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- PDB-3s1z: Crystal structure of acetamide bound Xanthomonas campestri OleA -

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Basic information

Entry
Database: PDB / ID: 3s1z
TitleCrystal structure of acetamide bound Xanthomonas campestri OleA
Components3-oxoacyl-[ACP] synthase III
KeywordsTRANSFERASE / Non-decarboxylative Claisen 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
ACETAMIDE / Acyl-CoA:acyl-CoA alkyltransferase
Similarity search - Component
Biological speciesXanthomonas campestris pv. campestris (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.0547 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 16, 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 / 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 / _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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)74,7324
Polymers74,6142
Non-polymers1182
Water7,656425
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4690 Å2
ΔGint-2 kcal/mol
Surface area25040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.628, 85.044, 103.050
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 37306.805 Da / Num. of mol.: 2
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-ACM / ACETAMIDE / Acetamide


Mass: 59.067 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H5NO
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 425 / 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: 2.4 Å3/Da / Density % sol: 48.68 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.2
Details: 18% PEG 8000, 80 mM potassium phosphate dibasic, 100 mM sodium citrate pH 4.2, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / 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: 2.05→50 Å / Num. all: 45354 / Num. obs: 45354 / % possible obs: 100 % / Observed criterion σ(F): -3 / Observed criterion σ(I): 0 / Redundancy: 8.1 % / Biso Wilson estimate: 25.41 Å2 / Rmerge(I) obs: 0.079 / Net I/σ(I): 33.6
Reflection shellResolution: 2.05→2.09 Å / Redundancy: 7.6 % / Rmerge(I) obs: 0.489 / Mean I/σ(I) obs: 7.6 / % possible all: 99.9

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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
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 3ROW

3row


Resolution: 2.0547→30.432 Å / SU ML: 0.23 / σ(F): 0 / Phase error: 17.51 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1919 2226 5.02 %R-free data carried over from 3ROW
Rwork0.1573 ---
obs0.1591 44377 97.81 %-
all-44377 --
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 43.395 Å2 / ksol: 0.359 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.6479 Å2-0 Å20 Å2
2---1.1098 Å20 Å2
3---0.4619 Å2
Refinement stepCycle: LAST / Resolution: 2.0547→30.432 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5078 0 8 425 5511
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075325
X-RAY DIFFRACTIONf_angle_d1.017251
X-RAY DIFFRACTIONf_dihedral_angle_d12.621995
X-RAY DIFFRACTIONf_chiral_restr0.071855
X-RAY DIFFRACTIONf_plane_restr0.004944
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0547-2.09940.22451410.1782388X-RAY DIFFRACTION91
2.0994-2.14820.19111220.16552559X-RAY DIFFRACTION95
2.1482-2.20190.2481310.1522511X-RAY DIFFRACTION96
2.2019-2.26150.19981340.15172579X-RAY DIFFRACTION97
2.2615-2.3280.21741450.15582570X-RAY DIFFRACTION97
2.328-2.40310.20811330.15362605X-RAY DIFFRACTION97
2.4031-2.48890.20451440.1552587X-RAY DIFFRACTION98
2.4889-2.58850.2121300.15542643X-RAY DIFFRACTION98
2.5885-2.70630.21541430.16672638X-RAY DIFFRACTION99
2.7063-2.84890.25911440.18242653X-RAY DIFFRACTION99
2.8489-3.02720.20831420.17472675X-RAY DIFFRACTION99
3.0272-3.26070.20671380.172696X-RAY DIFFRACTION99
3.2607-3.58840.18511410.15962687X-RAY DIFFRACTION100
3.5884-4.10650.15961470.14282728X-RAY DIFFRACTION100
4.1065-5.16970.15591410.12672755X-RAY DIFFRACTION100
5.1697-30.4350.16981500.17232877X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -12.1748 Å / Origin y: 15.1294 Å / Origin z: -14.2634 Å
111213212223313233
T0.1221 Å20.0012 Å2-0.0282 Å2-0.1049 Å2-0.0068 Å2--0.1164 Å2
L0.3838 °2-0.2716 °20.0942 °2-0.5217 °2-0.2205 °2--0.2879 °2
S0.0831 Å °0.0167 Å °-0.0845 Å °-0.1022 Å °-0.0085 Å °0.0911 Å °0.0781 Å °-0.0048 Å °-0.0108 Å °
Refinement TLS groupSelection details: (chain 'A') or (chain 'B')

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