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- PDB-1tt8: CHORISMATE LYASE WITH PRODUCT, 1.0 A RESOLUTION -

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Basic information

Entry
Database: PDB / ID: 1tt8
TitleCHORISMATE LYASE WITH PRODUCT, 1.0 A RESOLUTION
ComponentsChorismate-pyruvate lyase
KeywordsLYASE / NEW FOLD / UBIQUINONE PATHWAY / 123654 ANTIPARALLEL SHEET
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 / SAD / Resolution: 1 Å
AuthorsGallagher, D.T. / Mayhew, M. / Holden, M.J. / Vilker, V. / Howard, A.
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 22, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 28, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
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 23, 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

Downloads & links

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Assembly

Deposited unit
A: Chorismate-pyruvate lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,7742
Polymers18,6361
Non-polymers1381
Water6,684371
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)31.315, 33.849, 39.776
Angle α, β, γ (deg.)67.57, 87.83, 65.66
Int Tables number1
Space group name H-MP1
DetailsTHE ENZYME IS MONOMERIC. THIS ENTRY IS FOR ONE MONOMER.

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Components

#1: Protein Chorismate-pyruvate lyase


Mass: 18635.557 Da / Num. of mol.: 1 / Mutation: C14S,C81S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: ubiC,b4039 / Plasmid: pSE380 / Production host: 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.: 371 / 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: 1.8 Å3/Da / Density % sol: 30 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 26% PEG4K, 80 mM Hepes, 5%(V/V) ISOPROPANOL, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 297K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 0.7469 / Wavelength: 0.7469 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: May 18, 2000 / Details: DOUBLE MIRROR
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.7469 Å / Relative weight: 1
ReflectionResolution: 0.92→20 Å / Num. all: 89590 / Num. obs: 88226 / % possible obs: 0.92 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.6 % / Rmerge(I) obs: 0.066 / Net I/σ(I): 25.8
Reflection shellResolution: 0.92→0.94 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.262 / % possible all: 0.86

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Processing

Software
NameClassification
X-GENdata scaling
X-GENdata reduction
SHELXmodel building
SHELXL-97refinement
SHELXphasing
RefinementMethod to determine structure: SAD
Starting model: 1FW9

1fw9


Resolution: 1→8 Å / Num. parameters: 15076 / Num. restraintsaints: 17545 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
Details: ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) BY 0.02
RfactorNum. reflection% reflectionSelection details
Rfree0.1534 2175 3.4 %RANDOM
Rwork0.1231 ---
all0.1202 63630 --
obs0.1231 63630 86.6 %-
Refine analyzeNum. disordered residues: 3 / Occupancy sum hydrogen: 1360 / Occupancy sum non hydrogen: 1689
Refinement stepCycle: LAST / Resolution: 1→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2700 0 10 371 3081
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.017
X-RAY DIFFRACTIONs_angle_d0.035
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0324
X-RAY DIFFRACTIONs_zero_chiral_vol0.108
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.089
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.065
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.006
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.038
X-RAY DIFFRACTIONs_approx_iso_adps0.09
LS refinement shell
Resolution (Å)Rfactor RworkRefine-IDNum. reflection obs% reflection obs (%)
1-1.10.2X-RAY DIFFRACTION1239368
1.1-1.30.13X-RAY DIFFRACTION1949489
1.3-1.60.11X-RAY DIFFRACTION1447593
1.6-20.1X-RAY DIFFRACTION839496
2-80.12X-RAY DIFFRACTION887598

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