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- PDB-1ode: Crystal Analysis Of Chorismate Mutase From Thermus Thermophilus. -

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Basic information

Entry
Database: PDB / ID: 1ode
TitleCrystal Analysis Of Chorismate Mutase From Thermus Thermophilus.
ComponentsCHORISMATE MUTASE
KeywordsISOMERASE / CHORISMATE MUTASE / SHIKIMATE PATHWAY / MUTANT / RIKEN STRUCTURAL GENOMICS/PROTEOMICS INITIATIVE / RSGI / STRUCTURAL GENOMICS
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 speciesTHERMUS THERMOPHILUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsInagaki, E. / Miyano, M. / Tahirov, T.H.
CitationJournal: To be Published
Title: The Crystal Structure of Chorismate Mutase from Thermus Thermophilus
Authors: Inagaki, E. / Kuramitsu, S. / Yokoyama, S. / Miyano, M. / Tahirov, T.H.
History
DepositionFeb 18, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 27, 2003Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc ...exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / struct_biol
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 1.4Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CHORISMATE MUTASE
B: CHORISMATE MUTASE
C: CHORISMATE MUTASE


Theoretical massNumber of molelcules
Total (without water)41,0003
Polymers41,0003
Non-polymers00
Water5,981332
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)47.319, 78.540, 86.035
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein CHORISMATE MUTASE /


Mass: 13666.668 Da / Num. of mol.: 3 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: MUTATION OF PHE 55 TO SER / Source: (gene. exp.) THERMUS THERMOPHILUS (bacteria) / Strain: HB8 / Plasmid: PET11A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q84FH6*PLUS, chorismate mutase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 332 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED MUATION PHE 55 SER CHAINS A,B AND C
Sequence detailsCOMPOUND ENGINEERED MUTATION IN CHAIN A, PHE 55 TO SER 55 ENGINEERED MUTATION IN CHAIN B, PHE 55 TO ...COMPOUND ENGINEERED MUTATION IN CHAIN A, PHE 55 TO SER 55 ENGINEERED MUTATION IN CHAIN B, PHE 55 TO SER 55 ENGINEERED MUTATION IN CHAIN C, PHE 55 TO SER 55

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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: 1.9 Å3/Da / Density % sol: 36.9 %
Crystal growMethod: microbatch / pH: 8.4
Details: PROTEIN WAS CRYSTALLIZED USING MICRO BATCH METHOD UNDER OIL FROM 27.5% PEG 4000, 10% DIOXANE AND 100 MM, TRIS/HCL(PH 8.4).

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL45XU / Wavelength: 1.02
DetectorType: RIGAKU IMAGE PLATE RAXIS V / Detector: IMAGE PLATE / Date: Oct 15, 2002 / Details: CYLINDRICAL BEND MIRROR
RadiationMonochromator: DIAMOND / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.02 Å / Relative weight: 1
ReflectionResolution: 1.65→50 Å / Num. obs: 174516 / % possible obs: 99.5 % / Observed criterion σ(I): -0.5 / Redundancy: 4.4 % / Biso Wilson estimate: 15.4 Å2 / Rmerge(I) obs: 0.064 / Net I/σ(I): 23.5
Reflection shellResolution: 1.65→1.71 Å / Rmerge(I) obs: 0.383 / Mean I/σ(I) obs: 2.4 / % possible all: 99.5

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1DBF

1dbf


Resolution: 1.65→43.02 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 915251.25 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.239 1938 5 %RANDOM
Rwork0.213 ---
obs0.213 38745 98.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 43.9925 Å2 / ksol: 0.310146 e/Å3
Displacement parametersBiso mean: 22.7 Å2
Baniso -1Baniso -2Baniso -3
1-2.9 Å20 Å20 Å2
2---1.14 Å20 Å2
3----1.76 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.24 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.24 Å0.21 Å
Refinement stepCycle: LAST / Resolution: 1.65→43.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2731 0 0 332 3063
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.2
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.85
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it2.681.5
X-RAY DIFFRACTIONc_mcangle_it3.622
X-RAY DIFFRACTIONc_scbond_it4.182
X-RAY DIFFRACTIONc_scangle_it5.882.5
LS refinement shellResolution: 1.65→1.75 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.321 316 5.1 %
Rwork0.289 5930 -
obs--96.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP

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