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- PDB-1g81: CHORISMATE LYASE WITH BOUND PRODUCT, ORTHORHOMBIC CRYSTAL FORM -

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Basic information

Entry
Database: PDB / ID: 1g81
TitleCHORISMATE LYASE WITH BOUND PRODUCT, ORTHORHOMBIC CRYSTAL FORM
ComponentsCHORISMATE LYASE
KeywordsLYASE / NEW FOLD / UBIQUINONE PATHWAY / 123654 ANTIPARALLEL SHEET TOPOLOGY / PRODUCT INHIBITION
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 / SIRAS / Resolution: 1.71 Å
AuthorsGallagher, D.T. / Mayhew, M. / Holden, M.J. / Vilker, V.L. / Howard, A.
CitationJournal: 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.
History
DepositionNov 15, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 15, 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.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 1.5Feb 7, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CHORISMATE LYASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,7902
Polymers18,6521
Non-polymers1381
Water2,522140
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)31.962, 62.983, 71.894
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsENZYME IS A MONOMER

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Components

#1: Protein CHORISMATE LYASE


Mass: 18651.621 Da / Num. of mol.: 1 / Mutation: C14S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: UBIC / 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.: 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: 1.94 Å3/Da / Density % sol: 36.55 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 26% PEG 4K, 80 mM Hepes, 5% Isopropanol, 5mM PHB, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 297K
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: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 0.9879 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 28, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9879 Å / Relative weight: 1
ReflectionResolution: 1.7→20 Å / Num. all: 15812 / Num. obs: 15812 / % possible obs: 95 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4 % / Biso Wilson estimate: 14.1 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 16.7
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.12 / % possible all: 83
Reflection
*PLUS
% possible obs: 95 % / Num. measured all: 63214
Reflection shell
*PLUS
% possible obs: 83 %

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Processing

Software
NameVersionClassification
PHASESphasing
CNS1refinement
X-GENdata reduction
X-GENdata scaling
RefinementMethod to determine structure: SIRAS / Resolution: 1.71→8 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 481823.14 / 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
Rfree0.253 772 5.1 %EVERY NTH
Rwork0.202 ---
all0.21 15223 --
obs0.202 15223 94.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 74.79 Å2 / ksol: 0.444 e/Å3
Displacement parametersBiso mean: 16.2 Å2
Baniso -1Baniso -2Baniso -3
1-0.87 Å20 Å20 Å2
2--3.49 Å20 Å2
3----4.36 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.24 Å0.18 Å
Luzzati d res low-8 Å
Luzzati sigma a--0.1 Å
Refinement stepCycle: LAST / Resolution: 1.71→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1315 0 10 140 1465
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.017
X-RAY DIFFRACTIONc_angle_deg1.9
X-RAY DIFFRACTIONc_dihedral_angle_d26.3
X-RAY DIFFRACTIONc_improper_angle_d1.2
X-RAY DIFFRACTIONc_mcbond_it1.311.5
X-RAY DIFFRACTIONc_mcangle_it1.852
X-RAY DIFFRACTIONc_scbond_it2.182
X-RAY DIFFRACTIONc_scangle_it3.222.5
LS refinement shellResolution: 1.7→1.78 Å / Rfactor Rfree error: 0.031 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.261 71 4.8 %
Rwork0.242 1398 -
obs-1469 73 %
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
σ(F): 0 / % reflection Rfree: 5.1 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 16.2 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.9
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg26.3
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.2
X-RAY DIFFRACTIONc_mcbond_it1.5
X-RAY DIFFRACTIONc_scbond_it2
X-RAY DIFFRACTIONc_mcangle_it2
X-RAY DIFFRACTIONc_scangle_it2.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.261 / % reflection Rfree: 4.8 % / Rfactor Rwork: 0.242 / Rfactor obs: 0.25

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