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- PDB-4xaa: Crystal Structure of AviO1 from Streptomyces viridochromogenes Tue57 -

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Basic information

Entry
Database: PDB / ID: 4xaa
TitleCrystal Structure of AviO1 from Streptomyces viridochromogenes Tue57
ComponentsPutative oxygenase
KeywordsOXIDOREDUCTASE / double stranded beta helix
Function / homologyq2cbj1_9rhob like domain / Phytanoyl-CoA dioxygenase / Phytanoyl-CoA dioxygenase (PhyH) / Jelly Rolls / Sandwich / Mainly Beta / NICKEL (II) ION / Putative oxygenase
Function and homology information
Biological speciesStreptomyces viridochromogenes Tue57 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 Å
AuthorsMcCulloch, K.M. / McCranie, E.K. / Sarwar, M. / Mathieu, J.L. / Gitschlag, B.L. / Du, Y. / Bachmann, B.O. / Iverson, T.M.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2015
Title: Oxidative cyclizations in orthosomycin biosynthesis expand the known chemistry of an oxygenase superfamily.
Authors: McCulloch, K.M. / McCranie, E.K. / Smith, J.A. / Sarwar, M. / Mathieu, J.L. / Gitschlag, B.L. / Du, Y. / Bachmann, B.O. / Iverson, T.M.
History
DepositionDec 13, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 5, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 19, 2015Group: Database references
Revision 1.2Sep 30, 2015Group: Database references
Revision 1.3Feb 28, 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_conn_angle / pdbx_struct_oper_list / struct_conn
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative oxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,3852
Polymers24,3261
Non-polymers591
Water1,09961
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)72.119, 115.144, 33.864
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Detailsbiological unit is the same as asym.

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Components

#1: Protein Putative oxygenase /


Mass: 24326.391 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces viridochromogenes Tue57 (bacteria)
Gene: aviO1, STVIR_2892 / Plasmid: pET23 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q93KW4
#2: Chemical ChemComp-NI / NICKEL (II) ION / Nickel


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 61 / 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: 2.89 Å3/Da / Density % sol: 57.44 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 10
Details: 100 mM CAPS, 1.2 M NaH2PO4, 0.8 M K2HPO4, 0.2 M Li2SO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.485 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 27, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.485 Å / Relative weight: 1
ReflectionRedundancy: 8.5 % / Number: 88374 / Rmerge(I) obs: 0.111 / Χ2: 2.25 / D res high: 2.5 Å / D res low: 50 Å / Num. obs: 10455 / % possible obs: 98.6
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)IDRmerge(I) obsChi squaredRedundancy
6.785010.0624.3098.3
5.386.7810.0774.1329.1
4.75.3810.0764.1878.8
4.274.710.0833.9568.5
3.974.2710.0953.5928.3
3.733.9710.1073.0838.6
3.553.7310.1292.8348.5
3.393.5510.1612.3958.8
3.263.3910.192.1718.8
3.153.2610.2451.7579
3.053.1510.3081.7048.9
2.963.0510.3911.3379.1
2.892.9610.4681.2149.2
2.822.8910.551.1019.1
2.752.8210.6781.0978.9
2.692.7510.771.028.8
2.642.6910.8440.9258.3
2.592.6410.9030.957.6
2.542.5910.9870.9736.6
2.52.5410.9260.865.9
ReflectionResolution: 2.3→30 Å / % possible obs: 86.7 % / Redundancy: 4 % / Biso Wilson estimate: 44.71 Å2 / Rmerge(I) obs: 0.07 / Rpim(I) all: 0.038 / Rrim(I) all: 0.08 / Χ2: 1.958 / Net I/av σ(I): 26.689 / Net I/σ(I): 14.9 / Num. measured all: 45967
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.3-2.342.80.443970.8360.3210.551.29961.1
2.34-2.383.10.4414140.8570.2910.5331.34866.2
2.38-2.433.30.4035010.8780.2570.4821.43874.7
2.43-2.483.60.3915590.9070.2340.4591.5188.7
2.48-2.534.10.3395910.9590.1870.3891.51193.2
2.53-2.594.10.3376070.9390.1860.3871.61790.7
2.59-2.654.10.2675900.9670.1490.3081.57792.5
2.65-2.7340.235970.9590.1280.2651.72394.2
2.73-2.814.10.2066200.9810.1130.2371.84992.5
2.81-2.94.10.1715920.9830.0950.1971.77792.5
2.9-340.1415960.9910.0810.1642.07592.7
3-3.1240.1136130.9920.0630.1312.06192
3.12-3.2640.0916010.9920.0510.1052.20592.7
3.26-3.4340.0756020.9920.0430.0882.23689.1
3.43-3.654.10.0625930.9940.0360.0732.391.8
3.65-3.934.10.0595980.9940.0330.0682.41690.2
3.93-4.334.30.0525930.9970.0280.0592.27787.6
4.33-4.954.40.0516010.9950.0270.0582.37187.7
4.95-6.234.50.0495890.9980.0250.0562.28286.2
6.23-304.60.0455910.9980.0220.0512.15377.9

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHENIX(1.10pre_2083: ???)refinement
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.3→27.057 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.91 / Phase error: 25.9 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2213 1081 5.09 %
Rwork0.1881 20142 -
obs0.1897 21223 87.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 97.47 Å2 / Biso mean: 46.7252 Å2 / Biso min: 28.58 Å2
Refinement stepCycle: final / Resolution: 2.3→27.057 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1700 0 1 61 1762
Biso mean--58.16 46.46 -
Num. residues----220
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081745
X-RAY DIFFRACTIONf_angle_d1.1042392
X-RAY DIFFRACTIONf_chiral_restr0.045264
X-RAY DIFFRACTIONf_plane_restr0.005325
X-RAY DIFFRACTIONf_dihedral_angle_d12.976641
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3001-2.40470.29771090.27751911202066
2.4047-2.53140.27961580.24172490264889
2.5314-2.68990.30231540.22992671282593
2.6899-2.89740.29181240.22642702282693
2.8974-3.18850.27091290.21762714284394
3.1885-3.64890.22491430.18812618276192
3.6489-4.59360.18161510.1572567271890
4.5936-27.05870.17171130.16232469258285

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