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- PDB-1r52: Crystal structure of the bifunctional chorismate synthase from Sa... -

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Basic information

Entry
Database: PDB / ID: 1r52
TitleCrystal structure of the bifunctional chorismate synthase from Saccharomyces cerevisiae
ComponentsChorismate synthase
KeywordsLYASE / two layers alpha-beta
Function / homology
Function and homology information


FMN reductase (NADPH) / FMN reductase (NAD(P)H) activity / FMN reductase (NADPH) activity / chorismate synthase / chorismate synthase activity / riboflavin reductase (NADPH) activity / chorismate biosynthetic process / aromatic amino acid family biosynthetic process / amino acid biosynthetic process / FMN binding ...FMN reductase (NADPH) / FMN reductase (NAD(P)H) activity / FMN reductase (NADPH) activity / chorismate synthase / chorismate synthase activity / riboflavin reductase (NADPH) activity / chorismate biosynthetic process / aromatic amino acid family biosynthetic process / amino acid biosynthetic process / FMN binding / cytosol / cytoplasm
Similarity search - Function
Chorismate synthase signature 3. / Chorismate synthase, AroC fold / Chorismate synthase AroC / Chorismate synthase signature 2. / Chorismate synthase / Chorismate synthase, conserved site / Chorismate synthase AroC superfamily / Chorismate synthase / Chorismate synthase signature 1. / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chorismate synthase ARO2
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.89 Å
AuthorsQuevillon-Cheruel, S. / Leulliot, N. / Meyer, P. / Graille, M. / Bremang, M. / Blondeau, K. / Sorel, I. / Poupon, A. / Janin, J. / van Tilbeurgh, H.
CitationJournal: J.Biol.Chem. / Year: 2004
Title: Crystal structure of the bifunctional chorismate synthase from Saccharomyces cerevisiae
Authors: Quevillon-Cheruel, S. / Leulliot, N. / Meyer, P. / Graille, M. / Bremang, M. / Blondeau, K. / Sorel, I. / Poupon, A. / Janin, J. / van Tilbeurgh, H.
History
DepositionOct 9, 2003Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 23, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Chorismate synthase
B: Chorismate synthase
C: Chorismate synthase
D: Chorismate synthase


Theoretical massNumber of molelcules
Total (without water)166,8854
Polymers166,8854
Non-polymers00
Water1,76598
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16420 Å2
ΔGint-81 kcal/mol
Surface area39850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.816, 75.599, 91.327
Angle α, β, γ (deg.)114.44, 108.43, 89.98
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: PHE / End label comp-ID: PHE / Refine code: 4 / Auth seq-ID: 1 - 370 / Label seq-ID: 1 - 370

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC
4DD
Detailsthe biological assembly is the tetramer present in the asymetric unit

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Components

#1: Protein
Chorismate synthase / / 5-enolpyruvylshikimate-3-phosphate phospholyase


Mass: 41721.145 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: YGL148w / Plasmid: pET9 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3)pLysS / References: UniProt: P28777, chorismate synthase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 98 / 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: 2.82 Å3/Da / Density % sol: 56.09 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Na-citrate, HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 293 K / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
13 mg/mlprotein1drop
20.7 Msodium cirtate1reservoir
30.1 MHEPES1reservoirpH7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.934 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2.89→30 Å / Num. obs: 110781 / % possible obs: 90 % / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 21.5
Reflection
*PLUS
Highest resolution: 2.9 Å / Num. obs: 26514 / Num. measured all: 110781
Reflection shell
*PLUS
% possible obs: 62.3 % / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 9.4

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.89→29.75 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.912 / SU B: 14.136 / SU ML: 0.272 / Cross valid method: THROUGHOUT / ESU R Free: 0.395 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.22387 1344 5.1 %RANDOM
Rwork0.18792 ---
all0.18981 ---
obs0.18981 25170 89.58 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 32.347 Å2
Baniso -1Baniso -2Baniso -3
1-0.14 Å20.42 Å20.91 Å2
2---0.39 Å20.95 Å2
3---1.61 Å2
Refinement stepCycle: LAST / Resolution: 2.89→29.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8538 0 0 98 8636
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0228484
X-RAY DIFFRACTIONr_bond_other_d0.0020.027853
X-RAY DIFFRACTIONr_angle_refined_deg1.461.96211460
X-RAY DIFFRACTIONr_angle_other_deg0.85318315
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.11451108
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_chiral_restr0.0790.21333
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.029448
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021588
X-RAY DIFFRACTIONr_nbd_refined0.2210.22206
X-RAY DIFFRACTIONr_nbd_other0.250.29968
X-RAY DIFFRACTIONr_nbtor_other0.0890.25063
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1560.2239
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0480.23
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3120.235
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0340.24
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it0.9771.55580
X-RAY DIFFRACTIONr_mcangle_it1.85228960
X-RAY DIFFRACTIONr_scbond_it1.75432904
X-RAY DIFFRACTIONr_scangle_it3.1074.52500
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 4004 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Amedium positional0.070.5
2Bmedium positional0.090.5
3Cmedium positional0.080.5
4Dmedium positional0.090.5
1Amedium thermal0.242
2Bmedium thermal0.262
3Cmedium thermal0.252
4Dmedium thermal0.252
LS refinement shellResolution: 2.888→2.962 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.292 65
Rwork0.242 1155
Refinement
*PLUS
Lowest resolution: 29.7 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.224 / Rfactor Rwork: 0.188
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.015
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.46

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