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- PDB-1fnj: CRYSTAL STRUCTURE ANALYSIS OF CHORISMATE MUTASE MUTANT C88S/R90K -

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Basic information

Entry
Database: PDB / ID: 1fnj
TitleCRYSTAL STRUCTURE ANALYSIS OF CHORISMATE MUTASE MUTANT C88S/R90K
ComponentsPROTEIN (CHORISMATE MUTASE)
KeywordsISOMERASE / chorismate mutase / protein / mutant / pseudo-alpha beta-barrel / trimer
Function / homology
Function and homology information


chorismate metabolic process / chorismate mutase / chorismate mutase activity / aromatic amino acid family biosynthetic process / amino acid biosynthetic process / cytoplasm
Similarity search - Function
Chorismate mutase, AroH class / Chorismate mutase type I / Chorismate mutase domain profile. / RutC-like / RutC-like superfamily / 60s Ribosomal Protein L30; Chain: A; / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chorismate mutase AroH
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMEN / Resolution: 1.9 Å
AuthorsKast, P. / Grisostomi, C. / Chen, I.A. / Li, S. / Krengel, U. / Xue, Y. / Hilvert, D.
Citation
Journal: J.Biol.Chem. / Year: 2000
Title: A strategically positioned cation is crucial for efficient catalysis by chorismate mutase.
Authors: Kast, P. / Grisostomi, C. / Chen, I.A. / Li, S. / Krengel, U. / Xue, Y. / Hilvert, D.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 1996
Title: Exploring the active site of chorismate mutase by combinatorial mutagenesis and selection: the importance of electrostatic catalysis
Authors: Kast, P. / Asif-Ullah, M. / Jiang, N. / Hilvert, D.
#2: Journal: J.Am.Chem.Soc. / Year: 1999
Title: Heavy atom isotope effects reveal a highly polarized transition state for chorismate mutase
Authors: Gustin, D.J. / Mattei, P. / Kast, P. / Wiest, O. / Lee, L. / Cleland, W.W. / Hilvert, D.
History
DepositionAug 22, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 11, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Nov 3, 2021Group: Database references / Derived calculations / Category: database_2 / 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
Revision 1.5Aug 9, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.6Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROTEIN (CHORISMATE MUTASE)


Theoretical massNumber of molelcules
Total (without water)14,4801
Polymers14,4801
Non-polymers00
Water48627
1
A: PROTEIN (CHORISMATE MUTASE)

A: PROTEIN (CHORISMATE MUTASE)

A: PROTEIN (CHORISMATE MUTASE)


Theoretical massNumber of molelcules
Total (without water)43,4403
Polymers43,4403
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Buried area6120 Å2
ΔGint-43 kcal/mol
Surface area14900 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)82.600, 82.600, 42.843
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

#1: Protein PROTEIN (CHORISMATE MUTASE)


Mass: 14479.837 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria)
Plasmid details: PET-22B(+) FROM NOVAGEN (MADISON, WI) AND PKET3-W, A PET-22B(+) DERIVATIVE ALLOWING FOR T7 PROMOTOR-DRIVEN GENE EXPRESSION
Plasmid: PET-22B(+),PKET3-W / Production host: Escherichia coli (E. coli) / References: UniProt: P19080, chorismate mutase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 27 / 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: 2.2 Å3/Da / Density % sol: 45 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7
Details: Protein solution: 10 mM Tris-HCl, 2mM DTT, 0.125 mM EDTA, Reservoir solution: 30% PEG 400, 50 mM Tris-HCl, 50 mM Magnesium Chloride, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal grow
*PLUS
PH range low: 7.5 / PH range high: 7
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
115-20 mg/mlprotein1drop
230 %PEG4001reservoir
350 mMTris-HCl1reservoirpH7.0-7.5
450 mM1reservoirMgCl2

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Data collection

DiffractionMean temperature: 295 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Nov 1, 1996
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.75→30 Å / Num. obs: 10748 / % possible obs: 97.7 % / Observed criterion σ(I): 0 / Redundancy: 4.9 % / Rsym value: 0.06 / Net I/σ(I): 29
Reflection shellResolution: 1.75→1.81 Å / Redundancy: 2.5 % / Rsym value: 0.068 / % possible all: 82.1
Reflection
*PLUS
Highest resolution: 1.75 Å / Lowest resolution: 30 Å / Rmerge(I) obs: 0.06

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Processing

Software
NameVersionClassification
X-PLORmodel building
AMoREphasing
X-PLOR3.851refinement
SCALEPACKdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMEN
Starting model: PDB# 2CHT

2cht


Resolution: 1.9→30 Å / Cross valid method: R-FREE / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.221 419 5 %RANDOM
Rwork0.196 ---
obs0.196 7430 --
Refinement stepCycle: LAST / Resolution: 1.9→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms909 0 0 27 936
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.011
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.36
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d27.04
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.13
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 1.9→1.99 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.343 35 3.4 %
Rwork0.316 1018 -
Xplor fileSerial no: 1 / Param file: PARHCSDX.PRO / Topol file: TOPHCSDX.PRO
Refinement
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 30 Å / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_deg1.358
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg27.04
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.13
LS refinement shell
*PLUS
Rfactor Rfree: 0.343 / % reflection Rfree: 3.4 % / Rfactor Rwork: 0.316

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