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- PDB-6enk: The X-ray crystal structure of DesE bound to desferrioxamine B -

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Basic information

Entry
Database: PDB / ID: 6enk
TitleThe X-ray crystal structure of DesE bound to desferrioxamine B
ComponentsDesE
KeywordsTRANSFERASE / acetyltransferase siderophore
Function / homology
Function and homology information


outer membrane-bounded periplasmic space
Similarity search - Function
: / ABC transporter periplasmic binding domain / Periplasmic binding protein / Iron siderophore/cobalamin periplasmic-binding domain profile. / Nitrogenase molybdenum iron protein domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
desferrioxamine B / Secreted protein
Similarity search - Component
Biological speciesStreptomyces coelicolor (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.96 Å
AuthorsNaismith, J.H. / McMahon, S.A. / Challis, G.L. / Kadi, N. / Oke, M. / Liu, H. / Carter, L.G. / Johnson, K.A.
CitationJournal: Philos. Trans. R. Soc. Lond., B, Biol. Sci. / Year: 2018
Title: Desferrioxamine biosynthesis: diverse hydroxamate assembly by substrate-tolerant acyl transferase DesC.
Authors: Ronan, J.L. / Kadi, N. / McMahon, S.A. / Naismith, J.H. / Alkhalaf, L.M. / Challis, G.L.
History
DepositionOct 5, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 2, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: 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 / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
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_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DesE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,2585
Polymers34,5761
Non-polymers6824
Water5,747319
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, PDBePISA also suggests monomer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area270 Å2
ΔGint-15 kcal/mol
Surface area13390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.163, 58.055, 101.194
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 DesE


Mass: 34575.973 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces coelicolor (bacteria) / Gene: SCO2780 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9L074
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-BJ5 / desferrioxamine B


Mass: 613.505 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C25H45FeN6O8 / Feature type: SUBJECT OF INVESTIGATION / Comment: medication*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 319 / 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: 45.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 2.63M SODIUM MALONATE, 0.1M BISTRIS PH 6.0, 0.24M NACL.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
DetectorType: RIGAKU / Detector: CCD / Date: Feb 1, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.96→30.99 Å / Num. obs: 20684 / % possible obs: 94.3 % / Redundancy: 5.8 % / Rmerge(I) obs: 0.059 / Net I/σ(I): 19.8
Reflection shellResolution: 1.96→2.01 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.12 / Mean I/σ(I) obs: 10.3 / % possible all: 95.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2x4l

2x4l


Resolution: 1.96→30.99 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.919 / SU B: 2.683 / SU ML: 0.079 / Cross valid method: THROUGHOUT / ESU R: 0.166 / ESU R Free: 0.149 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20423 1123 5.1 %RANDOM
Rwork0.15947 ---
obs0.16172 20684 94.24 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 19.665 Å2
Baniso -1Baniso -2Baniso -3
1-0.04 Å20 Å20 Å2
2--0.06 Å20 Å2
3----0.09 Å2
Refinement stepCycle: 1 / Resolution: 1.96→30.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2267 0 43 319 2629
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.022378
X-RAY DIFFRACTIONr_bond_other_d0.0020.022272
X-RAY DIFFRACTIONr_angle_refined_deg1.4991.9763245
X-RAY DIFFRACTIONr_angle_other_deg0.9142.9625294
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0455303
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.21423.333108
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.72915397
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.571158
X-RAY DIFFRACTIONr_chiral_restr0.0770.2366
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212633
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02439
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9431.7811197
X-RAY DIFFRACTIONr_mcbond_other0.9411.7811196
X-RAY DIFFRACTIONr_mcangle_it1.4212.6651496
X-RAY DIFFRACTIONr_mcangle_other1.422.6651497
X-RAY DIFFRACTIONr_scbond_it1.5891.9911181
X-RAY DIFFRACTIONr_scbond_other1.5891.9931182
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.5062.8941747
X-RAY DIFFRACTIONr_long_range_B_refined4.32722.3052745
X-RAY DIFFRACTIONr_long_range_B_other4.32922.3112746
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.961→2.011 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.245 98 -
Rwork0.156 1462 -
obs--93.19 %

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