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- PDB-1qxo: Crystal structure of Chorismate synthase complexed with oxidized ... -

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Basic information

Entry
Database: PDB / ID: 1qxo
TitleCrystal structure of Chorismate synthase complexed with oxidized FMN and EPSP
ComponentsChorismate synthase
KeywordsLYASE / Beta-alpha-beta / flavoprotein / shikimate / anti-infective
Function / homology
Function and homology information


chorismate synthase / chorismate synthase activity / chorismate biosynthetic process / aromatic amino acid family biosynthetic process / FMN binding
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
Chem-EPS / FLAVIN MONONUCLEOTIDE / COBALT HEXAMMINE(III) / Chorismate synthase
Similarity search - Component
Biological speciesStreptococcus pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å
AuthorsMaclean, J. / Ali, S.
CitationJournal: Structure / Year: 2003
Title: The structure of chorismate synthase reveals a novel flavin binding site fundamental to a unique chemical reaction
Authors: Maclean, J. / Ali, S.
History
DepositionSep 8, 2003Deposition site: RCSB / Processing site: RCSB
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 1.3Oct 11, 2017Group: Refinement description / Category: software

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)179,89730
Polymers173,9784
Non-polymers5,91926
Water34,7511929
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area38730 Å2
ΔGint-79 kcal/mol
Surface area47990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.059, 124.582, 85.163
Angle α, β, γ (deg.)90.00, 115.15, 90.00
Int Tables number4
Space group name H-MP1211
DetailsAsymmetric unit contains one biological assembly (homotetramer)

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Components

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Protein , 1 types, 4 molecules ABCD

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


Mass: 43494.426 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Gene: AROC, SP1374 OR SPR1232 / Plasmid: PTX307 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) pLysS / References: UniProt: P0A2Y6, chorismate synthase

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Non-polymers , 5 types, 1955 molecules

#2: Chemical
ChemComp-NCO / COBALT HEXAMMINE(III)


Mass: 161.116 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: CoH18N6
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE / Flavin mononucleotide


Mass: 456.344 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C17H21N4O9P
#5: Chemical
ChemComp-EPS / 5-[(1-CARBOXYVINYL)OXY]-4-HYDROXY-3-(PHOSPHONOOXY)CYCLOHEX-1-ENE-1-CARBOXYLIC ACID / 5-ENOLPYRUVYLSHIKIMATE-3-PHOSPHATE / EPSP synthase


Mass: 324.178 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H13O10P
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1929 / 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: 2.24 Å3/Da / Density % sol: 45 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG 8000, Ethylene Glycol, HEPES, Cobalt hexamine trichloride, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 296K
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
16-10 mg/mlprotein1drop
210 mMTris-HCl1droppH7.5
320 mM1dropKCl
40.5 mMdithiothreitol1drop
52 mMEDTA1drop
69 %PEG80001drop
710 %ethlene glycol1drop
8100 mMHEPES1droppH7.5
92 mMFMN1reservoir
101 mMEPSP1reservoir
1112 mM1reservoir(NH3)6CoCl3

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.9788, 0.9790, 0.9755, 0.8855
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 28, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97881
20.9791
30.97551
40.88551
ReflectionResolution: 2→76.7 Å / Num. all: 103113 / Num. obs: 102745 / % possible obs: 99.6 % / Biso Wilson estimate: 23.9 Å2 / Rmerge(I) obs: 0.079 / Net I/σ(I): 22.9
Reflection shellResolution: 2→2.05 Å / Rmerge(I) obs: 0.383 / Mean I/σ(I) obs: 4.1 / % possible all: 100

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
SnBphasing
REFMACrefinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MAD / Resolution: 2→25 Å / Cross valid method: THROUGHOUT / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.222 4995 RANDOM
Rwork0.157 --
all0.16 102714 -
obs0.16 102714 -
Refinement stepCycle: LAST / Resolution: 2→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12137 0 361 1929 14427
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_refined_d0.013
X-RAY DIFFRACTIONr_angle_refined_deg2.59
LS refinement shellResolution: 2→2.102 Å
RfactorNum. reflection
Rfree0.285 615
Rwork0.188 -
obs-12587
Refinement
*PLUS
% reflection Rfree: 10 % / Rfactor Rfree: 0.2224 / Rfactor Rwork: 0.1569
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONbond_d0.013
X-RAY DIFFRACTIONangle_d
X-RAY DIFFRACTIONangle_deg2.585

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