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- PDB-5f9p: Crystal structure study of anthrone oxidase-like protein -

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Basic information

Entry
Database: PDB / ID: 5f9p
TitleCrystal structure study of anthrone oxidase-like protein
ComponentsAnthrone oxidase-like protein
KeywordsOXIDOREDUCTASE / anthrone oxidase-like protein / oxidative ring-B opening / activity site
Function / homologyAntibiotic biosynthesis monooxygenase / Antibiotic biosynthesis monooxygenase domain / Dimeric alpha-beta barrel / Anthrone oxidase-like protein
Function and homology information
Biological speciesStreptomyces ambofaciens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.078 Å
AuthorsGao, X. / Wu, D. / Fan, K. / Liu, Z.-J.
CitationJournal: ACS Chem. Biol. / Year: 2017
Title: Structure and Function of a C-C Bond Cleaving Oxygenase in Atypical Angucycline Biosynthesis
Authors: Pan, G. / Gao, X. / Fan, K. / Liu, J. / Meng, B. / Gao, J. / Wang, B. / Zhang, C. / Han, H. / Ai, G. / Chen, Y. / Wu, D. / Liu, Z.J. / Yang, K.
History
DepositionDec 10, 2015Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 14, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 8, 2017Group: Database references
Revision 1.2Jul 18, 2018Group: Data collection / Database references / Category: citation_author / diffrn_source
Item: _citation_author.name / _diffrn_source.pdbx_synchrotron_beamline ..._citation_author.name / _diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.pdbx_synchrotron_site / _diffrn_source.source
Revision 1.3Oct 23, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Anthrone oxidase-like protein
B: Anthrone oxidase-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,6774
Polymers53,4932
Non-polymers1842
Water5,621312
1
A: Anthrone oxidase-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,8382
Polymers26,7461
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area290 Å2
ΔGint-1 kcal/mol
Surface area11210 Å2
MethodPISA
2
B: Anthrone oxidase-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,8382
Polymers26,7461
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area310 Å2
ΔGint-2 kcal/mol
Surface area11080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.273, 90.273, 94.745
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number171
Space group name H-MP62
Components on special symmetry positions
IDModelComponents
11A-470-

HOH

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Components

#1: Protein Anthrone oxidase-like protein / Putative oxidase


Mass: 26746.357 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces ambofaciens (bacteria) / Gene: alpJ, DSMT0187 / Plasmid: pET-30a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: Q6VMI5
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 312 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.1 Å3/Da / Density % sol: 41.56 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.1M HEPES, 1.4M sodium citrate tribasic dehydrate

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Data collection

DiffractionMean temperature: 77.15 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 17, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.078→40.525 Å / Num. obs: 26423 / % possible obs: 100 % / Redundancy: 22.8 % / Net I/σ(I): 5.71
Reflection shellResolution: 2.078→2.152 Å / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.8.1_1168refinement
HKL-2000data processing
HKL-2000data scaling
PHENIX1.8.2_1309phasing
Coot0.7model building
RefinementMethod to determine structure: SAD / Resolution: 2.078→40.515 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 20.78 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2065 1340 5.07 %
Rwork0.155 --
obs0.1576 26423 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.078→40.515 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3711 0 12 312 4035
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073804
X-RAY DIFFRACTIONf_angle_d1.0325159
X-RAY DIFFRACTIONf_dihedral_angle_d13.0071373
X-RAY DIFFRACTIONf_chiral_restr0.07566
X-RAY DIFFRACTIONf_plane_restr0.004676
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.078-2.15230.25711330.17172483X-RAY DIFFRACTION100
2.1523-2.23850.23091340.15712494X-RAY DIFFRACTION100
2.2385-2.34040.23581440.15572501X-RAY DIFFRACTION100
2.3404-2.46370.23551360.16782482X-RAY DIFFRACTION100
2.4637-2.61810.23411160.17382534X-RAY DIFFRACTION100
2.6181-2.82020.22441160.17272521X-RAY DIFFRACTION100
2.8202-3.10390.23231500.16882481X-RAY DIFFRACTION100
3.1039-3.55280.20521450.15232502X-RAY DIFFRACTION100
3.5528-4.47520.17231300.12862528X-RAY DIFFRACTION100
4.4752-40.52250.16771360.15212557X-RAY DIFFRACTION100

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