113 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1698 3215 5.1 %RANDOM
Rwork0.1374 ---
obs0.1391 63570 98.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 44.26 Å2 / Biso mean: 10.1563 Å2 / Biso min: 3.08 Å2
Baniso -1Baniso -2Baniso -3
1--0.07 Å20 Å2-0 Å2
2--0.1 Å20 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 1.9→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6069 0 70 816 6955
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0196367
X-RAY DIFFRACTIONr_bond_other_d0.0010.024275
X-RAY DIFFRACTIONr_angle_refined_deg1.5821.9888678
X-RAY DIFFRACTIONr_angle_other_deg0.982310410
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8145881
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.97923.089246
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.79415952
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4491554
X-RAY DIFFRACTIONr_chiral_restr0.0930.2979
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0217375
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021307
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.25 229 -
Rwork0.192 3898 -
all-4127 -
obs--92.24 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.20170.0057-0.02890.26780.09210.36260.0003-0.0150.00520.03570.00060.00750.0102-0.0096-0.00090.00680.00240.0040.00390.00340.0066-16.5140.841-20.871
20.18380.0013-0.0450.26710.01280.2662-0.00560.0195-0.0008-0.02770.0138-0.0163-0.01420.0161-0.00820.0057-0.00350.00330.0051-0.00340.0061-11.152-0.59-50.349
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 422
2X-RAY DIFFRACTION2B0 - 422

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