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- PDB-2fcv: SyrB2 with Fe(II), bromide, and alpha-ketoglutarate -

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Basic information

Entry
Database: PDB / ID: 2fcv
TitleSyrB2 with Fe(II), bromide, and alpha-ketoglutarate
Componentssyringomycin biosynthesis enzyme 2
KeywordsBIOSYNTHETIC PROTEIN / mononuclear iron / cupin / halogenase
Function / homology
Function and homology information


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 / BROMIDE ION / Chem-DSU / : / : / Syringomycin biosynthesis enzyme 2
Similarity search - Component
Biological speciesPseudomonas syringae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / RIGID BODY / Resolution: 1.8 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: Non-polymer description / Version format compliance

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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)72,58511
Polymers71,3652
Non-polymers1,2209
Water8,377465
1
A: syringomycin biosynthesis enzyme 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,5416
Polymers35,6831
Non-polymers8585
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: syringomycin biosynthesis enzyme 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,0445
Polymers35,6831
Non-polymers3624
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
γ
α
β
Length a, b, c (Å)57.12, 89.35, 125.06
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#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) / 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

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Non-polymers , 5 types, 474 molecules

#2: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#3: Chemical
ChemComp-BR / BROMIDE ION / Bromide


Mass: 79.904 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Br
#4: 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
#5: Chemical ChemComp-AKG / 2-OXOGLUTARIC ACID / Α-Ketoglutaric acid


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


Mass: 18.015 Da / Num. of mol.: 465 / 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: 2.25 Å3/Da / Density % sol: 45.4 %
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: 0.9195 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: 0.9195 Å / Relative weight: 1
ReflectionResolution: 1.8→42.18 Å / Num. all: 57215 / Num. obs: 57215 / % possible obs: 95.3 % / Redundancy: 7.6 % / Biso Wilson estimate: 17.2 Å2 / Rsym value: 0.072 / Net I/σ(I): 18.2
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 5.9 % / Mean I/σ(I) obs: 2.4 / Num. unique all: 7474 / Rsym value: 0.337 / % possible all: 86.4

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Processing

Software
NameVersionClassificationNB
SCALAdata scaling
REFMAC5.2.0005refinement
PDB_EXTRACT1.701data extraction
MOSFLMdata reduction
CCP4(SCALA)data scaling
CNSphasing
RefinementMethod to determine structure: RIGID BODY
Starting model: SyrB2 with Fe(II), chloride, and alpha-ketoglutarate

Resolution: 1.8→42.18 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.938 / SU B: 2.307 / SU ML: 0.074 / Cross valid method: THROUGHOUT / ESU R: 0.131 / ESU R Free: 0.125 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21 3341 5.9 %Same as starting model
Rwork0.171 ---
all0.173 56498 --
obs0.173 56498 93.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.096 Å2
Baniso -1Baniso -2Baniso -3
1--0.23 Å20 Å20 Å2
2---0.11 Å20 Å2
3---0.35 Å2
Refine analyzeLuzzati coordinate error obs: 0.183 Å
Refinement stepCycle: LAST / Resolution: 1.8→42.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4814 0 60 465 5339
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0225020
X-RAY DIFFRACTIONr_bond_other_d0.0020.024267
X-RAY DIFFRACTIONr_angle_refined_deg1.5321.9346811
X-RAY DIFFRACTIONr_angle_other_deg1.34539943
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8365599
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.64423.91266
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.48615768
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.9231534
X-RAY DIFFRACTIONr_chiral_restr0.0970.2694
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.025687
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021097
X-RAY DIFFRACTIONr_nbd_refined0.2080.2926
X-RAY DIFFRACTIONr_nbd_other0.2030.24267
X-RAY DIFFRACTIONr_nbtor_refined0.1870.22384
X-RAY DIFFRACTIONr_nbtor_other0.0890.22572
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1520.2361
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.170.210
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2820.239
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.160.212
X-RAY DIFFRACTIONr_mcbond_it1.3871.53819
X-RAY DIFFRACTIONr_mcbond_other0.2521.51220
X-RAY DIFFRACTIONr_mcangle_it1.53524823
X-RAY DIFFRACTIONr_scbond_it2.47432422
X-RAY DIFFRACTIONr_scangle_it3.4374.51988
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.249 296 -
Rwork0.201 3309 -
obs-3605 82.01 %

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