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- PDB-1u1w: Structure and function of phenazine-biosynthesis protein PhzF fro... -

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Basic information

Entry
Database: PDB / ID: 1u1w
TitleStructure and function of phenazine-biosynthesis protein PhzF from Pseudomonas fluorescens 2-79
ComponentsPhenazine biosynthesis protein phzF
KeywordsISOMERASE / LYASE / phenazine biosynthesis / acid/base catalysis / closed form
Function / homology
Function and homology information


trans-2,3-dihydro-3-hydroxyanthranilate isomerase / trans-2,3-dihydro-3-hydroxy-anthranilate isomerase activity / phenazine biosynthetic process
Similarity search - Function
Phenazine biosynthesis PhzF protein / Phenazine biosynthesis-like protein / Diaminopimelate Epimerase; Chain A, domain 1 / Diaminopimelate Epimerase; Chain A, domain 1 / Roll / Alpha Beta
Similarity search - Domain/homology
3-HYDROXYANTHRANILIC ACID / ACETATE ION / Trans-2,3-dihydro-3-hydroxyanthranilate isomerase
Similarity search - Component
Biological speciesPseudomonas fluorescens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å
AuthorsBlankenfeldt, W. / Kuzin, A.P. / Skarina, T. / Korniyenko, Y. / Tong, L. / Bayer, P. / Janning, P. / Thomashow, L.S. / Mavrodi, D.V.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2004
Title: Structure and function of the phenazine biosynthetic protein PhzF from Pseudomonas fluorescens.
Authors: Blankenfeldt, W. / Kuzin, A.P. / Skarina, T. / Korniyenko, Y. / Tong, L. / Bayer, P. / Janning, P. / Thomashow, L.S. / Mavrodi, D.V.
History
DepositionJul 16, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 2, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Apr 16, 2014Group: Data collection
Revision 1.4Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / 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 phzF
B: Phenazine biosynthesis protein phzF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,0307
Polymers64,5132
Non-polymers5165
Water12,232679
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4180 Å2
ΔGint0 kcal/mol
Surface area20680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.600, 99.860, 57.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-1030-

HOH

21B-967-

HOH

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Components

#1: Protein Phenazine biosynthesis protein phzF


Mass: 32256.561 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas fluorescens (bacteria) / Gene: phzF / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta pLys S / References: UniProt: Q51792
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-3HA / 3-HYDROXYANTHRANILIC ACID / 2-AMINO-3-HYDROXYBENZOIC ACID


Mass: 153.135 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H7NO3
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 679 / 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: 2.04 Å3/Da / Density % sol: 39.78 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: preincubation with ligand, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 1.00133 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 7, 2003
RadiationMonochromator: diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00133 Å / Relative weight: 1
ReflectionResolution: 1.35→20 Å / Num. all: 116176 / Num. obs: 116176 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 3 / Redundancy: 4 % / Biso Wilson estimate: 20 Å2 / Rsym value: 0.068 / Net I/σ(I): 11.3
Reflection shellResolution: 1.35→1.45 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 3.1 / Rsym value: 0.415 / % possible all: 99.3

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Processing

Software
NameVersionClassification
REFMAC5.1.19refinement
XDdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1u1v

1u1v


Resolution: 1.35→19.73 Å / Cor.coef. Fo:Fc: 0.983 / Cor.coef. Fo:Fc free: 0.977 / SU B: 0.717 / SU ML: 0.029 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.046 / ESU R Free: 0.045 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1503 5844 5 %RANDOM
Rwork0.11844 ---
obs0.12005 110280 99.71 %-
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: 12.061 Å2
Baniso -1Baniso -2Baniso -3
1-0.41 Å20 Å20 Å2
2---0.34 Å20 Å2
3----0.06 Å2
Refinement stepCycle: LAST / Resolution: 1.35→19.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4248 0 36 679 4963
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0260.0214628
X-RAY DIFFRACTIONr_bond_other_d0.0670.024220
X-RAY DIFFRACTIONr_angle_refined_deg2.0581.9516329
X-RAY DIFFRACTIONr_angle_other_deg1.75639774
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4375608
X-RAY DIFFRACTIONr_chiral_restr0.1490.2698
X-RAY DIFFRACTIONr_gen_planes_refined0.040.025391
X-RAY DIFFRACTIONr_gen_planes_other0.0680.02969
X-RAY DIFFRACTIONr_nbd_refined0.2540.2849
X-RAY DIFFRACTIONr_nbd_other0.2820.25227
X-RAY DIFFRACTIONr_nbtor_other0.0890.22733
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2130.2476
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2250.232
X-RAY DIFFRACTIONr_symmetry_vdw_other0.360.297
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2630.252
X-RAY DIFFRACTIONr_mcbond_it2.2581.52944
X-RAY DIFFRACTIONr_mcangle_it3.00424755
X-RAY DIFFRACTIONr_scbond_it4.22531684
X-RAY DIFFRACTIONr_scangle_it5.9344.51574
X-RAY DIFFRACTIONr_rigid_bond_restr2.40524628
X-RAY DIFFRACTIONr_sphericity_free10.3852679
X-RAY DIFFRACTIONr_sphericity_bonded4.34924504
LS refinement shellResolution: 1.35→1.385 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.242 447
Rwork0.222 7962
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)
10.53650.1154-0.26380.19210.00380.30910.00030.03070.03740.0070.0231-0.0017-0.0325-0.0284-0.02350.0086-0.0032-0.00350.02990.02040.03027.09430.99324.816
20.2185-0.01790.12160.1287-0.12741.0904-0.01170.038-0.0032-0.02940.0376-0.02250.1385-0.0388-0.0260.0453-0.022-0.00870.02380.01140.005617.10710.3141.796
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 27821 - 298
2X-RAY DIFFRACTION1AE700
3X-RAY DIFFRACTION2BB1 - 27821 - 298
4X-RAY DIFFRACTION2BF701

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