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- PDB-3row: Crystal Structure of Xanthomonas campestri OleA -

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Basic information

Entry
Database: PDB / ID: 3row
TitleCrystal Structure of 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
Acyl-CoA:acyl-CoA alkyltransferase
Similarity search - Component
Biological speciesXanthomonas campestris pv. campestris (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8487 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
DepositionApr 26, 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 / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)74,6142
Polymers74,6142
Non-polymers00
Water10,701594
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4270 Å2
ΔGint-11 kcal/mol
Surface area25470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.204, 85.379, 102.706
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, beta-ketoacyl-[acyl-carrier-protein] synthase I
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 594 / 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: 2.42 Å3/Da / Density % sol: 49.07 %
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-D / Wavelength: 1.03 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Jun 25, 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: 1.8487→50 Å / Num. all: 61685 / Num. obs: 61685 / % possible obs: 98.8 % / Observed criterion σ(F): -3 / Observed criterion σ(I): 0 / Redundancy: 8.2 % / Rmerge(I) obs: 0.055 / Net I/σ(I): 40.2
Reflection shellResolution: 1.8487→1.88 Å / Redundancy: 8.1 % / Rmerge(I) obs: 0.385 / Mean I/σ(I) obs: 5.3 / % possible all: 97.9

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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 3FK5

3fk5


Resolution: 1.8487→44.006 Å / SU ML: 0.18 / σ(F): 0 / Phase error: 17.44 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1912 3059 5.04 %
Rwork0.1597 --
obs0.1613 60653 97.04 %
all-60652 -
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 47.481 Å2 / ksol: 0.368 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.7162 Å2-0 Å20 Å2
2---3.369 Å20 Å2
3---1.6528 Å2
Refinement stepCycle: LAST / Resolution: 1.8487→44.006 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5087 0 0 594 5681
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075352
X-RAY DIFFRACTIONf_angle_d1.0387299
X-RAY DIFFRACTIONf_dihedral_angle_d12.9322018
X-RAY DIFFRACTIONf_chiral_restr0.073865
X-RAY DIFFRACTIONf_plane_restr0.004948
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8487-1.87760.28591230.19382364X-RAY DIFFRACTION88
1.8776-1.90840.21391330.17132485X-RAY DIFFRACTION92
1.9084-1.94130.20531370.16032472X-RAY DIFFRACTION94
1.9413-1.97660.22081400.14862535X-RAY DIFFRACTION95
1.9766-2.01460.19271320.15452538X-RAY DIFFRACTION95
2.0146-2.05570.18491350.14862542X-RAY DIFFRACTION95
2.0557-2.10040.17381420.15032524X-RAY DIFFRACTION96
2.1004-2.14930.19511270.14972603X-RAY DIFFRACTION97
2.1493-2.2030.20141430.14732592X-RAY DIFFRACTION97
2.203-2.26260.20441390.15772610X-RAY DIFFRACTION98
2.2626-2.32910.20781350.14832605X-RAY DIFFRACTION98
2.3291-2.40430.19551370.15882615X-RAY DIFFRACTION98
2.4043-2.49020.19921530.15392627X-RAY DIFFRACTION98
2.4902-2.58990.20461360.15682655X-RAY DIFFRACTION99
2.5899-2.70780.18981390.17022664X-RAY DIFFRACTION99
2.7078-2.85050.23751450.17542679X-RAY DIFFRACTION99
2.8505-3.02910.19521390.17462688X-RAY DIFFRACTION99
3.0291-3.26290.20411390.16652686X-RAY DIFFRACTION99
3.2629-3.59110.16631450.15812715X-RAY DIFFRACTION100
3.5911-4.11040.16161450.14382740X-RAY DIFFRACTION100
4.1104-5.17740.1771430.14272760X-RAY DIFFRACTION100
5.1774-44.01870.18511520.18662895X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -11.8539 Å / Origin y: 15.3434 Å / Origin z: -14.3255 Å
111213212223313233
T0.0673 Å2-0.0021 Å2-0.0178 Å2-0.0766 Å2-0.0087 Å2--0.0711 Å2
L0.2544 °2-0.1629 °2-0.0202 °2-0.8684 °2-0.1304 °2--0.3574 °2
S0.0383 Å °0.0311 Å °-0.0364 Å °-0.1023 Å °-0.0233 Å °0.1043 Å °0.0106 Å °-0.0142 Å °-0.0016 Å °
Refinement TLS groupSelection details: (chain 'A') or (chain 'B')

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