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- PDB-1q1l: Crystal Structure of Chorismate Synthase -

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Basic information

Entry
Database: PDB / ID: 1q1l
TitleCrystal Structure of Chorismate Synthase
ComponentsChorismate synthase
KeywordsLYASE / beta alpha beta sandwich / Structural Genomics / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


chorismate synthase / chorismate synthase activity / chorismate biosynthetic process / aromatic amino acid family biosynthetic process / amino acid biosynthetic process / FMN binding / cytosol
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 speciesAquifex aeolicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.05 Å
AuthorsViola, C.M. / Saridakis, V. / Christendat, D. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: PROTEINS: STRUCT.,FUNCT.,GENET. / Year: 2004
Title: Crystal structure of chorismate synthase from Aquifex aeolicus reveals a novel beta alpha beta sandwich topology
Authors: Viola, C.M. / Saridakis, V. / Christendat, D.
History
DepositionJul 21, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 30, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.4Jun 13, 2018Group: Data collection / Category: diffrn_radiation / Item: _diffrn_radiation.pdbx_diffrn_protocol
Revision 1.5Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _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)179,7254
Polymers179,7254
Non-polymers00
Water10,088560
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area24170 Å2
ΔGint-91 kcal/mol
Surface area42220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)153.428, 95.959, 113.462
Angle α, β, γ (deg.)90.00, 93.04, 90.00
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 44931.195 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus (bacteria) / Gene: AROC / Plasmid: pET15B / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O66493, chorismate synthase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 560 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.32 Å3/Da / Density % sol: 46.97 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 7.5
Details: 30% isopropanol, 0.1M Na Hepes, 0.2M magnesium chloride, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 100K
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
130 %isopropanol1reservoir
20.2 M1reservoirMgCl2
30.1 Msodium HEPES1reservoirpH7.5

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 14-BM-C11
SYNCHROTRONAPS 14-ID-B20.979
Detector
TypeIDDetectorDate
MARRESEARCH1CCDJun 11, 2003
ADSC QUANTUM 42CCDJun 12, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
111
20.9791
ReflectionResolution: 2.05→30 Å / Num. obs: 164607 / Redundancy: 6.5 % / Biso Wilson estimate: 16.7 Å2 / Rmerge(I) obs: 0.073 / Net I/σ(I): 26.4
Reflection shellResolution: 2.05→2.12 Å / Mean I/σ(I) obs: 3.3 / Num. unique all: 19497 / Rsym value: 0.503 / % possible all: 100
Reflection
*PLUS
Num. obs: 99491 / % possible obs: 97.5 % / Num. measured all: 651230
Reflection shell
*PLUS
% possible obs: 92.8 % / Rmerge(I) obs: 0.503

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
RESOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.05→24.63 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 534076.69 / Data cutoff high rms absF: 534076.69 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.246 6458 3.9 %RANDOM
Rwork0.209 ---
obs0.209 164607 81.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 63.8403 Å2 / ksol: 0.360776 e/Å3
Displacement parametersBiso mean: 45.7 Å2
Baniso -1Baniso -2Baniso -3
1-1.87 Å20 Å2-4.4 Å2
2--8.78 Å20 Å2
3----10.65 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.3 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.33 Å0.27 Å
Refinement stepCycle: LAST / Resolution: 2.05→24.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10531 0 0 560 11091
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d22.1
X-RAY DIFFRACTIONc_improper_angle_d0.73
X-RAY DIFFRACTIONc_mcbond_it1.41.5
X-RAY DIFFRACTIONc_mcangle_it2.282
X-RAY DIFFRACTIONc_scbond_it2.032
X-RAY DIFFRACTIONc_scangle_it3.082.5
LS refinement shellResolution: 2.05→2.18 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.298 808 4 %
Rwork0.281 19497 -
obs--60 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
Refinement
*PLUS
Lowest resolution: 30 Å / % reflection Rfree: 4 % / Rfactor Rfree: 0.25
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.1
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.73
LS refinement shell
*PLUS
Lowest resolution: 2.12 Å

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