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- PDB-3ex9: Crystal structure of PhzA/B from Burkholderia cepacia R18194 crys... -

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Basic information

Entry
Database: PDB / ID: 3ex9
TitleCrystal structure of PhzA/B from Burkholderia cepacia R18194 crystallized in C2221
ComponentsPhenazine biosynthesis protein A/B
KeywordsBIOSYNTHETIC PROTEIN / phenazine biosynthesis / KSI
Function / homologyPhenazine biosynthesis protein A/B / Phenazine biosynthesis protein A/B / Nuclear Transport Factor 2; Chain: A, - #50 / antibiotic biosynthetic process / NTF2-like domain superfamily / Nuclear Transport Factor 2; Chain: A, / Roll / Alpha Beta / Phenazine biosynthesis protein A/B
Function and homology information
Biological speciesBurkholderia sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsAhuja, E.G. / 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 16, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 30, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Phenazine biosynthesis protein A/B


Theoretical massNumber of molelcules
Total (without water)21,5311
Polymers21,5311
Non-polymers00
Water61334
1
A: Phenazine biosynthesis protein A/B

A: Phenazine biosynthesis protein A/B


Theoretical massNumber of molelcules
Total (without water)43,0622
Polymers43,0622
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-1/21
Buried area3460 Å2
ΔGint-16 kcal/mol
Surface area14630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.940, 79.680, 64.240
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Phenazine biosynthesis protein A/B


Mass: 21531.025 Da / Num. of mol.: 1 / Fragment: PhzA/B
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia sp. (bacteria) / Strain: R18194 / Gene: Bcep18194_B1568 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2 pLysS / References: UniProt: Q396C9
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 34 / 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: 2.35 Å3/Da / Density % sol: 47.57 %
Crystal growTemperature: 284 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: 0.1M Bis-TRIS, 0.2M NH4OAc, 20% (w/v) PEG 3350, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 284K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 20, 2008
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→42.26 Å / Num. all: 10609 / Num. obs: 10338 / % possible obs: 97.4 % / Observed criterion σ(I): 5.5 / Redundancy: 9.2 % / Biso Wilson estimate: 48 Å2 / Rsym value: 0.064 / Net I/σ(I): 20.1
Reflection shellResolution: 2.1→2.3 Å / Redundancy: 8.6 % / Rmerge(I) obs: 0.429 / Mean I/σ(I) obs: 5.5 / Num. unique all: 1305 / % possible all: 95.7

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Processing

Software
NameVersionClassification
MOLREPphasing
REFMAC5.2.0019refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3B4O

3b4o


Resolution: 2.2→20 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.916 / SU B: 16.581 / SU ML: 0.179 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.23 / ESU R Free: 0.197 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS; TLS-REFINEMENT WAS USED THROUGOUT (1 BODY)
RfactorNum. reflection% reflectionSelection details
Rfree0.23968 535 5.2 %RANDOM
Rwork0.19218 ---
obs0.19476 9803 97.45 %-
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: 54.538 Å2
Baniso -1Baniso -2Baniso -3
1--1.84 Å20 Å20 Å2
2--3.08 Å20 Å2
3----1.23 Å2
Refinement stepCycle: LAST / Resolution: 2.2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1253 0 0 34 1287
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0211299
X-RAY DIFFRACTIONr_bond_other_d0.0020.02933
X-RAY DIFFRACTIONr_angle_refined_deg1.8311.9051757
X-RAY DIFFRACTIONr_angle_other_deg0.966
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.534
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.708
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.399
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.307
X-RAY DIFFRACTIONr_chiral_restr0.116
X-RAY DIFFRACTIONr_gen_planes_refined0.008
X-RAY DIFFRACTIONr_gen_planes_other0.001
X-RAY DIFFRACTIONr_nbd_refined0.211
X-RAY DIFFRACTIONr_nbd_other0.216
X-RAY DIFFRACTIONr_nbtor_refined0.191
X-RAY DIFFRACTIONr_nbtor_other0.095
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.193
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.193
X-RAY DIFFRACTIONr_symmetry_vdw_other0.314
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.182
X-RAY DIFFRACTIONr_mcbond_it1.097
X-RAY DIFFRACTIONr_mcbond_other0.265
X-RAY DIFFRACTIONr_mcangle_it1.632
X-RAY DIFFRACTIONr_scbond_it2.563
X-RAY DIFFRACTIONr_scangle_it3.958
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.448 30 -
Rwork0.35 716 -
obs--96.88 %
Refinement TLS params.Method: refined / Origin x: -11.0642 Å / Origin y: 1.1891 Å / Origin z: -14.952 Å
111213212223313233
T-0.1496 Å2-0.0656 Å2-0.0418 Å2--0.1007 Å20.0081 Å2---0.2039 Å2
L6.0507 °20.0597 °2-4.3093 °2-2.528 °20.1162 °2--5.6751 °2
S-0.0004 Å °0.8618 Å °0.1077 Å °-0.0057 Å °0.0197 Å °0.0549 Å °0.4001 Å °-1.0647 Å °-0.0193 Å °

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