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- PDB-5hmc: Crystal structure of S. sahachiroi AziG complexed with 5-methyl n... -

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Basic information

Entry
Database: PDB / ID: 5hmc
TitleCrystal structure of S. sahachiroi AziG complexed with 5-methyl naphthoic acid
ComponentsAzi13
KeywordsHYDROLASE / azinomycin biosynthesis / polyketide synthase / thioesterase / naphthoate
Function / homology
Function and homology information


1,4-dihydroxy-2-naphthoyl-CoA thioesterase activity / cytosol
Similarity search - Function
Phenylacetic acid degradation-related domain / Thioesterase domain / Thioesterase superfamily / Hotdog Thioesterase / Thiol Ester Dehydrase; Chain A / HotDog domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
5-methylnaphthalene-1-carboxylic acid / Azi13
Similarity search - Component
Biological speciesStreptomyces sahachiroi (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.2 Å
AuthorsZhang, Y. / Erb, M.S. / Ealick, S.E.
CitationJournal: Biochemistry / Year: 2016
Title: Polyketide Ring Expansion Mediated by a Thioesterase, Chain Elongation and Cyclization Domain, in Azinomycin Biosynthesis: Characterization of AziB and AziG.
Authors: Mori, S. / Simkhada, D. / Zhang, H. / Erb, M.S. / Zhang, Y. / Williams, H. / Fedoseyenko, D. / Russell, W.K. / Kim, D. / Fleer, N. / Ealick, S.E. / Watanabe, C.M.
History
DepositionJan 15, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 3, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 17, 2016Group: Database references
Revision 1.2Mar 6, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Azi13
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,7954
Polymers15,4161
Non-polymers3783
Water54030
1
A: Azi13
hetero molecules

A: Azi13
hetero molecules

A: Azi13
hetero molecules

A: Azi13
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,17816
Polymers61,6654
Non-polymers1,51312
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z1
crystal symmetry operation10_645-x+1,-y-1,z1
crystal symmetry operation15_645y+1,x-1,-z1
Buried area8960 Å2
ΔGint-139 kcal/mol
Surface area18170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.771, 67.771, 140.278
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number98
Space group name H-MI4122
Components on special symmetry positions
IDModelComponents
11A-417-

HOH

21A-425-

HOH

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Components

#1: Protein Azi13


Mass: 15416.212 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces sahachiroi (bacteria) / Gene: azi13 / Plasmid: pET24 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: B4XYA6
#2: Chemical ChemComp-5NE / 5-methylnaphthalene-1-carboxylic acid


Mass: 186.207 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H10O2
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 30 / 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: 2.61 Å3/Da / Density % sol: 52.91 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 1.25 M ammonium sulfate and 0.1 M cacodylate pH 6.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 12, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.95→70.14 Å / Num. obs: 12265 / % possible obs: 99.4 % / Redundancy: 7 % / Biso Wilson estimate: 44.15 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.056 / Rpim(I) all: 0.023 / Net I/σ(I): 20.9 / Num. measured all: 85401
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
1.95-2.066.21.1161.3196.6
6.17-70.146.20.01780.2199.3

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Processing

Software
NameVersionClassification
Aimless0.1.27data scaling
PHENIXrefinement
PDB_EXTRACT3.15data extraction
MOLREPphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: D_1000217232

Resolution: 2.2→61.023 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 26.96
RfactorNum. reflection% reflection
Rfree0.2192 418 4.84 %
Rwork0.1844 --
obs0.1861 8634 99.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 94.36 Å2 / Biso mean: 48.3142 Å2 / Biso min: 32.81 Å2
Refinement stepCycle: final / Resolution: 2.2→61.023 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms928 0 24 30 982
Biso mean--54.03 50.96 -
Num. residues----125
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006979
X-RAY DIFFRACTIONf_angle_d0.7841342
X-RAY DIFFRACTIONf_chiral_restr0.053152
X-RAY DIFFRACTIONf_plane_restr0.006174
X-RAY DIFFRACTIONf_dihedral_angle_d15.207552
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 3

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2004-2.51880.27291440.22022670281499
2.5188-3.17340.2961290.219527012830100
3.1734-61.04610.18921450.166428452990100

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