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- PDB-3jun: Crystal Structure of PhzA/B from Burkholderia cepacia R18194 in s... -

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Basic information

Entry
Database: PDB / ID: 3jun
TitleCrystal Structure of PhzA/B from Burkholderia cepacia R18194 in simultaneous complex with racemic 5-bromo-2-(piperidin-3-ylamino)benzoic acid
ComponentsPhenazine biosynthesis protein A/B
KeywordsBIOSYNTHETIC PROTEIN / chirality / drug design / phenazine biosynthesis / racemate / racemic mixture
Function / homology
Function and homology information


antibiotic biosynthetic process
Similarity search - Function
Phenazine biosynthesis protein A/B / Phenazine biosynthesis protein A/B / Nuclear Transport Factor 2; Chain: A, - #50 / NTF2-like domain superfamily / Nuclear Transport Factor 2; Chain: A, / Roll / Alpha Beta
Similarity search - Domain/homology
5-bromo-2-[(3R)-piperidin-3-ylamino]benzoic acid / 5-bromo-2-[(3S)-piperidin-3-ylamino]benzoate / Phenazine biosynthesis protein A/B
Similarity search - Component
Biological speciesBurkholderia sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.8 Å
AuthorsMentel, M. / Breinbauer, R. / Blankenfeldt, W.
Citation
Journal: Angew.Chem.Int.Ed.Engl. / Year: 2009
Title: The Active Site of an Enzyme Can Host Both Enantiomers of a Racemic Ligand Simultaneously
Authors: Mentel, M. / Blankenfeldt, W. / Breinbauer, R.
#1: Journal: J.Am.Chem.Soc. / Year: 2008
Title: PhzA/B catalyzes the formation of the tricycle in phenazine biosynthesis
Authors: Ahuja, E.G. / Janning, P. / Graebsch, A. / Breinbauer, R. / Hiller, W. / Costisella, B. / Thomashow, L.S. / Mavrodi, D.V. / Blankenfeldt, W.
History
DepositionSep 15, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 29, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description ...Advisory / Refinement description / Source and taxonomy / Version format compliance
Revision 1.2Feb 21, 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

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Assembly

Deposited unit
A: Phenazine biosynthesis protein A/B
B: Phenazine biosynthesis protein A/B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,2576
Polymers43,0622
Non-polymers1,1954
Water2,972165
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3640 Å2
ΔGint-12 kcal/mol
Surface area14780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.660, 64.660, 161.310
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Detailsbiological unit is the same as asym.

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Components

#1: Protein Phenazine biosynthesis protein A/B


Mass: 21531.025 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia sp. (bacteria) / Strain: 383 / Gene: Bcep18194_B1568 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2(DE3) pLysS / References: UniProt: Q396C9
#2: Chemical ChemComp-AJD / 5-bromo-2-[(3R)-piperidin-3-ylamino]benzoic acid


Mass: 299.164 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H15BrN2O2
#3: Chemical ChemComp-AKD / 5-bromo-2-[(3S)-piperidin-3-ylamino]benzoate


Mass: 298.156 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H14BrN2O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 165 / 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: 45.59 %
Crystal growTemperature: 284 K
Details: 16-20% (w/v) PEG3350, 0.2 M NH4OAc, 0.1 M Bis-Tris pH 6.1-6.7; complex prepared by overnight soaking in mother liquor containing 4 mM racemic 5-bromo-2-(piperidin-3-ylamino)benzoic acid, ...Details: 16-20% (w/v) PEG3350, 0.2 M NH4OAc, 0.1 M Bis-Tris pH 6.1-6.7; complex prepared by overnight soaking in mother liquor containing 4 mM racemic 5-bromo-2-(piperidin-3-ylamino)benzoic acid, vapor diffusion, hanging drop, temperature 284K
PH range: 6.1 - 6.7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.98407
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 27, 2007 / Details: SI(111)
RadiationMonochromator: SI(111) MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98407 Å / Relative weight: 1
ReflectionResolution: 1.8→19.7 Å / Num. obs: 37044 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 37.23 Å2
Reflection shellResolution: 1.8→1.9 Å / Rmerge(I) obs: 0.442 / Mean I/σ(I) obs: 4.2 / % possible all: 99.9

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
REFMAC5.2.0019refinement
PDB_EXTRACT3.004data extraction
RefinementResolution: 1.8→19.7 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.947 / SU B: 5.105 / SU ML: 0.072 / TLS residual ADP flag: LIKELY RESIDUAL / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflection
Rfree0.217 1837 5 %
Rwork0.175 --
obs0.177 37044 99.9 %
Solvent computationSolvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 23.73 Å2
Refinement stepCycle: LAST / Resolution: 1.8→19.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2538 0 68 165 2771
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0260.0212684
X-RAY DIFFRACTIONr_bond_other_d0.0010.021926
X-RAY DIFFRACTIONr_angle_refined_deg1.9271.9323626
X-RAY DIFFRACTIONr_angle_other_deg0.9843.0054514
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2385302
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.44422.692156
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.53115428
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4231532
X-RAY DIFFRACTIONr_chiral_restr0.1320.2346
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0213028
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02628
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_refined0.2160.2158
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2980.28
X-RAY DIFFRACTIONr_symmetry_vdw_other0.4030.228
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3020.26
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.3561.51505
X-RAY DIFFRACTIONr_mcbond_other0.4731.5619
X-RAY DIFFRACTIONr_mcangle_it2.40422419
X-RAY DIFFRACTIONr_scbond_it3.73231179
X-RAY DIFFRACTIONr_scangle_it5.9524.51207
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.85 Å
RfactorNum. reflection% reflection
Rfree0.253 136 -
Rwork0.198 2543 -
obs--99.96 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.02540.026-0.0661.2394-0.53691.82780.005-0.0544-0.00080.0602-0.074-0.22480.06160.07460.0690.04340.0269-0.01360.08220.00740.041642.92270.513887.227
20.8361-0.1850.37051.5097-0.43181.2509-0.03320.07110.0819-0.14550.11560.0482-0.029-0.1875-0.08240.0650.0311-0.00470.12110.02940.021529.847110.963572.3272
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A12 - 162
2X-RAY DIFFRACTION1A500 - 600
3X-RAY DIFFRACTION1A166 - 243
4X-RAY DIFFRACTION2B8 - 160
5X-RAY DIFFRACTION2B500 - 600
6X-RAY DIFFRACTION2B166 - 252

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