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- PDB-1u1v: Structure and function of phenazine-biosynthesis protein PhzF fro... -

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Basic information

Entry
Database: PDB / ID: 1u1v
TitleStructure and function of phenazine-biosynthesis protein PhzF from Pseudomonas fluorescens 2-79
ComponentsPhenazine biosynthesis protein phzF
KeywordsISOMERASE / LYASE / phenazine biosynthesis / open form / acid/base catalysis
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 / cytoplasm
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
Trans-2,3-dihydro-3-hydroxyanthranilate isomerase
Similarity search - Component
Biological speciesPseudomonas fluorescens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.7 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: Advisory / Version format compliance
Revision 1.3Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / 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_conn.pdbx_leaving_atom_flag / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,9634
Polymers32,6791
Non-polymers2843
Water5,963331
1
A: Phenazine biosynthesis protein phzF
hetero molecules

A: Phenazine biosynthesis protein phzF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,9268
Polymers65,3572
Non-polymers5686
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Unit cell
Length a, b, c (Å)56.260, 56.260, 156.400
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-528-

HOH

21A-611-

HOH

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Components

#1: Protein Phenazine biosynthesis protein phzF


Mass: 32678.611 Da / Num. of mol.: 1
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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 331 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.19 Å3/Da / Density % sol: 43.75 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 0.1M Na-Citrate, 0.2M Ammonium Sulphate, 10% (w/v) PEG 3350, pH 5.6, temperature 292K, VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 12, 2003
RadiationMonochromator: diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 1.7→20 Å / Num. all: 31965 / Num. obs: 31965 / % possible obs: 98.2 % / Redundancy: 20.6 % / Biso Wilson estimate: 22 Å2 / Rsym value: 0.075 / Net I/σ(I): 27.4
Reflection shellResolution: 1.7→1.8 Å / Redundancy: 15.3 % / Mean I/σ(I) obs: 9.8 / Rsym value: 0.268 / % possible all: 91.1

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Processing

Software
NameVersionClassification
REFMAC5.1.19refinement
XDSdata reduction
XDSdata scaling
SHELXDphasing
RefinementMethod to determine structure: SAD / Resolution: 1.7→19.21 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.967 / SU B: 1.425 / SU ML: 0.047 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.079 / ESU R Free: 0.077 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.15338 1633 5.1 %RANDOM
Rwork0.12967 ---
obs0.1309 30304 98.41 %-
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: 13.84 Å2
Baniso -1Baniso -2Baniso -3
1-0.21 Å20.1 Å20 Å2
2--0.21 Å20 Å2
3----0.31 Å2
Refinement stepCycle: LAST / Resolution: 1.7→19.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2119 0 16 331 2466
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.0212220
X-RAY DIFFRACTIONr_bond_other_d0.0020.022060
X-RAY DIFFRACTIONr_angle_refined_deg1.5621.9523021
X-RAY DIFFRACTIONr_angle_other_deg0.91834767
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1065277
X-RAY DIFFRACTIONr_chiral_restr0.1060.2342
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.022479
X-RAY DIFFRACTIONr_gen_planes_other0.0190.02458
X-RAY DIFFRACTIONr_nbd_refined0.20.2378
X-RAY DIFFRACTIONr_nbd_other0.2570.22392
X-RAY DIFFRACTIONr_nbtor_other0.0820.21346
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2040.2217
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2170.210
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3550.268
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2270.241
X-RAY DIFFRACTIONr_mcbond_it0.9631.51392
X-RAY DIFFRACTIONr_mcangle_it1.76522248
X-RAY DIFFRACTIONr_scbond_it3.163828
X-RAY DIFFRACTIONr_scangle_it5.0444.5773
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.173 102
Rwork0.149 1859
Refinement TLS params.Method: refined / Origin x: 18.266 Å / Origin y: 22.212 Å / Origin z: 16.474 Å
111213212223313233
T0.0329 Å2-0.0087 Å2-0.0075 Å2-0.0063 Å20.0105 Å2--0.0203 Å2
L0.0211 °2-0.087 °20.006 °2-0.3854 °2-0.1775 °2--0.1697 °2
S-0.0057 Å °-0.0033 Å °-0.0066 Å °-0.0132 Å °0.0091 Å °0.0192 Å °0.0002 Å °0.0001 Å °-0.0034 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 27821 - 298
2X-RAY DIFFRACTION1AB - C401 - 4021
3X-RAY DIFFRACTION1AD5011

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