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- PDB-3s23: Crystal structure of cerulenin bound Xanthomonas campestri oleA (... -

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Basic information

Entry
Database: PDB / ID: 3s23
TitleCrystal structure of cerulenin bound Xanthomonas campestri oleA (co-crystal) Xe Derivative
Components3-oxoacyl-[ACP] synthase III
KeywordsTRANSFERASE / Non-decarboxylative Claisen Condensation Reaction
Function / homology
Function and homology information


acyl-CoA:acyl-CoA alkyltransferase / secondary metabolite biosynthetic process / 3-oxoacyl-[acyl-carrier-protein] synthase activity / fatty acid biosynthetic process / metal ion binding / cytoplasm
Similarity search - Function
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
Chem-CER / : / XENON / Acyl-CoA:acyl-CoA alkyltransferase
Similarity search - Component
Biological speciesXanthomonas campestris pv. campestris (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.9484 Å
AuthorsGoblirsch, B.R. / Wilmot, C.M.
CitationJournal: Biochemistry / Year: 2012
Title: Crystal Structures of Xanthomonas campestris OleA Reveal Features That Promote Head-to-Head Condensation of Two Long-Chain Fatty Acids.
Authors: Goblirsch, B.R. / Frias, J.A. / Wackett, L.P. / Wilmot, C.M.
History
DepositionMay 16, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 9, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 6, 2012Group: Database references
Revision 1.2Sep 13, 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 / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _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_conn.ptnr2_label_seq_id / _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

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Assembly

Deposited unit
A: 3-oxoacyl-[ACP] synthase III
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,2028
Polymers37,4201
Non-polymers7827
Water2,396133
1
A: 3-oxoacyl-[ACP] synthase III
hetero molecules

A: 3-oxoacyl-[ACP] synthase III
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,40416
Polymers74,8402
Non-polymers1,56414
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+1/31
Buried area7510 Å2
ΔGint-19 kcal/mol
Surface area26030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.027, 90.027, 69.513
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

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Protein , 1 types, 1 molecules A

#1: Protein 3-oxoacyl-[ACP] synthase III


Mass: 37419.961 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xanthomonas campestris pv. campestris (bacteria)
Gene: fabH, XCC0212 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8PDX2

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Non-polymers , 5 types, 140 molecules

#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-CER / (2S, 3R)-3-HYDROXY-4-OXO-7,10-TRANS,TRANS-DODECADIENAMIDE / CERULENIN


Mass: 225.284 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H19NO3 / Comment: antifungal, antibiotic*YM
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-XE / XENON


Mass: 131.293 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Xe
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 133 / 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: 2.17 Å3/Da / Density % sol: 43.4 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 17% PEG 4000, 80 manganese chloride, 100 mM MES pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.03 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 19, 2011
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03 Å / Relative weight: 1
ReflectionResolution: 1.948→50 Å / Num. all: 24115 / Num. obs: 24115 / % possible obs: 99.9 % / Observed criterion σ(F): -3 / Observed criterion σ(I): 0 / Redundancy: 11.1 % / Rmerge(I) obs: 0.058 / Net I/σ(I): 55
Reflection shellResolution: 1.948→1.98 Å / Redundancy: 11.1 % / Rmerge(I) obs: 0.408 / Mean I/σ(I) obs: 7.1 / % possible all: 99.8

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHENIX(phenix.refine: 1.7_650)model building
PHENIX(phenix.refine: 1.7_650)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIX1.7_650phasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 3S21

3s21


Resolution: 1.9484→31.745 Å / SU ML: 0.23 / σ(F): 0 / Phase error: 19.88 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2171 1225 5.16 %
Rwork0.18 --
obs0.1819 23739 98.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 47.763 Å2 / ksol: 0.372 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.0183 Å2-0 Å2-0 Å2
2--0.0183 Å2-0 Å2
3----0.0365 Å2
Refinement stepCycle: LAST / Resolution: 1.9484→31.745 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2532 0 32 133 2697
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082676
X-RAY DIFFRACTIONf_angle_d1.0063637
X-RAY DIFFRACTIONf_dihedral_angle_d13.4241003
X-RAY DIFFRACTIONf_chiral_restr0.071430
X-RAY DIFFRACTIONf_plane_restr0.004469
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9484-2.02640.25341390.20042344X-RAY DIFFRACTION94
2.0264-2.11860.25411300.18732416X-RAY DIFFRACTION96
2.1186-2.23020.22431490.18172470X-RAY DIFFRACTION98
2.2302-2.36990.21781290.18362509X-RAY DIFFRACTION99
2.3699-2.55280.24161460.18112467X-RAY DIFFRACTION99
2.5528-2.80960.21021330.18382530X-RAY DIFFRACTION100
2.8096-3.21580.25911400.17432532X-RAY DIFFRACTION100
3.2158-4.05030.21171350.17362570X-RAY DIFFRACTION100
4.0503-31.74920.1781240.18042676X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 47.9877 Å / Origin y: 0.9476 Å / Origin z: -3.5482 Å
111213212223313233
T0.2112 Å2-0.085 Å20.0508 Å2-0.1405 Å2-0.027 Å2--0.0994 Å2
L1.003 °20.8776 °20.5155 °2-1.9421 °20.901 °2--0.742 °2
S-0.1945 Å °0.2325 Å °-0.0745 Å °-0.3695 Å °0.3105 Å °-0.1648 Å °-0.194 Å °0.1431 Å °0.1151 Å °
Refinement TLS groupSelection details: chain 'A'

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