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- PDB-3rem: Structure of the Isochorismate-Pyruvate Lyase from Pseudomonas ae... -

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Basic information

Entry
Database: PDB / ID: 3rem
TitleStructure of the Isochorismate-Pyruvate Lyase from Pseudomonas aerugionsa with Bound Salicylate and Pyruvate
ComponentsSalicylate biosynthesis protein pchB
KeywordsLYASE / INTERTWINED DIMER / Mutase
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsOlucha, J. / Ouellette, A.N. / Luo, Q. / Lamb, A.L.
CitationJournal: Biochemistry / Year: 2011
Title: pH Dependence of Catalysis by Pseudomonas aeruginosa Isochorismate-Pyruvate Lyase: Implications for Transition State Stabilization and the Role of Lysine 42.
Authors: Olucha, J. / Ouellette, A.N. / Luo, Q. / Lamb, A.L.
History
DepositionApr 4, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 27, 2011Provider: repository / Type: Initial release
Revision 1.1Aug 31, 2011Group: Database references
Revision 1.2Sep 13, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
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

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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)23,3466
Polymers22,8942
Non-polymers4524
Water79344
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6190 Å2
ΔGint-18 kcal/mol
Surface area9130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.316, 60.254, 60.607
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

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Components

#1: Protein Salicylate biosynthesis protein pchB


Mass: 11447.064 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: PAO1 / Gene: PA4230, pchB / Plasmid: PET29B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS
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.: 44 / 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: 1.89 Å3/Da / Density % sol: 34.81 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 0.2 M lithium sulfate, 0.1 M sodium acetate, 6% glycerol, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 1 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Apr 30, 2010 / Details: Rh coated flat mirror, toroidal focusing mirror
RadiationMonochromator: Double crystal monochromator, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.95→31.71 Å / Num. all: 13010 / Num. obs: 12438 / % possible obs: 95.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Rsym value: 0.058 / Net I/σ(I): 15.4
Reflection shellResolution: 1.95→2.06 Å / Redundancy: 3.4 % / Mean I/σ(I) obs: 5.2 / Num. unique all: 1816 / Rsym value: 0.226 / % possible all: 97.1

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
REFMAC5.5.0072 & PHENIX 1.7-650refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2H9D

2h9d


Resolution: 1.95→31.71 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.918 / SU B: 4.498 / SU ML: 0.13 / Cross valid method: THROUGHOUT / ESU R: 0.285 / ESU R Free: 0.23
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29084 1235 10 %RANDOM
Rwork0.23086 ---
all0.23665 12438 --
obs0.23665 11177 94.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.308 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2---0.02 Å20 Å2
3---0.03 Å2
Refinement stepCycle: LAST / Resolution: 1.95→31.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1564 0 32 44 1640
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0221635
X-RAY DIFFRACTIONr_angle_refined_deg1.2111.9662213
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.6695194
X-RAY DIFFRACTIONr_dihedral_angle_2_deg26.59122.68382
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.67915273
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7311520
X-RAY DIFFRACTIONr_chiral_restr0.0860.2231
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211286
X-RAY DIFFRACTIONr_mcbond_it0.5461.5976
X-RAY DIFFRACTIONr_mcangle_it1.03821563
X-RAY DIFFRACTIONr_scbond_it1.8373659
X-RAY DIFFRACTIONr_scangle_it3.0944.5650
LS refinement shellResolution: 1.952→2.002 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.382 115 -
Rwork0.264 801 -
obs--96.83 %

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