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- PDB-5vxe: Crystal structure of Xanthomonas campestris OleA E117A bound with... -

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Basic information

Entry
Database: PDB / ID: 5vxe
TitleCrystal structure of Xanthomonas campestris OleA E117A bound with Cerulenin
Components3-oxoacyl-[ACP] synthase III
KeywordsTRANSFERASE / Thiolase / Condensation
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: 1.66 Å
AuthorsJensen, M.R. / Wilmot, C.M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM-008700 United States
CitationJournal: Biochem. J. / Year: 2017
Title: OleA Glu117 is key to condensation of two fatty-acyl coenzyme A substrates in long-chain olefin biosynthesis.
Authors: Jensen, M.R. / Goblirsch, B.R. / Christenson, J.K. / Esler, M.A. / Mohamed, F.A. / Wackett, L.P. / Wilmot, C.M.
History
DepositionMay 23, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 25, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 4, 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
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_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_symmetry

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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)39,1574
Polymers38,7841
Non-polymers3723
Water1,964109
1
A: 3-oxoacyl-[ACP] synthase III
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)78,3138
Polymers77,5692
Non-polymers7456
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z+2/31
Buried area5840 Å2
ΔGint-12 kcal/mol
Surface area26530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.965, 89.965, 69.577
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

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


Mass: 38784.406 Da / Num. of mol.: 1 / Mutation: E117A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xanthomonas campestris pv. campestris (strain ATCC 33913 / DSM 3586 / NCPPB 528 / LMG 568 / P 25) (bacteria)
Strain: ATCC 33913 / DSM 3586 / NCPPB 528 / LMG 568 / P 25 / Gene: fabH, XCC0212 / Plasmid: pET28b+ / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8PDX2
#2: 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
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 109 / 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: 2.26 Å3/Da / Density % sol: 41.31 % / Mosaicity: 0.313 °
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 13% PEG 4000, 100 MM MANGANESE CHLORIDE, 100 MM MES PH 6.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.03317 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Jun 14, 2015
RadiationMonochromator: SI 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03317 Å / Relative weight: 1
ReflectionResolution: 1.66→50 Å / Num. obs: 38595 / % possible obs: 99.3 % / Redundancy: 5.6 % / Biso Wilson estimate: 21.7 Å2 / Rmerge(I) obs: 0.077 / Rpim(I) all: 0.035 / Rrim(I) all: 0.085 / Χ2: 1.053 / Net I/av σ(I): 21.6 / Net I/σ(I): 10.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.66-1.695.60.8652.070.6940.3980.9541.02899
1.69-1.725.60.7360.7410.3380.8121.00999.1
1.72-1.755.70.6340.8140.290.6981.04298.3
1.75-1.795.60.5030.8670.230.5541.0698.6
1.79-1.835.60.4190.9040.1910.4621.07299.2
1.83-1.875.70.3620.9270.1650.3981.0899.4
1.87-1.925.70.2850.9510.130.3131.08299.1
1.92-1.975.70.2350.9680.1070.2591.06699.1
1.97-2.035.70.2010.9740.0910.2211.09399.2
2.03-2.095.70.1640.9830.0740.181.07899.4
2.09-2.175.70.130.9880.0590.1431.05399.5
2.17-2.255.70.1110.9920.0510.1221.05999.1
2.25-2.365.70.0920.9930.0420.1011.0899.7
2.36-2.485.70.0860.9920.040.0951.08699.7
2.48-2.635.70.0830.9920.0380.0911.02399.7
2.63-2.845.70.0750.9940.0340.0821.02899.7
2.84-3.125.70.060.9960.0270.0661.08499.9
3.12-3.585.60.0510.9970.0240.0570.99499.8
3.58-4.55.60.0520.9970.0240.0571.07799.9
4.5-505.40.0570.9950.0270.0630.96198.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
HKL-2000v705data scaling
PDB_EXTRACT3.22data extraction
PHASER5.8.0158phasing
HKLdata scaling
HKL-2000v705data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3S21

3s21


Resolution: 1.66→50 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.953 / SU B: 4.45 / SU ML: 0.073 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.095 / ESU R Free: 0.096 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2096 1925 5 %RANDOM
Rwork0.1741 ---
obs0.1759 36667 99.21 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 107.14 Å2 / Biso mean: 34.301 Å2 / Biso min: 11.77 Å2
Baniso -1Baniso -2Baniso -3
1--0.06 Å2-0.03 Å2-0 Å2
2---0.06 Å20 Å2
3---0.2 Å2
Refinement stepCycle: final / Resolution: 1.66→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2517 0 23 109 2649
Biso mean--35.81 31.99 -
Num. residues----332
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0310.0192643
X-RAY DIFFRACTIONr_bond_other_d0.0020.022534
X-RAY DIFFRACTIONr_angle_refined_deg2.7571.9673585
X-RAY DIFFRACTIONr_angle_other_deg1.2935861
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9885345
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.31424.22109
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.44515456
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.3661518
X-RAY DIFFRACTIONr_chiral_restr0.1640.2420
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.022979
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02522
LS refinement shellResolution: 1.658→1.701 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.28 144 -
Rwork0.244 2599 -
all-2743 -
obs--97.1 %
Refinement TLS params.Method: refined / Origin x: 20.6023 Å / Origin y: -36.873 Å / Origin z: 8.0781 Å
111213212223313233
T0.0144 Å20.0168 Å20.0024 Å2-0.1446 Å20.0279 Å2--0.0379 Å2
L1.9842 °20.1067 °2-0.9376 °2-0.581 °2-0.281 °2--0.6812 °2
S0.123 Å °0.4572 Å °0.1126 Å °-0.0167 Å °-0.0079 Å °0.0252 Å °-0.0483 Å °-0.2127 Å °-0.1151 Å °

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