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- PDB-2fcu: SyrB2 with alpha-ketoglutarate -

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Basic information

Entry
Database: PDB / ID: 2fcu
TitleSyrB2 with alpha-ketoglutarate
Componentssyringomycin biosynthesis enzyme 2
KeywordsBIOSYNTHETIC PROTEIN / mononuclear iron / cupin / halogenase
Function / homology
Function and homology information


L-threonyl-[L-threonyl-carrier protein] 4-chlorinase / 2-oxoglutarate-dependent dioxygenase activity / iron ion binding
Similarity search - Function
Chlorinating enzyme / Phytanoyl-CoA dioxygenase / Phytanoyl-CoA dioxygenase (PhyH) / q2cbj1_9rhob like domain / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
2-OXOGLUTARIC ACID / Chem-DSU / : / L-threonyl-[L-threonyl-carrier protein] 4-chlorinase
Similarity search - Component
Biological speciesPseudomonas syringae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.6 Å
AuthorsBlasiak, L.C. / Drennan, C.L.
CitationJournal: Nature / Year: 2006
Title: Crystal structure of the non-haem iron halogenase SyrB2 in syringomycin biosynthesis.
Authors: Blasiak, L.C. / Vaillancourt, F.H. / Walsh, C.T. / Drennan, C.L.
History
DepositionDec 12, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 21, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: syringomycin biosynthesis enzyme 2
B: syringomycin biosynthesis enzyme 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,1545
Polymers71,3652
Non-polymers7893
Water7,819434
1
A: syringomycin biosynthesis enzyme 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,3253
Polymers35,6831
Non-polymers6432
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: syringomycin biosynthesis enzyme 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,8292
Polymers35,6831
Non-polymers1461
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.263, 90.032, 128.769
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein syringomycin biosynthesis enzyme 2


Mass: 35682.543 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas syringae (bacteria) / Strain: pv. syringae / Gene: SyrB2 / Plasmid: pET28b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: GenBank: 5748808, UniProt: Q9RBY6*PLUS
#2: Chemical ChemComp-DSU / ((2R,3S,4S,5S)-3,4-DIHYDROXY-5-(HYDROXYMETHYL)-5-((2R,3S,4S,5S,6R)-3,4,5-TRIHYDROXY-6-METHOXY-TETRAHYDRO-2H-PYRAN-2-YLOXY)-TETRAHYDROFURAN-2-YL)METHYL NONANOATE


Mass: 496.546 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H40O12
#3: Chemical ChemComp-AKG / 2-OXOGLUTARIC ACID


Mass: 146.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H6O5
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 434 / 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: 47.5 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 15% PEG 3350, 250 mM Na formate, spermine tetra-HCl, n-decanoyl sucrose, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 1.0332 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jun 4, 2005 / Details: double crystal monochromator
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.6→42.8 Å / Num. all: 87345 / Num. obs: 87345 / % possible obs: 98.7 % / Redundancy: 5 % / Rsym value: 0.071 / Net I/σ(I): 14.2
Reflection shellResolution: 1.6→1.64 Å / Redundancy: 4.7 % / Mean I/σ(I) obs: 3 / Rsym value: 0.396 / % possible all: 96.1

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Processing

Software
NameVersionClassificationNB
SCALAdata scaling
REFMAC5.2.0005refinement
PDB_EXTRACT1.701data extraction
MOSFLMdata reduction
CCP4(SCALA)data scaling
SHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 1.6→42.8 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.946 / SU B: 1.479 / SU ML: 0.054 / Cross valid method: THROUGHOUT / ESU R: 0.092 / ESU R Free: 0.089 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21179 5784 6.6 %RANDOM
Rwork0.18768 ---
obs0.18912 81490 98.58 %-
all-87274 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.36 Å2
Baniso -1Baniso -2Baniso -3
1--0.22 Å20 Å20 Å2
2--0.31 Å20 Å2
3----0.1 Å2
Refine analyzeLuzzati coordinate error obs: 0.175 Å
Refinement stepCycle: LAST / Resolution: 1.6→42.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4850 0 54 434 5338
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0225068
X-RAY DIFFRACTIONr_bond_other_d0.0010.023438
X-RAY DIFFRACTIONr_angle_refined_deg1.381.9366870
X-RAY DIFFRACTIONr_angle_other_deg1.67438312
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5865604
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.74523.918268
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.77715790
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.8851535
X-RAY DIFFRACTIONr_chiral_restr0.0850.2700
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.025727
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021102
X-RAY DIFFRACTIONr_nbd_refined0.2090.2928
X-RAY DIFFRACTIONr_nbd_other0.2020.23720
X-RAY DIFFRACTIONr_nbtor_refined0.1840.22439
X-RAY DIFFRACTIONr_nbtor_other0.0870.22525
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1060.2291
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1280.26
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3130.224
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1350.28
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1261.53862
X-RAY DIFFRACTIONr_mcbond_other0.1891.51226
X-RAY DIFFRACTIONr_mcangle_it1.28824865
X-RAY DIFFRACTIONr_scbond_it2.03332441
X-RAY DIFFRACTIONr_scangle_it2.9274.52005
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.28 527 -
Rwork0.24 5699 -
obs--95.76 %

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