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- PDB-1jd3: Chorismate lyase G90A mutant with bound product -

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Basic information

Entry
Database: PDB / ID: 1jd3
TitleChorismate lyase G90A mutant with bound product
Componentschorismate lyase
KeywordsLYASE / active site mutant / product complex
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 / FOURIER SYNTHESIS / Resolution: 2.03 Å
AuthorsMayhew, M. / Smith, N. / Holden, M.J. / Gallagher, D.T.
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
DepositionJun 12, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 20, 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.classification / _software.name
Revision 1.4Oct 27, 2021Group: Database references / Derived calculations / Category: 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
Revision 1.5Aug 16, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: chorismate lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,7882
Polymers18,6501
Non-polymers1381
Water1,17165
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)32.246, 64.773, 72.674
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein chorismate lyase /


Mass: 18649.582 Da / Num. of mol.: 1 / Mutation: C14S,C81S,G90A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: UniProt: P26602, Lyases
#2: Chemical ChemComp-PHB / P-HYDROXYBENZOIC ACID / 4-Hydroxybenzoic acid


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


Mass: 18.015 Da / Num. of mol.: 65 / 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: 2.03 Å3/Da / Density % sol: 39.51 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 7
Details: PEG 4K, hepes, isopropanol, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 297K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: SIEMENS / Wavelength: 1.54 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 21, 2001 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. all: 9861 / Num. obs: 9861 / % possible obs: 94 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Biso Wilson estimate: 22.2 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 10.1
Reflection shellResolution: 2→2.15 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.22 / % possible all: 83

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Processing

Software
NameClassification
CNSrefinement
MAR345data collection
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 1g81.pdb

1g81


Resolution: 2.03→8 Å / Rfactor Rfree error: 0.013 / Data cutoff high absF: 415677.86 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.253 375 4 %OTHER
Rwork0.183 ---
all-9372 --
obs-9372 92.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 71.45 Å2 / ksol: 0.412 e/Å3
Displacement parametersBiso mean: 24.3 Å2
Baniso -1Baniso -2Baniso -3
1--4.64 Å20 Å20 Å2
2--6.29 Å20 Å2
3----1.65 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.3 Å0.21 Å
Luzzati d res low-12 Å
Luzzati sigma a0.14 Å0.17 Å
Refinement stepCycle: LAST / Resolution: 2.03→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1316 0 10 65 1391
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.028
X-RAY DIFFRACTIONc_angle_deg2.5
X-RAY DIFFRACTIONc_dihedral_angle_d26.1
X-RAY DIFFRACTIONc_improper_angle_d1.76
X-RAY DIFFRACTIONc_mcbond_it1.451.5
X-RAY DIFFRACTIONc_mcangle_it2.172
X-RAY DIFFRACTIONc_scbond_it2.322
X-RAY DIFFRACTIONc_scangle_it3.452.5
LS refinement shellResolution: 2.03→2.12 Å / Rfactor Rfree error: 0.033 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.209 41 4.2 %
Rwork0.229 935 -
obs-935 79.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3PHB.PARAMPHB.TOP

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