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

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Basic information

Entry
Database: PDB / ID: 3jup
TitleCrystal Structure of PhzA/B from Burkholderia cepacia R18194 in complex with (S)-5-bromo-2-(piperidin-3-ylamino)benzoic acid
ComponentsPhenazine biosynthesis protein A/B
KeywordsBIOSYNTHETIC PROTEIN / chirality / drug design / phenazine biosynthesis / medicinal chemistry / inhibitor
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-[(3S)-piperidin-3-ylamino]benzoate / Phenazine biosynthesis protein A/B
Similarity search - Component
Biological speciesBurkholderia sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.9 Å
AuthorsMentel, M. / Jain, I.H. / 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)43,6584
Polymers43,0622
Non-polymers5962
Water3,711206
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4240 Å2
ΔGint-20 kcal/mol
Surface area15040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.720, 64.720, 160.760
Angle α, β, γ (deg.)90.000, 90.000, 120.000
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-AKD / 5-bromo-2-[(3S)-piperidin-3-ylamino]benzoate


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


Mass: 18.015 Da / Num. of mol.: 206 / 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: 45.5 %
Crystal growTemperature: 284 K / Method: vapor diffusion, hanging drop
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 5 mM (S)-5-bromo-2-(piperidin-3-ylamino)benzoic acid, vapor ...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 5 mM (S)-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: 0.97886 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 5, 2008 / Details: SI(111)
RadiationMonochromator: SI(111) MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97886 Å / Relative weight: 1
ReflectionResolution: 1.9→19.7 Å / Num. obs: 31529 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 40.736 Å2 / Rmerge(I) obs: 0.049 / Net I/σ(I): 27.14
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.9-20.574.6440374395100
2-2.10.3398400463632100
2.1-2.20.23810.9330992994100
2.2-30.07925.813476912248100
3-40.03652509044720100
4-50.03260.617865169799.9
5-60.03260785976799.9
6-70.0359.54014403100
7-80.03612269231100
8-90.02960.61325141100
9-100.02858.87268298.8
10-110.03159.46196897.1
11-120.03156.63213997.5
12-140.02854.54495690.3
14-160.03558.62362790
16-180.03749.31071680
18-200.03548.8841392.9
20

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
REFMAC5.5.0070refinement
PDB_EXTRACT3.004data extraction
RefinementResolution: 1.9→19.7 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.95 / SU B: 7.388 / SU ML: 0.096 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.132 / ESU R Free: 0.131 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.218 1592 5 %RANDOM
Rwork0.173 ---
obs0.175 31529 99.93 %-
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: 27.845 Å2
Baniso -1Baniso -2Baniso -3
1-0.73 Å20.36 Å20 Å2
2--0.73 Å20 Å2
3----1.09 Å2
Refinement stepCycle: LAST / Resolution: 1.9→19.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2605 0 34 206 2845
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0212771
X-RAY DIFFRACTIONr_bond_other_d0.0010.021974
X-RAY DIFFRACTIONr_angle_refined_deg1.8461.9233763
X-RAY DIFFRACTIONr_angle_other_deg0.9473.0034680
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7015328
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.06422.866164
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.3315446
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.571533
X-RAY DIFFRACTIONr_chiral_restr0.1210.2365
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0213167
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02648
X-RAY DIFFRACTIONr_mcbond_it1.1221.51582
X-RAY DIFFRACTIONr_mcbond_other0.4031.5646
X-RAY DIFFRACTIONr_mcangle_it1.91922557
X-RAY DIFFRACTIONr_scbond_it3.23331189
X-RAY DIFFRACTIONr_scangle_it4.9564.51198
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.267 131 -
Rwork0.222 2114 -
all-2245 -
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)
11.23220.18020.14222.9827-0.90372.8530.07080.0295-0.07940.275-0.0189-0.57320.16920.0957-0.05190.07160.0405-0.0780.0594-0.01840.157842.99830.984385.882
21.54480.19190.59772.9963-1.01071.9369-0.12060.13950.093-0.17220.29560.08130.0004-0.3497-0.1750.0450.015-0.00910.1640.04980.056730.451711.478572.9455
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A9 - 165
2X-RAY DIFFRACTION1A500
3X-RAY DIFFRACTION1A166 - 263
4X-RAY DIFFRACTION2B9 - 165
5X-RAY DIFFRACTION2B500
6X-RAY DIFFRACTION2B166 - 273

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