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- PDB-1fw9: CHORISMATE LYASE WITH BOUND PRODUCT -

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Basic information

Entry
Database: PDB / ID: 1fw9
TitleCHORISMATE LYASE WITH BOUND PRODUCT
ComponentsCHORISMATE LYASE
KeywordsLYASE / new fold / ubiquinone pathway / 123654 antiparallel sheet topology
Function / homology
Function and homology information


chorismate lyase / chorismate lyase activity / pyruvate biosynthetic process / ubiquinone biosynthetic process / cytosol
Similarity search - Function
Chorismate--pyruvate lyase / Chorismate lyase / Chorismate lyase / Chorismate lyase-like / Chorismate pyruvate-lyase/UbiC transcription regulator-associated domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
P-HYDROXYBENZOIC ACID / Chorismate pyruvate-lyase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.4 Å
AuthorsGallagher, D.T. / Mayhew, M. / Holden, M. / Vilker, V. / Howard, A.
CitationJournal: Proteins / Year: 2001
Title: The crystal structure of chorismate lyase shows a new fold and a tightly retained product.
Authors: Gallagher, D.T. / Mayhew, M. / Holden, M.J. / Howard, A. / Kim, K.J. / Vilker, V.L.
History
DepositionSep 22, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 22, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow
Item: _exptl_crystal_grow.pdbx_details / _exptl_crystal_grow.temp
Revision 1.5Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CHORISMATE LYASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,7742
Polymers18,6361
Non-polymers1381
Water4,288238
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)31.693, 33.859, 39.891
Angle α, β, γ (deg.)67.37, 87.37, 65.26
Int Tables number1
Space group name H-MP1
Detailsasymmetric unit contains one biologically active monomer

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Components

#1: Protein CHORISMATE LYASE


Mass: 18635.557 Da / Num. of mol.: 1 / Fragment: COMPLETE ENZYME / Mutation: DOUBLE MUTANT C14S,C81S / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P26602, Lyases
#2: Chemical ChemComp-PHB / P-HYDROXYBENZOIC ACID


Mass: 138.121 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H6O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 238 / 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: 1.91 Å3/Da / Density % sol: 35.47 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 100 mM Hepes buffer, 22% (v/v) PEG 4K, 5% (v/v) isopropanol , pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 24K
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion / Details: Stover, C., (2000) J. Struct. Biol., 129, 96.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
126 %(v/v)PEG40001reservoir
280 mMHEPES1reservoir
35 %(v/v)isopropanol1reservoir
45 mMprotein1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 0.7469
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 4, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.7469 Å / Relative weight: 1
ReflectionResolution: 1.4→8 Å / Num. all: 67243 / Num. obs: 63699 / % possible obs: 95 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 4.6 % / Biso Wilson estimate: 10.5 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 21
Reflection shellResolution: 1.4→1.5 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.07 / % possible all: 95
Reflection
*PLUS
Num. obs: 26149 / Num. measured all: 136107 / Rmerge(I) obs: 0.05
Reflection shell
*PLUS
% possible obs: 94 %

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Processing

Software
NameVersionClassification
PHASESphasing
CNS1refinement
X-GENdata reduction
X-GENdata scaling
RefinementResolution: 1.4→7.99 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 279060.49 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.182 904 3.5 %EVERY NTH
Rwork0.164 ---
all0.2 25896 --
obs0.164 25896 95.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 89.95 Å2 / ksol: 0.415 e/Å3
Displacement parametersBiso mean: 13.7 Å2
Baniso -1Baniso -2Baniso -3
1-0.87 Å2-1.35 Å20.09 Å2
2--0.38 Å21.03 Å2
3----1.25 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.15 Å0.13 Å
Luzzati d res low-8 Å
Luzzati sigma a0.12 Å0.06 Å
Refinement stepCycle: LAST / Resolution: 1.4→7.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1315 0 10 238 1563
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.022
X-RAY DIFFRACTIONc_angle_deg2
X-RAY DIFFRACTIONc_dihedral_angle_d26.5
X-RAY DIFFRACTIONc_improper_angle_d1.42
X-RAY DIFFRACTIONc_mcbond_it1.071.5
X-RAY DIFFRACTIONc_mcangle_it1.542
X-RAY DIFFRACTIONc_scbond_it2.092
X-RAY DIFFRACTIONc_scangle_it2.682.5
LS refinement shellResolution: 1.4→1.46 Å / Rfactor Rfree error: 0.025 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.253 106 3.3 %
Rwork0.19 3089 -
obs--93.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER.PARAMWATER.TOP
X-RAY DIFFRACTION3PHB.PARAMPHB.TOP
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg26.5
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.42

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