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- PDB-3hgx: Crystal Structure of Pseudomonas aeruginosa Isochorismate-Pyruvat... -

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Basic information

Entry
Database: PDB / ID: 3hgx
TitleCrystal Structure of Pseudomonas aeruginosa Isochorismate-Pyruvate Lyase K42A mutant in complex with salicylate and pyruvate
ComponentsSalicylate biosynthesis protein pchB
KeywordsLYASE / siderophore biosynthesis / pyochelin / isochorismate-pyruvate lyase / chorismate mutase / PchB
Function / homology
Function and homology information


pyochelin biosynthetic process / isochorismate lyase / carbon-oxygen lyase activity / isochorismate pyruvate lyase activity / salicylic acid biosynthetic process / chorismate metabolic process / chorismate mutase / chorismate mutase activity
Similarity search - Function
Salicylate biosynthesis protein PchB / : / Chorismate mutase / Chorismate Mutase Domain, subunit A / Chorismate mutase domain superfamily / Chorismate mutase domain profile. / Chorismate mutase type II / Chorismate mutase type II superfamily / Chorismate mutase II, prokaryotic-type / Chorismate mutase type II ...Salicylate biosynthesis protein PchB / : / Chorismate mutase / Chorismate Mutase Domain, subunit A / Chorismate mutase domain superfamily / Chorismate mutase domain profile. / Chorismate mutase type II / Chorismate mutase type II superfamily / Chorismate mutase II, prokaryotic-type / Chorismate mutase type II / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
PYRUVIC ACID / 2-HYDROXYBENZOIC ACID / Isochorismate pyruvate lyase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsLuo, Q. / Lamb, A.L.
CitationJournal: Biochemistry / Year: 2009
Title: Structure-function analyses of isochorismate-pyruvate lyase from Pseudomonas aeruginosa suggest differing catalytic mechanisms for the two pericyclic reactions of this bifunctional enzyme.
Authors: Luo, Q. / Olucha, J. / Lamb, A.L.
History
DepositionMay 14, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 30, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Revision 1.3Oct 13, 2021Group: Advisory / Database references / Derived calculations
Category: database_2 / pdbx_unobs_or_zero_occ_atoms ...database_2 / pdbx_unobs_or_zero_occ_atoms / 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
Revision 1.4Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Category: atom_site / chem_comp_atom / chem_comp_bond
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Salicylate biosynthesis protein pchB
B: Salicylate biosynthesis protein pchB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,2306
Polymers22,7782
Non-polymers4524
Water28816
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5770 Å2
ΔGint-30 kcal/mol
Surface area10020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.015, 53.150, 82.336
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Salicylate biosynthesis protein pchB


Mass: 11388.963 Da / Num. of mol.: 2 / Mutation: K42A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: PAO1 / Gene: pchB, PA4230 / Plasmid: pET29b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q51507, Lyases; Carbon-carbon lyases; Other carbon-carbon lyases
#2: Chemical ChemComp-SAL / 2-HYDROXYBENZOIC ACID / SALICYLIC ACID


Mass: 138.121 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H6O3
#3: Chemical ChemComp-PYR / PYRUVIC ACID


Mass: 88.062 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H4O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 16 / 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: 2.34 Å3/Da / Density % sol: 47.33 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1M Tris-HCl, pH 8.5, 2M ammonium phosphate, 13% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 291.15K

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Data collection

DiffractionMean temperature: 113.15 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jun 19, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.5→100 Å / Num. obs: 7706 / % possible obs: 99.9 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.101 / Χ2: 0.897 / Net I/σ(I): 15.234
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.5-2.596.70.2777490.95399.9
2.59-2.696.70.2287461.001100
2.69-2.826.60.1977561.002100
2.82-2.966.80.1757590.964100
2.96-3.156.70.1477550.988100
3.15-3.396.80.1057620.895100
3.39-3.736.50.0927690.905100
3.73-4.276.60.0697680.839100
4.27-5.396.50.0637950.763100
5.39-1005.90.0498470.65898.9

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.2.0019refinement
PDB_EXTRACT3.005data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2H9D

2h9d


Resolution: 2.5→41.49 Å / Cor.coef. Fo:Fc: 0.915 / Cor.coef. Fo:Fc free: 0.873 / Occupancy max: 1 / Occupancy min: 0 / SU B: 9.959 / SU ML: 0.227 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.733 / ESU R Free: 0.329
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.276 350 4.5 %RANDOM
Rwork0.216 ---
obs0.218 7346 99.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 45.92 Å2 / Biso mean: 15.597 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1-0.07 Å20 Å20 Å2
2---0.01 Å20 Å2
3----0.06 Å2
Refinement stepCycle: LAST / Resolution: 2.5→41.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1578 0 32 16 1626
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0221627
X-RAY DIFFRACTIONr_angle_refined_deg1.2191.9642203
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.6135196
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.46122.82178
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.73215263
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.8461518
X-RAY DIFFRACTIONr_chiral_restr0.0940.2232
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021276
X-RAY DIFFRACTIONr_nbd_refined0.1940.2752
X-RAY DIFFRACTIONr_nbtor_refined0.2990.21101
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1180.247
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1550.226
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1140.24
X-RAY DIFFRACTIONr_mcbond_it0.51.51027
X-RAY DIFFRACTIONr_mcangle_it0.81321575
X-RAY DIFFRACTIONr_scbond_it1.23711
X-RAY DIFFRACTIONr_scangle_it1.8794.5628
LS refinement shellResolution: 2.503→2.567 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.281 23 -
Rwork0.228 513 -
all-536 -
obs--97.99 %

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