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- PDB-2fct: SyrB2 with Fe(II), chloride, and alpha-ketoglutarate -

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Basic information

Entry
Database: PDB / ID: 2fct
TitleSyrB2 with Fe(II), chloride, and 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 / q2cbj1_9rhob like domain / Phytanoyl-CoA dioxygenase / Phytanoyl-CoA dioxygenase (PhyH) / 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 pv. 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: Non-polymer description / 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 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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)72,40711
Polymers71,3652
Non-polymers1,0429
Water9,314517
1
A: syringomycin biosynthesis enzyme 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,4526
Polymers35,6831
Non-polymers7695
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: syringomycin biosynthesis enzyme 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,9555
Polymers35,6831
Non-polymers2734
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.15, 89.60, 124.89
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 pv. syringae (bacteria)
Species: Pseudomonas syringae / 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

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Non-polymers , 5 types, 526 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-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#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


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


Mass: 18.015 Da / Num. of mol.: 517 / 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: 2.26 Å3/Da / Density % sol: 45.51 %
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: ALS / Beamline: 4.2.2 / Wavelength: 1.1271 Å
DetectorType: NOIR-1 / Detector: CCD / Date: Feb 9, 2005
Details: Rosenbaum-Rock monochromator #1 high-resolution double-crystal sagittal focusing, Rosenbaum-Rock monochromator #2 double crystal, Rosenbaum-Rock vertical focusing mirror
RadiationMonochromator: Rosenbaum-Rock monochromator #1 high-resolution double-crystal sagittal focusing, Rosenbaum-Rock monochromator #2 double crystal
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1271 Å / Relative weight: 1
ReflectionResolution: 1.6→44.8 Å / Num. all: 81779 / Num. obs: 81779 / % possible obs: 95.9 % / Redundancy: 6.51 % / Rsym value: 0.059 / Net I/σ(I): 13.3
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 5.44 % / Mean I/σ(I) obs: 3.9 / Num. unique all: 446 / Rsym value: 0.459 / % possible all: 92.2

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0005refinement
PDB_EXTRACT1.701data extraction
d*TREKdata reduction
d*TREKdata scaling
SHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 1.6→44.8 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.948 / SU B: 1.495 / SU ML: 0.054 / Cross valid method: THROUGHOUT / ESU R: 0.094 / ESU R Free: 0.093 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.204 3867 5 %RANDOM
Rwork0.175 ---
all0.176 77713 --
obs0.176 77713 91.11 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.693 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å20 Å20 Å2
2--0.01 Å20 Å2
3---0.02 Å2
Refine analyzeLuzzati coordinate error obs: 0.173 Å
Refinement stepCycle: LAST / Resolution: 1.6→44.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4818 0 60 517 5395
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0225024
X-RAY DIFFRACTIONr_bond_other_d0.0020.024272
X-RAY DIFFRACTIONr_angle_refined_deg1.4071.9346815
X-RAY DIFFRACTIONr_angle_other_deg1.30639957
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6025599
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.25223.91266
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.26915772
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.4631534
X-RAY DIFFRACTIONr_chiral_restr0.0870.2694
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.025687
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021097
X-RAY DIFFRACTIONr_nbd_refined0.210.2945
X-RAY DIFFRACTIONr_nbd_other0.1930.24447
X-RAY DIFFRACTIONr_nbtor_refined0.1870.22447
X-RAY DIFFRACTIONr_nbtor_other0.0870.22688
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1360.2388
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1730.27
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2420.238
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1150.211
X-RAY DIFFRACTIONr_mcbond_it1.111.53831
X-RAY DIFFRACTIONr_mcbond_other0.1921.51220
X-RAY DIFFRACTIONr_mcangle_it1.27424824
X-RAY DIFFRACTIONr_scbond_it2.08132422
X-RAY DIFFRACTIONr_scangle_it2.9564.51991
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.27 256 -
Rwork0.228 5005 -
obs-5261 84.55 %

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