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- PDB-4xc9: Crystal Structure of apo HygX from Streptomyces hygroscopicus -

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Basic information

Entry
Database: PDB / ID: 4xc9
TitleCrystal Structure of apo HygX from Streptomyces hygroscopicus
Componentsoxidase/hydroxylase
KeywordsOXIDOREDUCTASE / double stranded beta helix
Function / homologyPhytanoyl-CoA dioxygenase / Phytanoyl-CoA dioxygenase (PhyH) / q2cbj1_9rhob like domain / 2-oxoglutarate-dependent dioxygenase activity / Jelly Rolls / Sandwich / Mainly Beta / metal ion binding / Putative oxidase/hydroxylase
Function and homology information
Biological speciesStreptomyces hygroscopicus subsp. hygroscopicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 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 17, 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 1.3Sep 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: oxidase/hydroxylase
B: oxidase/hydroxylase
C: oxidase/hydroxylase
D: oxidase/hydroxylase
E: oxidase/hydroxylase
F: oxidase/hydroxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)174,62212
Polymers173,8896
Non-polymers7336
Water8,107450
1
A: oxidase/hydroxylase
B: oxidase/hydroxylase
C: oxidase/hydroxylase
D: oxidase/hydroxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,4148
Polymers115,9264
Non-polymers4894
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14510 Å2
ΔGint-51 kcal/mol
Surface area35500 Å2
MethodPISA
2
E: oxidase/hydroxylase
F: oxidase/hydroxylase
hetero molecules

E: oxidase/hydroxylase
F: oxidase/hydroxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,4148
Polymers115,9264
Non-polymers4894
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area13880 Å2
ΔGint-61 kcal/mol
Surface area35980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.113, 274.427, 52.825
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
DetailsThe biological assembly is a tetramer. The asymmetric unit contains one complete biological unit (chains A, B, C, & D) and half of a second biological unit (chains E & F). The second tetramer is generated by the operation: -x, -y, z

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Components

#1: Protein
oxidase/hydroxylase


Mass: 28981.477 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces hygroscopicus subsp. hygroscopicus (bacteria)
Gene: hygX / Plasmid: pET28a(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q2MFS1
#2: Chemical
ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 450 / 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: 2.34 Å3/Da / Density % sol: 47.36 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.8 / Details: 100 mM Bis-Tris, 100 mM MgCl2, 12% PEG8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.979 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 23, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 61662 / % possible obs: 92.9 % / Redundancy: 3.7 % / Biso Wilson estimate: 38.69 Å2 / Rmerge(I) obs: 0.08 / Χ2: 0.965 / Net I/av σ(I): 14.736 / Net I/σ(I): 9.7 / Num. measured all: 228727
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.4-2.493.60.44359100.66791.1
2.49-2.593.60.34558790.67390.1
2.59-2.73.60.24958740.72689.8
2.7-2.853.60.17958660.73889.7
2.85-3.023.50.13259300.79690.1
3.02-3.263.50.09960020.93491
3.26-3.583.50.07261501.11292.8
3.58-4.13.60.07164431.35296.7
4.1-5.173.90.07666511.44598.7
5.17-504.60.04669571.00398.7

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Processing

Software
NameVersionClassification
HKL-2000data reduction
PHENIXrefinement
PDB_EXTRACT3.15data extraction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4XCA

4xca


Resolution: 2.4→49.295 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 26.85 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2458 3132 5.09 %
Rwork0.1835 58457 -
obs0.1868 61589 91.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 94.51 Å2 / Biso mean: 40.6367 Å2 / Biso min: 18.43 Å2
Refinement stepCycle: final / Resolution: 2.4→49.295 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11732 0 48 450 12230
Biso mean--49.86 38.65 -
Num. residues----1477
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00812023
X-RAY DIFFRACTIONf_angle_d1.1216292
X-RAY DIFFRACTIONf_chiral_restr0.0421787
X-RAY DIFFRACTIONf_plane_restr0.0052143
X-RAY DIFFRACTIONf_dihedral_angle_d14.5764436
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 22

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.374-2.41110.28291100.22021884199466
2.4111-2.45070.33821320.21242600273292
2.4507-2.49290.28611420.22432589273190
2.4929-2.53820.30571250.22512552267790
2.5382-2.58710.30031350.21912587272291
2.5871-2.63990.32731430.22032549269289
2.6399-2.69730.31711300.22512570270091
2.6973-2.760.27711430.22012571271489
2.76-2.8290.371380.2282541267990
2.829-2.90550.34181360.23452593272990
2.9055-2.9910.29381350.22892574270990
2.991-3.08750.29621470.22492605275290
3.0875-3.19780.31661450.22772626277191
3.1978-3.32580.28321190.22452643276291
3.3258-3.47720.2551480.19082696284494
3.4772-3.66040.25541460.1762748289494
3.6604-3.88970.24921510.1652781293296
3.8897-4.18990.18271660.14272861302798
4.1899-4.61120.19441590.13582878303798
4.6112-5.27780.18681530.13882962311599
5.2778-6.64690.241410.17182988312999
6.6469-49.30580.18511880.17573059324798

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