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- PDB-3s21: Crystal structure of cerulenin bound Xanthomonas campestri OleA (... -

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Basic information

Entry
Database: PDB / ID: 3s21
TitleCrystal structure of cerulenin bound Xanthomonas campestri OleA (co-crystal)
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 / : / Acyl-CoA:acyl-CoA alkyltransferase
Similarity search - Component
Biological speciesXanthomonas campestris pv. campestris (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7001 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)37,8845
Polymers37,4201
Non-polymers4644
Water3,963220
1
A: 3-oxoacyl-[ACP] synthase III
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)75,76910
Polymers74,8402
Non-polymers9298
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+1/31
Buried area6500 Å2
ΔGint-7 kcal/mol
Surface area26460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.516, 90.516, 69.793
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

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


Mass: 54.938 Da / Num. of mol.: 1 / 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: 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 220 / 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: 2.21 Å3/Da / Density % sol: 44.23 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 16% PEG 4000, 80 mM 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-B / Wavelength: 1.03 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Nov 5, 2010
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: 1.7→50 Å / Num. all: 36644 / Num. obs: 36296 / % possible obs: 99 % / Observed criterion σ(F): -3 / Observed criterion σ(I): 0 / Redundancy: 7.4 % / Rmerge(I) obs: 0.044 / Net I/σ(I): 44.5
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.445 / Mean I/σ(I) obs: 5 / % possible all: 100

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
PHENIX(phenix.refine: 1.7_650)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3ROW

3row


Resolution: 1.7001→27.635 Å / SU ML: 0.18 / σ(F): 1.35 / Phase error: 19.95 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2092 1852 5.1 %
Rwork0.1779 --
obs0.1795 36294 99.04 %
all-36294 -
Solvent computationShrinkage radii: 0.49 Å / VDW probe radii: 0.8 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 72.003 Å2 / ksol: 0.402 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.3265 Å20 Å20 Å2
2---0.3265 Å20 Å2
3---0.653 Å2
Refinement stepCycle: LAST / Resolution: 1.7001→27.635 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2532 0 29 220 2781
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072670
X-RAY DIFFRACTIONf_angle_d1.0133627
X-RAY DIFFRACTIONf_dihedral_angle_d11.959999
X-RAY DIFFRACTIONf_chiral_restr0.068429
X-RAY DIFFRACTIONf_plane_restr0.005467
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7001-1.74610.25171300.22392646X-RAY DIFFRACTION100
1.7461-1.79740.2431310.20542640X-RAY DIFFRACTION100
1.7974-1.85540.2361540.20112615X-RAY DIFFRACTION100
1.8554-1.92170.2661270.18672682X-RAY DIFFRACTION100
1.9217-1.99860.18651450.18662654X-RAY DIFFRACTION100
1.9986-2.08960.21151680.18132593X-RAY DIFFRACTION100
2.0896-2.19970.20191390.18242679X-RAY DIFFRACTION100
2.1997-2.33750.20551520.18242632X-RAY DIFFRACTION99
2.3375-2.51780.23271510.18932645X-RAY DIFFRACTION99
2.5178-2.7710.19551410.18482671X-RAY DIFFRACTION99
2.771-3.17150.2111500.17112629X-RAY DIFFRACTION98
3.1715-3.99380.2031360.16342657X-RAY DIFFRACTION98
3.9938-27.6390.19991280.17192699X-RAY DIFFRACTION95
Refinement TLS params.Method: refined / Origin x: 48.2951 Å / Origin y: 0.9646 Å / Origin z: -3.5817 Å
111213212223313233
T0.1812 Å2-0.062 Å20.0278 Å2-0.143 Å2-0.0165 Å2--0.1164 Å2
L0.8708 °20.7492 °20.4357 °2-1.7155 °20.7992 °2--1.0274 °2
S-0.1478 Å °0.1988 Å °-0.0453 Å °-0.241 Å °0.2471 Å °-0.1183 Å °-0.136 Å °0.1628 Å °0.0367 Å °
Refinement TLS groupSelection details: chain 'A'

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