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- PDB-1g1b: CHORISMATE LYASE (WILD-TYPE) WITH BOUND PRODUCT -

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Basic information

Entry
Database: PDB / ID: 1g1b
TitleCHORISMATE LYASE (WILD-TYPE) WITH BOUND PRODUCT
ComponentsCHORISMATE LYASE
KeywordsLYASE / 6-stranded-antiparallel-sheet topology=(123654)
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 / Resolution: 1.99 Å
AuthorsGallagher, D.T. / Mayhew, M. / Holden, M.J. / Kim, K.J. / Howard, A. / Vilker, V.L.
Citation
Journal: 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.
#1: Journal: J.Struct.Biol. / Year: 2000
Title: Crystallization and 1.1-A Diffraction of Chorismate Lyase from Escherichia coli
Authors: Stover, C. / Mayhew, M.P. / Holden, M.J. / Howard, A. / Gallagher, D.T.
History
DepositionOct 11, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 11, 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 1.4Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
B: CHORISMATE LYASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,6124
Polymers37,3352
Non-polymers2762
Water4,504250
1
A: CHORISMATE LYASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,8062
Polymers18,6681
Non-polymers1381
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: CHORISMATE LYASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,8062
Polymers18,6681
Non-polymers1381
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.753, 60.363, 65.870
Angle α, β, γ (deg.)90.00, 94.43, 90.00
Int Tables number4
Space group name H-MP1211
DetailsAsymmetric unit contains two monomers, each with bound product. Biological unit is a monomer.

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Components

#1: Protein CHORISMATE LYASE /


Mass: 18667.686 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) 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.: 2 / Source method: obtained synthetically / Formula: C7H6O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 250 / 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: 2.11 Å3/Da / Density % sol: 41.68 %
Crystal growTemperature: 298 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 298.0K
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: ROTATING ANODE / Type: SIEMENS / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 20, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. all: 20385 / Num. obs: 20385 / % possible obs: 93.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.5 % / Biso Wilson estimate: 15.4 Å2 / Rmerge(I) obs: 0.062 / Net I/σ(I): 18.1
Reflection shellResolution: 1.98→2.07 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.22 / Num. unique all: 2093 / % possible all: 77.7
Reflection
*PLUS
% possible obs: 94 % / Num. measured all: 111649 / Rmerge(I) obs: 0.06
Reflection shell
*PLUS
Highest resolution: 2 Å / % possible obs: 78 %

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Processing

Software
NameClassification
CNSrefinement
MAR345data collection
SCALEPACKdata scaling
CNSphasing
RefinementResolution: 1.99→7.99 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 423436.69 / 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
Rfree0.265 1022 5.1 %EVERY NTH
Rwork0.196 ---
all0.2 20385 --
obs0.196 19858 93.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 113.1 Å2 / ksol: 0.62 e/Å3
Displacement parametersBiso mean: 16.3 Å2
Baniso -1Baniso -2Baniso -3
1-5.49 Å20 Å2-0.13 Å2
2---1.56 Å20 Å2
3----3.93 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.16 Å0.11 Å
Luzzati d res low-8 Å
Luzzati sigma a0.14 Å-0.04 Å
Refinement stepCycle: LAST / Resolution: 1.99→7.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2630 0 20 250 2900
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.025
X-RAY DIFFRACTIONc_angle_deg2.4
X-RAY DIFFRACTIONc_dihedral_angle_d26.2
X-RAY DIFFRACTIONc_improper_angle_d1.57
LS refinement shellResolution: 1→1.05 Å / Total num. of bins used: 8 /
RfactorNum. reflection
Rwork0.265 0
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
Refinement
*PLUS
Highest resolution: 2 Å / Lowest resolution: 8 Å / Num. reflection Rfree: 1018 / % reflection Rfree: 5 % / Rfactor Rfree: 0.27 / Rfactor Rwork: 0.2
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg26.2
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.57
LS refinement shell
*PLUS
Highest resolution: 2 Å / Lowest resolution: 2.07 Å / Rfactor Rfree: 0.28 / Rfactor Rwork: 0.19 / Num. reflection obs: 1817

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