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- PDB-1ui9: Crystal analysis of chorismate mutase from thermus thermophilus -

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Basic information

Entry
Database: PDB / ID: 1ui9
TitleCrystal analysis of chorismate mutase from thermus thermophilus
Componentschorismate mutase
KeywordsISOMERASE / CHORISMATE MUTASE / SHIKIMATE PATHWAY / 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. / Kuramitsu, S. / Yokoyama, S. / Miyano, M. / Tahirov, T.H. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
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
DepositionJul 15, 2003Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 29, 2003Provider: 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 25, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: chorismate mutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,2906
Polymers13,7271
Non-polymers5645
Water1,820101
1
A: chorismate mutase
hetero molecules

A: chorismate mutase
hetero molecules

A: chorismate mutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,87118
Polymers41,1803
Non-polymers1,69115
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555-z+1/2,-x,y+1/21
crystal symmetry operation10_545-y,z-1/2,-x+1/21
Buried area9210 Å2
ΔGint-34 kcal/mol
Surface area14810 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)74.804, 74.804, 74.804
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213
DetailsThe biological assembly is a trimer generated from the monomer in the asymmetric unit by the operations: -y, z-1/2, -x+1/2 and -z+1/2, -x, y+1/2.

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Components

#1: Protein chorismate mutase


Mass: 13726.764 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Plasmid: pET 11a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q84FH6, chorismate mutase
#2: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 101 / 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: 2.35 Å3/Da / Density % sol: 47.36 %
Crystal growTemperature: 295 K / Method: microbatch / pH: 6.3
Details: Sodium malonate, MES, pH 6.3, Micro Batch, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å
DetectorType: RIGAKU RAXIS V / Detector: IMAGE PLATE / Date: Jun 23, 2003 / Details: MIRRORS
RadiationMonochromator: SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.65→50 Å / Num. all: 17108 / Num. obs: 16749 / % possible obs: 97.9 % / Observed criterion σ(I): -1 / Redundancy: 3.8 % / Biso Wilson estimate: 15.6 Å2 / Rmerge(I) obs: 0.046
Reflection shellResolution: 1.65→1.71 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.328 / % possible all: 99.9

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Processing

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

1ufy


Resolution: 1.65→33.45 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 1438630.21 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.227 845 5.1 %RANDOM
Rwork0.204 ---
obs0.204 16729 97.9 %-
all-17108 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 54.7121 Å2 / ksol: 0.407688 e/Å3
Displacement parametersBiso mean: 22.3 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.21 Å0.19 Å
Luzzati d res low-5 Å
Luzzati sigma a0.16 Å0.16 Å
Refinement stepCycle: LAST / Resolution: 1.65→33.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms919 0 36 101 1056
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d23.6
X-RAY DIFFRACTIONc_improper_angle_d0.87
LS refinement shellResolution: 1.65→1.75 Å / Rfactor Rfree error: 0.027 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.292 120 4.3 %
Rwork0.269 2668 -
obs--99.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3SOLVENT.PARAMSOLVENT.TOP

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