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- PDB-1sq1: Crystal Structure of the Chorismate Synthase from Campylobacter j... -

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Basic information

Entry
Database: PDB / ID: 1sq1
TitleCrystal Structure of the Chorismate Synthase from Campylobacter jejuni, Northeast Structural Genomics Target BR19
ComponentsChorismate synthase
KeywordsLYASE / Structural Genomics / Bifunctional alpha/beta tetrameric protein / PSI / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homology
Function and homology information


chorismate synthase / chorismate synthase activity / chorismate biosynthetic process / aromatic amino acid family biosynthetic process
Similarity search - Function
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
Biological speciesCampylobacter jejuni (Campylobacter)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.8 Å
AuthorsForouhar, F. / Lee, I. / Vorobiev, S.M. / Xiao, R. / Acton, T.B. / Montelione, G.T. / Tong, L. / Hunt, J.F. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Crystal Structure of the Chorismate Synthase from Campylobacter jejuni, Northeast Structural Genomics Target BR19
Authors: Forouhar, F. / Lee, I. / Vorobiev, S.M. / Xiao, R. / Acton, T.B. / Montelione, G.T. / Tong, L. / Hunt, J.F.
History
DepositionMar 17, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 6, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Chorismate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,8973
Polymers40,7051
Non-polymers1922
Water1267
1
A: Chorismate synthase
hetero molecules

A: Chorismate synthase
hetero molecules

A: Chorismate synthase
hetero molecules

A: Chorismate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)163,58912
Polymers162,8214
Non-polymers7698
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_666-y+1,-x+1,-z+11
crystal symmetry operation10_665-x+1,-y+1,z1
crystal symmetry operation15_556y,x,-z+11
Buried area19080 Å2
ΔGint-227 kcal/mol
Surface area40700 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)73.600, 73.600, 338.559
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122

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Components

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


Mass: 40705.129 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Campylobacter jejuni (Campylobacter) / Strain: NCTC 11168 / Gene: AROC OR CJ1634 / Plasmid: pET21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+Magic / References: UniProt: Q9PM41, chorismate synthase
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 7 / 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: 3.81 Å3/Da / Density % sol: 67.43 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: Protein solution: 10mM Tris (pH 7.5), 5mM DTT, 100mM NaCl. Well solution: 50mM NaAcetate (pH 4.6), 1M ammonium sulfate, 10mM DTT, 25mM octanoylsucrose, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97914 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 30, 2004 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97914 Å / Relative weight: 1
ReflectionResolution: 2.8→29.6 Å / Num. obs: 21612 / % possible obs: 98.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.6 % / Biso Wilson estimate: -1.9 Å2 / Rmerge(I) obs: 0.061 / Rsym value: 0.062 / Net I/σ(I): 22.4
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.188 / Mean I/σ(I) obs: 6 / Num. unique all: 2148 / Rsym value: 0.19 / % possible all: 98.3

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
SnBphasing
SOLVEphasing
CNSrefinement
RefinementMethod to determine structure: SAD / Resolution: 2.8→29.6 Å / Isotropic thermal model: Overall anisotropic / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber / Details: Used weighted full matrix least squares procedure.
RfactorNum. reflection% reflectionSelection details
Rfree0.279 1802 -Random
Rwork0.224 ---
obs0.224 18999 9.5 %-
all-21612 --
Displacement parametersBiso mean: 69.1 Å2
Baniso -1Baniso -2Baniso -3
1-21 Å20 Å20 Å2
2--21.99 Å20 Å2
3----43.98 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.44 Å0.35 Å
Luzzati d res low-5 Å
Luzzati sigma a0.42 Å0.41 Å
Refinement stepCycle: LAST / Resolution: 2.8→29.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2151 0 10 7 2168
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_d1.2
X-RAY DIFFRACTIONc_dihedral_angle_d24
X-RAY DIFFRACTIONc_improper_angle_d0.73
LS refinement shellResolution: 2.8→2.98 Å / Rfactor Rfree error: 0.024
RfactorNum. reflection% reflection
Rfree0.351 222 -
Rwork0.291 --
obs-2092 9.6 %

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