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- PDB-1nf9: Crystal Structure of PhzD protein from Pseudomonas aeruginosa -

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Basic information

Entry
Database: PDB / ID: 1nf9
TitleCrystal Structure of PhzD protein from Pseudomonas aeruginosa
Componentsphenazine biosynthesis protein phzD
KeywordsHYDROLASE / isochorismatase / enzyme / phenazine pathway
Function / homology
Function and homology information


trans-2,3-dihydro-3-hydroxyanthranilic acid synthase / isochorismatase activity / phenazine biosynthetic process
Similarity search - Function
Isochorismatase / Isochorismatase-like / Isochorismatase-like / Isochorismatase-like superfamily / Isochorismatase family / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
FORMIC ACID / Phenazine biosynthesis protein PhzD1 / Phenazine biosynthesis protein PhzD2
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SAD S / Resolution: 1.5 Å
AuthorsParsons, F. / Calabrese, K. / Eisenstein, E. / Ladner, J.E.
CitationJournal: Biochemistry / Year: 2003
Title: Structure and mechanism of Pseudomonas aeruginosa PhzD, an isochorismatase from the phenazine biosynthetic pathway
Authors: Parsons, J.F. / Calabrese, K. / Eisenstein, E. / Ladner, J.E.
History
DepositionDec 13, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 17, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: phenazine biosynthesis protein phzD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,5593
Polymers23,2211
Non-polymers3382
Water5,242291
1
A: phenazine biosynthesis protein phzD
hetero molecules

A: phenazine biosynthesis protein phzD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,1186
Polymers46,4412
Non-polymers6774
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_556-x,y,-z+3/21
Unit cell
Length a, b, c (Å)68.850, 77.030, 82.550
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-443-

HOH

DetailsThe second part of the biological dimer is generated by the two fold axis: -x,y,-z+3/2

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Components

#1: Protein phenazine biosynthesis protein phzD / PhzD isochorismatase


Mass: 23220.541 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: PhzD / Plasmid: pET28a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL-21(DE3)
References: UniProt: Q7DC80, UniProt: P0DPB9*PLUS, isochorismatase
#2: Sugar ChemComp-BOG / octyl beta-D-glucopyranoside / Beta-Octylglucoside / octyl beta-D-glucoside / octyl D-glucoside / octyl glucoside / Octyl glucoside


Type: D-saccharide / Mass: 292.369 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C14H28O6 / Comment: detergent*YM
IdentifierTypeProgram
b-octylglucosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#3: Chemical ChemComp-FMT / FORMIC ACID / Formic acid


Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 291 / 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: 2.03 Å3/Da / Density % sol: 47.78 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 10-20% polyethylene glycol 4000, 0.2M ammonium formate, 0.2% beta-octylglucoside, 1mM aminodeoxychorismate, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
pH: 7.2 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
150 mMMOPS1drop
21 mMdithiothreitol1drop
31 mMEDTA1droppH7.2
417 mg/mlprotein1drop
50.2 %beta-octylglucoside1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Sep 16, 2002 / Details: OSMIC
RadiationMonochromator: osmic / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.5→20 Å / Num. all: 33819 / Num. obs: 33819 / % possible obs: 92.7 % / Redundancy: 11 % / Rmerge(I) obs: 0.032 / Net I/σ(I): 25.6
Reflection shellResolution: 1.5→1.55 Å / Redundancy: 2 % / Rmerge(I) obs: 0.097 / Mean I/σ(I) obs: 3.2 / % possible all: 80.4
Reflection
*PLUS
Num. measured all: 357616
Reflection shell
*PLUS
% possible obs: 80.4 %

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Processing

Software
NameClassification
d*TREKdata scaling
CrystalCleardata reduction
SHELXmodel building
SHELXL-97refinement
SOLVEphasing
RESOLVEphasing
RefinementMethod to determine structure: SAD S / Resolution: 1.5→20 Å / Num. parameters: 17525 / Num. restraintsaints: 20980 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER / Details: ANISOTROPIC REFINEMENT REDUCED FREE R BY 0.035
RfactorNum. reflection% reflectionSelection details
Rfree0.225 1607 5.1 %RANDOM
Rwork0.155 ---
all0.156 31344 --
obs0.156 31344 87.2 %-
Refine analyzeNum. disordered residues: 0 / Occupancy sum hydrogen: 1607 / Occupancy sum non hydrogen: 1945.5
Refinement stepCycle: LAST / Resolution: 1.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1632 0 20 294 1946
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.01
X-RAY DIFFRACTIONs_angle_d0.031
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0285
X-RAY DIFFRACTIONs_zero_chiral_vol0.055
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.057
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.044
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.003
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.059
X-RAY DIFFRACTIONs_approx_iso_adps0.082
Software
*PLUS
Name: SHELXL / Version: 97 / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.5 Å / Lowest resolution: 20 Å / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_plane_restr0.029
X-RAY DIFFRACTIONs_chiral_restr0.055

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