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- PDB-2x3e: Crystal structure of 3-oxoacyl-(acyl carrier protein) synthase II... -

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Basic information

Entry
Database: PDB / ID: 2x3e
TitleCrystal structure of 3-oxoacyl-(acyl carrier protein) synthase III, FabH from Pseudomonas aeruginosa PAO1
Components3-OXOACYL-[ACYL-CARRIER-PROTEIN] SYNTHASE 3
KeywordsTRANSFERASE / HED / ACYLTRANSFERASE / LIPID SYNTHESIS / MULTIFUNCTIONAL ENZYME / FATTY ACID BIOSYNTHESIS
Function / homology
Function and homology information


beta-ketoacyl-[acyl-carrier-protein] synthase III / beta-ketoacyl-acyl-carrier-protein synthase III activity / 3-oxoacyl-[acyl-carrier-protein] synthase activity / fatty acid metabolic process / fatty acid biosynthetic process / cytoplasm
Similarity search - Function
3-oxoacyl-[acyl-carrier-protein] synthase 3 / 3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III / 3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III / 3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III, C-terminal / 3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III C terminal / Thiolase/Chalcone synthase / Peroxisomal Thiolase; Chain A, domain 1 / Thiolase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
3-oxoacyl-[acyl-carrier-protein] synthase 3
Similarity search - Component
Biological speciesPSEUDOMONAS AERUGINOSA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.81 Å
AuthorsOke, M. / Carter, L.G. / Johnson, K.A. / Liu, H. / Mcmahon, S.A. / White, M.F. / Naismith, J.H.
CitationJournal: J.Struct.Funct.Genomics / Year: 2010
Title: The Scottish Structural Proteomics Facility: Targets, Methods and Outputs.
Authors: Oke, M. / Carter, L.G. / Johnson, K.A. / Liu, H. / Mcmahon, S.A. / Yan, X. / Kerou, M. / Weikart, N.D. / Kadi, N. / Sheikh, M.A. / Schmelz, S. / Dorward, M. / Zawadzki, M. / Cozens, C. / ...Authors: Oke, M. / Carter, L.G. / Johnson, K.A. / Liu, H. / Mcmahon, S.A. / Yan, X. / Kerou, M. / Weikart, N.D. / Kadi, N. / Sheikh, M.A. / Schmelz, S. / Dorward, M. / Zawadzki, M. / Cozens, C. / Falconer, H. / Powers, H. / Overton, I.M. / Van Niekerk, C.A.J. / Peng, X. / Patel, P. / Garrett, R.A. / Prangishvili, D. / Botting, C.H. / Coote, P.J. / Dryden, D.T.F. / Barton, G.J. / Schwarz-Linek, U. / Challis, G.L. / Taylor, G.L. / White, M.F. / Naismith, J.H.
History
DepositionJan 24, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 28, 2010Provider: repository / Type: Initial release
Revision 1.1May 7, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 24, 2018Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name ..._entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain / _entity_src_gen.pdbx_host_org_variant
Revision 1.4Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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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 3
B: 3-OXOACYL-[ACYL-CARRIER-PROTEIN] SYNTHASE 3


Theoretical massNumber of molelcules
Total (without water)68,1192
Polymers68,1192
Non-polymers00
Water8,359464
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4680 Å2
ΔGint-39.4 kcal/mol
Surface area21670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.240, 69.240, 212.190
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein 3-OXOACYL-[ACYL-CARRIER-PROTEIN] SYNTHASE 3 / 3-OXOACYL-[ACYL-CARRIER-PROTEIN] SYNTHASE III / BETA-KETOACYL-ACP SYNTHASE III / KAS III / 3- ...3-OXOACYL-[ACYL-CARRIER-PROTEIN] SYNTHASE III / BETA-KETOACYL-ACP SYNTHASE III / KAS III / 3-OXOACYL-ACP SYNTHASE III


Mass: 34059.453 Da / Num. of mol.: 2 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PSEUDOMONAS AERUGINOSA (bacteria) / Strain: PA01 / Plasmid: PDEST14 / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / Variant (production host): C43
References: UniProt: Q9HYR2, beta-ketoacyl-[acyl-carrier-protein] synthase III
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 464 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, CYS 111 TO ALA ENGINEERED RESIDUE IN CHAIN B, CYS 111 TO ALA

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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: 2.2 Å3/Da / Density % sol: 45 % / Description: NONE
Crystal growpH: 4.5
Details: 2.8M DI-AMMONIUM-PHOSPHATE, 0.1M SODIUM CITRATE, PH4.5, 120MM AMMONIUM ACETATE.CRYOPROTECTED WITH 3.6M DI-AMMONIUM-PHOSPHATE, 50MM NACITRATE, PH4.5, 100MM AMMONIUM ACETATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.939
DetectorType: ADSC CCD / Detector: CCD / Date: Jul 4, 2008 / Details: MIRRORS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.939 Å / Relative weight: 1
ReflectionResolution: 1.81→100 Å / Num. obs: 49430 / % possible obs: 99 % / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 0 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 16.9
Reflection shellResolution: 1.81→1.85 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.61 / Mean I/σ(I) obs: 2 / % possible all: 90

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Processing

Software
NameVersionClassification
REFMAC5.5.0090refinement
XDSdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1UB7

1ub7


Resolution: 1.81→213.2 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.935 / SU B: 5.898 / SU ML: 0.082 / Cross valid method: THROUGHOUT / ESU R: 0.133 / ESU R Free: 0.122 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE STRUCTURE IS ONLY ORDERED FROM RESIDUES 3 TO 327 ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE STRUCTURE IS ONLY ORDERED FROM RESIDUES 3 TO 327 ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS.
RfactorNum. reflection% reflectionSelection details
Rfree0.20377 2655 5.1 %RANDOM
Rwork0.16915 ---
obs0.1709 49430 99.15 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 9.929 Å2
Baniso -1Baniso -2Baniso -3
1-0.11 Å20.06 Å2-0 Å2
2--0.11 Å2-0 Å2
3----0.17 Å2
Refinement stepCycle: LAST / Resolution: 1.81→213.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4640 0 0 464 5104
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0214822
X-RAY DIFFRACTIONr_bond_other_d0.0010.023131
X-RAY DIFFRACTIONr_angle_refined_deg1.0781.966590
X-RAY DIFFRACTIONr_angle_other_deg0.81637624
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8825674
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.33822.887194
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.64615728
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.7571545
X-RAY DIFFRACTIONr_chiral_restr0.060.2784
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.025600
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021009
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_it0.3421.53212
X-RAY DIFFRACTIONr_mcbond_other0.0731.51349
X-RAY DIFFRACTIONr_mcangle_it0.64825091
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.12131610
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.8494.51481
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.807→1.854 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.275 194 -
Rwork0.241 3318 -
obs--90.66 %
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)
11.93371.2033-0.37932.9295-0.17710.9827-0.05720.1303-0.2728-0.2715-0.0062-0.10130.166-0.19880.06340.0809-0.0253-0.03020.1012-0.00570.087-15.576-25.473-12.958
21.5928-0.18110.39891.1349-0.12911.27540.0059-0.0422-0.1786-0.1096-0.00060.14680.162-0.2543-0.00540.0653-0.0338-0.00160.0861-0.0140.0679-9.635-26.273-11.724
30.72360.0128-0.1010.77090.00651.1252-0.02630.0081-0.0370.0240.01860.06390.0942-0.0650.00770.0139-0.0091-0.01070.0287-0.00020.0577-7.855-21.147-2.807
41.48850.1913-0.0513.18210.23732.55070.0008-0.0833-0.07610.216-0.08160.23250.0298-0.12270.08080.0376-0.01740.00620.11420.00320.1258-20.9-12.7123.981
51.3659-0.3598-0.18770.90510.05951.2536-0.00840.11350.0604-0.093-0.04340.0766-0.0158-0.22520.05190.0475-0.0237-0.02880.0975-0.00270.1084-22.741-14.912-7.155
61.2337-0.73770.49572.6865-1.90572.37370.02620.13580.0653-0.182-0.05610.02310.0324-0.03280.02990.033-0.0122-0.00430.0564-0.00170.0587-14.47-10.633-5.068
71.1084-0.9628-0.42994.20750.55851.5441-0.084-0.0955-0.19210.16160.01440.20420.360.21250.06960.09170.0403-0.00440.10990.02450.083516.632-30.53111.991
81.3015-0.0989-0.1610.6452-0.06911.22020.0012-0.059-0.16850.016-0.0562-0.05740.2470.19410.0550.08470.0350.01340.04590.03340.077610.58-29.85210.678
90.8699-0.0035-0.07690.5988-0.04261.2483-0.02330.0159-0.0472-0.04480.0225-0.02410.14220.05160.00080.02020.004-0.00390.0270.01410.05359.929-23.5172.528
101.37770.3967-0.36241.67730.2741.0201-0.02250.0394-0.0722-0.105-0.0185-0.10540.06030.19830.0410.02970.012-0.01150.10980.00520.092224.332-17.295-3.599
111.04160.6756-0.38151.67170.11770.9816-0.0278-0.1256-0.00820.1309-0.0039-0.16440.04890.3070.03160.0460.0275-0.02610.12650.02910.120225.729-21.3137.212
121.9891.43161.64883.25783.24854.45970.1098-0.24930.04340.384-0.0717-0.03930.37940.0147-0.03820.04790.0023-0.00520.05950.01680.072218.837-15.0096.084
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 28
2X-RAY DIFFRACTION2A29 - 94
3X-RAY DIFFRACTION3A95 - 216
4X-RAY DIFFRACTION4A217 - 256
5X-RAY DIFFRACTION5A257 - 300
6X-RAY DIFFRACTION6A301 - 327
7X-RAY DIFFRACTION7B3 - 28
8X-RAY DIFFRACTION8B29 - 94
9X-RAY DIFFRACTION9B95 - 216
10X-RAY DIFFRACTION10B217 - 256
11X-RAY DIFFRACTION11B257 - 300
12X-RAY DIFFRACTION12B301 - 322

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