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- PDB-3juq: Crystal Structure of PhzA/B from Burkholderia cepacia R18194 cocr... -

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Basic information

Entry
Database: PDB / ID: 3juq
TitleCrystal Structure of PhzA/B from Burkholderia cepacia R18194 cocrystallized with 2 mM 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: 1.75 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
Water4,161231
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4120 Å2
ΔGint-20 kcal/mol
Surface area14790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.401, 64.401, 160.520
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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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.: 231 / 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: 2.23 Å3/Da / Density % sol: 44.88 %
Crystal growTemperature: 284 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: 28% (w/v) PEG3350, 0.2 M NH4OAc, 0.1 M Bis-Tris pH 6.1-6.7; complex prepared by cocrystallization with 2 mM racemic 5-bromo-2-(piperidin-3-ylamino)benzoic acid, vapor diffusion, hanging drop, temperature 284K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.98407 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 27, 2007 / Details: SI(111)
RadiationMonochromator: SI(111) MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98407 Å / Relative weight: 1
ReflectionResolution: 1.75→19.61 Å / Num. obs: 75067 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 39.344 Å2 / Rmerge(I) obs: 0.109 / Net I/σ(I): 21.37
Reflection shell

Rmerge(I) obs: 0.03 / Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Mean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.75-1.853.314858511517100
1.85-26.417498713261100
2-2.111.1921986866100
2.1-2.214.2763035646100
2.2-2.317.764525478199.9
2.3-2.422.3531893920100
2.4-2.526.3454563346100
2.5-332.514791310860100
3-445.51175758645100
4-551.6411923062100
5-651.8182611352100
6-851.7143081081100
8-1049.24262370100
10-1546.12994288100
15-2044.167872100
20-30
30-40
40-50
50

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
REFMAC5.5.0070refinement
PDB_EXTRACT3.004data extraction
RefinementResolution: 1.75→19.61 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.953 / SU B: 5.188 / SU ML: 0.075 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.104 / ESU R Free: 0.107 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.214 1987 5 %RANDOM
Rwork0.172 ---
obs0.174 39771 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 24.657 Å2
Baniso -1Baniso -2Baniso -3
1-0.95 Å20.47 Å20 Å2
2--0.95 Å20 Å2
3----1.42 Å2
Refinement stepCycle: LAST / Resolution: 1.75→19.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2591 0 68 231 2890
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.0212871
X-RAY DIFFRACTIONr_bond_other_d0.0020.022061
X-RAY DIFFRACTIONr_angle_refined_deg1.9311.943900
X-RAY DIFFRACTIONr_angle_other_deg0.9763.0074815
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1615331
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.04922.695167
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.34815452
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.6111534
X-RAY DIFFRACTIONr_chiral_restr0.1320.2369
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0213263
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02671
X-RAY DIFFRACTIONr_mcbond_it1.2921.51581
X-RAY DIFFRACTIONr_mcbond_other0.4951.5647
X-RAY DIFFRACTIONr_mcangle_it2.23322554
X-RAY DIFFRACTIONr_scbond_it3.53731290
X-RAY DIFFRACTIONr_scangle_it5.4254.51336
LS refinement shellResolution: 1.75→1.795 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.232 155 -
Rwork0.2 2717 -
all-2872 -
obs--100 %
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)
11.3531-0.0371-0.14051.6281-0.83592.88540.0142-0.06810.00410.1336-0.0803-0.2920.09040.12590.06610.02940.0109-0.030.03470.00350.097443.09790.52886.1867
21.5093-0.09080.58012.244-0.88911.8645-0.06480.08250.0789-0.09930.19550.121-0.0297-0.3379-0.13070.02910.0177-0.00050.11160.03530.063529.955211.046672.2817
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A9 - 164
2X-RAY DIFFRACTION1A500 - 600
3X-RAY DIFFRACTION1A166 - 282
4X-RAY DIFFRACTION2B8 - 163
5X-RAY DIFFRACTION2B500 - 600
6X-RAY DIFFRACTION2B166 - 279

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