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- PDB-1nf8: Crystal structure of PhzD protein active site mutant with substrate -

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Basic information

Entry
Database: PDB / ID: 1nf8
TitleCrystal structure of PhzD protein active site mutant with substrate
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 domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-ISC / Phenazine biosynthesis protein PhzD1 / Phenazine biosynthesis protein PhzD2
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.6 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 1.3Sep 14, 2011Group: Non-polymer description
Revision 1.4Jul 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 1.5Oct 27, 2021Group: Database references / Structure summary / Category: chem_comp / database_2 / struct_ref_seq_dif
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.6Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.7Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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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)23,6953
Polymers23,1771
Non-polymers5192
Water5,368298
1
A: phenazine biosynthesis protein phzD
hetero molecules

A: phenazine biosynthesis protein phzD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,3906
Polymers46,3532
Non-polymers1,0374
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_556-x,y,-z+3/21
Unit cell
Length a, b, c (Å)68.400, 77.010, 82.440
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-508-

HOH

21A-545-

HOH

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

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Components

#1: Protein phenazine biosynthesis protein phzD


Mass: 23176.529 Da / Num. of mol.: 1 / Mutation: D38A
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


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-ISC / (5S,6S)-5-[(1-carboxyethenyl)oxy]-6-hydroxycyclohexa-1,3-diene-1-carboxylic acid / ISOCHORISMIC ACID


Mass: 226.183 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H10O6
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 298 / 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: 2.02 Å3/Da / Density % sol: 47.45 %
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 isochorismate, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 %PEG40001drop
20.2 Mammonium formate1drop
310-20 %PEG40001reservoir
40.2 Mammonium formate1reservoir
517 mg/mlprotein1drop

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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: Jul 15, 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: 1.6→20 Å / Num. obs: 27572 / % possible obs: 99.7 % / Redundancy: 3 % / Rmerge(I) obs: 0.042 / Net I/σ(I): 22
Reflection shellResolution: 1.6→1.7 Å / Redundancy: 3 % / Rmerge(I) obs: 0.207 / Mean I/σ(I) obs: 3.1 / Num. unique all: 3895 / % possible all: 99
Reflection
*PLUS
Num. measured all: 82842
Reflection shell
*PLUS
% possible obs: 99 %

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Processing

Software
NameVersionClassification
SHELXmodel building
SHELXL-97refinement
CrystalClear(MSC/RIGAKU)data reduction
d*TREKdata scaling
SHELXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Native structure

Resolution: 1.6→20 Å / Num. parameters: 17662 / Num. restraintsaints: 21130 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.21 1423 5.2 %RANDOM
Rwork0.134 ---
all0.134 27403 --
obs0.134 27403 92.9 %-
Refine analyzeNum. disordered residues: 0 / Occupancy sum hydrogen: 1608 / Occupancy sum non hydrogen: 1962
Refinement stepCycle: LAST / Resolution: 1.6→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1629 0 36 298 1963
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.008
X-RAY DIFFRACTIONs_angle_d0.026
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0279
X-RAY DIFFRACTIONs_zero_chiral_vol0.047
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.049
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.021
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.003
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.055
X-RAY DIFFRACTIONs_approx_iso_adps0.08
Software
*PLUS
Name: SHELXL / Version: 97 / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.6 Å / Lowest resolution: 20 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.21
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_plane_restr0.028
X-RAY DIFFRACTIONs_chiral_restr0.047

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