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- PDB-1xlr: CHORISMATE LYASE WITH INHIBITOR VANILLATE -

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Basic information

Entry
Database: PDB / ID: 1xlr
TitleCHORISMATE LYASE WITH INHIBITOR VANILLATE
ComponentsChorismate--pyruvate lyase
KeywordsLYASE / secondary inhibitor site
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
4-HYDROXY-3-METHOXYBENZOATE / Chorismate pyruvate-lyase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.94 Å
AuthorsGallagher, D.T. / Smith, N.
CitationJournal: Arch.Biochem.Biophys. / Year: 2006
Title: Structural analysis of ligand binding and catalysis in chorismate lyase.
Authors: Smith, N. / Roitberg, A.E. / Rivera, E. / Howard, A. / Holden, M.J. / Mayhew, M. / Kaistha, S. / Gallagher, D.T.
History
DepositionSep 30, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 9, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Feb 14, 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--pyruvate lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,9843
Polymers18,6501
Non-polymers3342
Water2,522140
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)32.270, 65.190, 72.670
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Detailsbiological unit is a monomer, equal to one asymmetric unit.

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Components

#1: Protein Chorismate--pyruvate lyase / chorismate lyase


Mass: 18649.582 Da / Num. of mol.: 1 / Mutation: C14S, C81S, G90A
Source method: isolated from a genetically manipulated source
Details: MUTATIONS: C14S, C81S, G90A / Source: (gene. exp.) Escherichia coli (E. coli) / Gene: UbiC / Production host: Escherichia coli (E. coli) / References: UniProt: P26602, chorismate lyase
#2: Chemical ChemComp-VNL / 4-HYDROXY-3-METHOXYBENZOATE / vanillate


Mass: 167.139 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H7O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 140 / 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: 1.9 Å3/Da / Density % sol: 34 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 25% PEG 4000, 80 mM Hepes, 5%(v/v) isopropanol, 20mM vanillate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 295 K
Diffraction sourceSource: ROTATING ANODE / Type: SIEMENS / Wavelength: 1.5418 Å
DetectorType: SIEMENS HI-STAR / Detector: AREA DETECTOR / Date: May 15, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.93→20 Å / Num. all: 11533 / Num. obs: 10973 / % possible obs: 92 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.1 % / Biso Wilson estimate: 15.3 Å2 / Rmerge(I) obs: 0.061 / Net I/σ(I): 12.3
Reflection shellResolution: 1.93→2.05 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.2 / Mean I/σ(I) obs: 2.9 / Num. unique all: 1504 / % possible all: 74

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Processing

Software
NameVersionClassification
CNS1refinement
X-GENdata reduction
X-GENdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.94→7.98 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 122521.12 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflection
Rfree0.236 557 5.2 %
Rwork0.173 --
all0.175 11435 -
obs0.173 10792 91.6 %
Solvent computationSolvent model: FLAT MODEL / Bsol: 59.2762 Å2 / ksol: 0.400962 e/Å3
Displacement parametersBiso mean: 22 Å2
Baniso -1Baniso -2Baniso -3
1--1.31 Å20 Å20 Å2
2--4.08 Å20 Å2
3----2.77 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.26 Å0.19 Å
Luzzati d res low-12 Å
Luzzati sigma a0.19 Å0.21 Å
Refinement stepCycle: LAST / Resolution: 1.94→7.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1316 0 24 140 1480
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.022
X-RAY DIFFRACTIONc_angle_deg2.2
X-RAY DIFFRACTIONc_dihedral_angle_d26.3
X-RAY DIFFRACTIONc_improper_angle_d1.39
X-RAY DIFFRACTIONc_mcbond_it1.611.5
X-RAY DIFFRACTIONc_mcangle_it2.452
X-RAY DIFFRACTIONc_scbond_it2.432
X-RAY DIFFRACTIONc_scangle_it3.692.5
LS refinement shellResolution: 1.94→2.02 Å / Rfactor Rfree error: 0.039 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.285 54 5.2 %
Rwork0.253 986 -
obs-1465 70.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3VAN.PARAMVAN.TOP

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