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- PDB-2ahc: Chorismate lyase with inhibitor Vanilate -

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Basic information

Entry
Database: PDB / ID: 2ahc
TitleChorismate lyase with inhibitor Vanilate
ComponentsChorismate lyase
KeywordsLYASE / unique fold / ubiquinone pathway / 123654 antiparallel sheet / internal active 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsGallagher, D.T. / Smith, N.N.
CitationJournal: Arch.Biochem.Biophys. / Year: 2006
Title: Structural analysis of ligand binding and catalysis in chorismate lyase
Authors: Smith, N.N. / Roitberg, A.E. / Rivera, E. / Howard, A. / Holden, M.J. / Mayhew, M. / Kaistha, S. / Gallagher, D.T.
History
DepositionJul 27, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 31, 2006Provider: 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 1.4Aug 23, 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_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
Remark 300BIOMOLECULE: 1, 2, 3, 4 QUATERNARY STRUCTURE FOR THIS ENTRY: MONOMERIC THIS ENTRY CONTAINS THE ...BIOMOLECULE: 1, 2, 3, 4 QUATERNARY STRUCTURE FOR THIS ENTRY: MONOMERIC THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 4 CHAIN(S). SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S).

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Chorismate lyase
B: Chorismate lyase
C: Chorismate lyase
D: Chorismate lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,2118
Polymers74,5424
Non-polymers6694
Water2,144119
1
A: Chorismate lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,8032
Polymers18,6361
Non-polymers1671
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Chorismate lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,8032
Polymers18,6361
Non-polymers1671
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Chorismate lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,8032
Polymers18,6361
Non-polymers1671
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Chorismate lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,8032
Polymers18,6361
Non-polymers1671
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.173, 58.560, 70.646
Angle α, β, γ (deg.)70.24, 67.40, 67.17
Int Tables number1
Space group name H-MP1
DetailsThis entry contains 4 monomers. The monomer is the biological unit. Thus Chain A is one biol. unit.

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Components

#1: Protein
Chorismate lyase


Mass: 18635.557 Da / Num. of mol.: 4 / Mutation: C14S, C81S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: ubiC / Plasmid: pse380 / 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.: 4 / Source method: obtained synthetically / Formula: C8H7O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 119 / 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: 2.54 Å3/Da / Density % sol: 44.3 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Mar 8, 2001
RadiationMonochromator: double mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→12 Å / Num. all: 33651 / Num. obs: 33472 / % possible obs: 87 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.1 % / Biso Wilson estimate: 22.3 Å2 / Rmerge(I) obs: 0.052 / Net I/σ(I): 18.3
Reflection shellResolution: 2.3→2.4 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.093 / Mean I/σ(I) obs: 6.3 / Num. unique all: 3873 / % possible all: 82

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Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
X-GENdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1FW9

1fw9


Resolution: 2.4→8 Å / Rfactor Rfree error: 0.016 / Data cutoff high absF: 999999 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.314 1091 3.8 %RANDOM
Rwork0.262 ---
all0.264 27664 --
obs0.262 27664 97.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 56.2301 Å2 / ksol: 0.40114 e/Å3
Displacement parametersBiso mean: 26.1 Å2
Baniso -1Baniso -2Baniso -3
1--2.11 Å20 Å20 Å2
2--3.98 Å20 Å2
3----2.56 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.31 Å0.32 Å
Luzzati d res low-12 Å
Luzzati sigma a0.24 Å0.38 Å
Refinement stepCycle: LAST / Resolution: 2.4→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5260 0 48 119 5427
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.016
X-RAY DIFFRACTIONc_angle_deg2.3
X-RAY DIFFRACTIONc_dihedral_angle_d22.9
X-RAY DIFFRACTIONc_improper_angle_d1.6
X-RAY DIFFRACTIONc_mcbond_it1.821.5
X-RAY DIFFRACTIONc_mcangle_it2.732
X-RAY DIFFRACTIONc_scbond_it2.912
X-RAY DIFFRACTIONc_scangle_it3.362.5
LS refinement shellResolution: 2.4→2.55 Å / Rfactor Rfree error: 0.039 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.331 157 4.1 %
Rwork0.281 4191 -
obs-4348 91.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3VNL.paramVNL.top

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