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- PDB-5vxi: Crystal structure of Xanthomonas campestris OleA E117D bound with... -

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Basic information

Entry
Database: PDB / ID: 5vxi
TitleCrystal structure of Xanthomonas campestris OleA E117D 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 / FOURIER SYNTHESIS / Resolution: 2.08 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)39,1093
Polymers38,8281
Non-polymers2802
Water81145
1
A: 3-oxoacyl-[ACP] synthase III
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)78,2176
Polymers77,6572
Non-polymers5604
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+1/31
Buried area5230 Å2
ΔGint-16 kcal/mol
Surface area26410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.765, 89.765, 69.509
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: 38828.418 Da / Num. of mol.: 1 / Mutation: E117D
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-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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 45 / 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: 2.24 Å3/Da / Density % sol: 45.01 % / Mosaicity: 1.267 °
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 12% PEG 4000, 70 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: 19-BM / Wavelength: 1.02235 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Feb 17, 2017
RadiationMonochromator: SI 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.02235 Å / Relative weight: 1
ReflectionResolution: 2.08→50 Å / Num. obs: 19937 / % possible obs: 98.8 % / Redundancy: 10.3 % / Biso Wilson estimate: 36.1 Å2 / Rmerge(I) obs: 0.143 / Rpim(I) all: 0.047 / Rrim(I) all: 0.151 / Χ2: 1.024 / Net I/σ(I): 11.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.08-2.12100.720.7460.2370.7591.365100
2.12-2.1510.10.5620.910.1850.5921.03100
2.15-2.210.10.530.9380.1740.5581.039100
2.2-2.2410.20.4510.9570.1480.4750.968100
2.24-2.2910.30.4320.9330.1410.4540.965100
2.29-2.3410.20.3770.9530.1230.3971.021100
2.34-2.410.30.3520.9510.1140.371.011100
2.4-2.4710.40.3280.9610.1060.3451.017100
2.47-2.5410.50.2890.970.0930.3040.969100
2.54-2.6210.60.2560.9770.0820.2690.992100
2.62-2.7110.70.2290.9720.0730.2410.966100
2.71-2.8210.80.2080.9770.0660.2181.04999.9
2.82-2.9510.90.1830.9850.0580.1921.031100
2.95-3.1110.80.1730.9840.0560.1821.098100
3.11-3.310.70.1520.9880.0490.161.07499.7
3.3-3.5610.50.1380.9850.0450.1460.94998.5
3.56-3.9110.20.1240.9850.0410.1310.91998.1
3.91-4.489.80.1120.9860.0390.1190.95194.6
4.48-5.64100.0980.9910.0330.1041.09695.1
5.64-509.40.0810.9910.0280.0860.9690.2

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Processing

Software
NameVersionClassification
HKL-2000v705data scaling
REFMAC5.8.0158refinement
PDB_EXTRACT3.22data extraction
REFMAC5.8.0158phasing
HKL-2000v705data scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 3S21

3s21


Resolution: 2.08→50 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.936 / SU B: 9.942 / SU ML: 0.129 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.199 / ESU R Free: 0.179 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2289 1004 5 %RANDOM
Rwork0.1711 ---
obs0.1741 18913 98.53 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 115.02 Å2 / Biso mean: 48.522 Å2 / Biso min: 23.48 Å2
Baniso -1Baniso -2Baniso -3
1--0.31 Å2-0.16 Å2-0 Å2
2---0.31 Å20 Å2
3---1.02 Å2
Refinement stepCycle: final / Resolution: 2.08→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2534 0 17 45 2596
Biso mean--65.88 41.35 -
Num. residues----334
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.0192588
X-RAY DIFFRACTIONr_bond_other_d0.0020.022500
X-RAY DIFFRACTIONr_angle_refined_deg2.3061.973502
X-RAY DIFFRACTIONr_angle_other_deg1.16435773
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7775332
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.94824.095105
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.63415448
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.4721518
X-RAY DIFFRACTIONr_chiral_restr0.1340.2413
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.022878
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02506
LS refinement shellResolution: 2.08→2.119 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.26 54 -
Rwork0.203 1360 -
obs--96.98 %
Refinement TLS params.Method: refined / Origin x: 47.9171 Å / Origin y: 0.5718 Å / Origin z: -3.5394 Å
111213212223313233
T0.134 Å2-0.0612 Å20.0353 Å2-0.0472 Å2-0.0137 Å2--0.0214 Å2
L0.8254 °20.4696 °20.1247 °2-1.7959 °20.9346 °2--0.6979 °2
S-0.1498 Å °0.1359 Å °-0.0317 Å °-0.3386 Å °0.2495 Å °-0.1299 Å °-0.1617 Å °0.1112 Å °-0.0997 Å °

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