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- PDB-5hmb: Crystal structure of S. sahachiroi AziG -

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Basic information

Entry
Database: PDB / ID: 5hmb
TitleCrystal structure of S. sahachiroi AziG
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
Biological speciesStreptomyces sahachiroi (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.151 Å
AuthorsErb, M.S. / Zhang, Y. / 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 1.2Sep 27, 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 / citation / database_2 / pdbx_initial_refinement_model / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Azi13
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,6083
Polymers15,4161
Non-polymers1922
Water43224
1
A: Azi13
hetero molecules

A: Azi13
hetero molecules

A: Azi13
hetero molecules

A: Azi13
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,43312
Polymers61,6654
Non-polymers7698
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 area7930 Å2
ΔGint-134 kcal/mol
Surface area19380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.466, 68.466, 139.616
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-415-

HOH

21A-420-

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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 24 / 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: 2.65 Å3/Da / Density % sol: 53.64 %
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: CHESS / Beamline: F1 / Wavelength: 0.9183 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Jun 25, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9183 Å / Relative weight: 1
ReflectionResolution: 2.15→50 Å / Num. obs: 9373 / % possible obs: 99.5 % / Redundancy: 6.7 % / Biso Wilson estimate: 42.76 Å2 / Rmerge(I) obs: 0.091 / Χ2: 2.92 / Net I/av σ(I): 37.312 / Net I/σ(I): 13.9 / Num. measured all: 62888
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.15-2.195.70.3864592.074100
2.19-2.2360.3454621.94100
2.23-2.276.40.2754452.104100
2.27-2.3270.3544592.046100
2.32-2.3770.2844672.196100
2.37-2.427.10.2424682.224100
2.42-2.487.10.2344512.383100
2.48-2.5570.2014642.45699.8
2.55-2.627.10.1924682.487100
2.62-2.7170.1524522.653100
2.71-2.8170.1294692.93499.8
2.81-2.9270.1184673.107100
2.92-3.056.80.1044683.46100
3.05-3.216.80.0974673.79899.8
3.21-3.416.60.0784713.94799.4
3.41-3.686.40.0764724.22399.8
3.68-4.056.70.0784794.03898.8
4.05-4.636.60.0754714.26499.2
4.63-5.836.70.0774893.24899
5.83-506.10.085252.63896

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACT3.15data extraction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3S4K

3s4k


Resolution: 2.151→29.908 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2289 447 4.79 %Random selection
Rwork0.2073 8886 --
obs0.2084 9333 99.33 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 107.18 Å2 / Biso mean: 52.063 Å2 / Biso min: 30.56 Å2
Refinement stepCycle: final / Resolution: 2.151→29.908 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms926 0 10 24 960
Biso mean--67.11 53.08 -
Num. residues----125
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006985
X-RAY DIFFRACTIONf_angle_d0.7661350
X-RAY DIFFRACTIONf_chiral_restr0.052153
X-RAY DIFFRACTIONf_plane_restr0.006178
X-RAY DIFFRACTIONf_dihedral_angle_d26.798338
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 (%)
2.1514-2.46260.24681510.241128853036100
2.4626-3.10210.291430.256129473090100
3.1021-29.9110.20971530.18653054320799

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