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- PDB-3b4p: Crystal structure of phenazine biosynthesis protein PhzA/B from B... -

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Basic information

Entry
Database: PDB / ID: 3b4p
TitleCrystal structure of phenazine biosynthesis protein PhzA/B from Burkholderia cepacia R18194, complex with 2-(cyclohexylamino)benzoic acid
ComponentsPhenazine biosynthesis protein A/B
KeywordsBIOSYNTHETIC PROTEIN / phenazine biosynthesis / imine / Schiff base
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
2-(cyclohexylamino)benzoic acid / ACETATE ION / AZIDE ION / Phenazine biosynthesis protein A/B
Similarity search - Component
Biological speciesBurkholderia sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.7 Å
AuthorsAhuja, E.G. / Janning, P. / Mentel, M. / Graebsch, A. / Breinbauer, R. / Blankenfeldt, W.
CitationJournal: J.Am.Chem.Soc. / Year: 2008
Title: PhzA/B catalyzes the formation of the tricycle in phenazine biosynthesis.
Authors: Ahuja, E.G. / Janning, P. / Mentel, M. / Graebsch, A. / Breinbauer, R. / Hiller, W. / Costisella, B. / Thomashow, L.S. / Mavrodi, D.V. / Blankenfeldt, W.
History
DepositionOct 24, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 30, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Phenazine biosynthesis protein A/B
B: Phenazine biosynthesis protein A/B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,6026
Polymers43,0622
Non-polymers5404
Water4,486249
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.550, 64.550, 160.390
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: R18194 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2 pLysS / References: UniProt: Q396C9
#2: Chemical ChemComp-3B4 / 2-(cyclohexylamino)benzoic acid


Mass: 219.280 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H17NO2
#3: Chemical ChemComp-AZI / AZIDE ION


Mass: 42.020 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: N3
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 249 / 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: 2.24 Å3/Da / Density % sol: 45.09 %
Crystal growTemperature: 285 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 16-20% (w/v) PEG 3350, 0.2 M NH4-acetate, 0.1 M Bis-TRIS pH 6.1-6.7, soak with 10 mM 2-(cyclohexylamino)benzoic acid in ML, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 285K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9789 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 30, 2007 / Details: Si(111)monochromator
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 1.7→19.65 Å / Num. all: 43508 / Num. obs: 43465 / % possible obs: 99.9 % / Observed criterion σ(I): 4 / Redundancy: 14.1 % / Biso Wilson estimate: 35 Å2 / Rmerge(I) obs: 0.047 / Net I/σ(I): 24.2
Reflection shellResolution: 1.7→1.8 Å / Redundancy: 10.6 % / Rmerge(I) obs: 0.313 / Mean I/σ(I) obs: 4.2 / Num. unique all: 6744 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
XDSdata scaling
XDSdata reduction
XSCALEdata scaling
SHELXDphasing
RefinementMethod to determine structure: SAD / Resolution: 1.7→19.65 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.952 / SU B: 4.842 / SU ML: 0.073 / Cross valid method: THROUGHOUT / ESU R: 0.093 / ESU R Free: 0.099 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21406 2191 5 %RANDOM
Rwork0.1695 ---
obs0.17169 41272 99.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 28.096 Å2
Refinement stepCycle: LAST / Resolution: 1.7→19.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2666 0 39 249 2954
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0260.0212788
X-RAY DIFFRACTIONr_bond_other_d0.0020.021990
X-RAY DIFFRACTIONr_angle_refined_deg2.081.9233776
X-RAY DIFFRACTIONr_angle_other_deg1.0343.0024705
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2375325
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.99922.866164
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.61615450
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9161533
X-RAY DIFFRACTIONr_chiral_restr0.2590.2363
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.023190
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02652
X-RAY DIFFRACTIONr_nbd_refined0.2470.2572
X-RAY DIFFRACTIONr_nbd_other0.2280.22194
X-RAY DIFFRACTIONr_nbtor_refined0.1950.21335
X-RAY DIFFRACTIONr_nbtor_other0.0930.21596
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2370.2228
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2230.212
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3290.242
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1820.24
X-RAY DIFFRACTIONr_mcbond_it1.9421.52025
X-RAY DIFFRACTIONr_mcbond_other0.491.5650
X-RAY DIFFRACTIONr_mcangle_it2.1722574
X-RAY DIFFRACTIONr_scbond_it3.78631397
X-RAY DIFFRACTIONr_scangle_it5.3894.51200
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.228 171 -
Rwork0.2 2974 -
obs--100 %

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