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

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Basic information

Entry
Database: PDB / ID: 1ufy
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
MALONATE ION / Chorismate mutase AroH
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.96 Å
AuthorsInagaki, E. / 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
DepositionJun 11, 2003Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 1, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Source and taxonomy / 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 / pdbx_struct_special_symmetry / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

Downloads & links

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Assembly

Deposited unit
A: Chorismate mutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,5857
Polymers13,6671
Non-polymers9186
Water2,378132
1
A: Chorismate mutase
hetero molecules

A: Chorismate mutase
hetero molecules

A: Chorismate mutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,75521
Polymers41,0003
Non-polymers2,75518
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_765-y+2,x-y+1,z1
crystal symmetry operation3_675-x+y+1,-x+2,z1
Buried area9810 Å2
ΔGint-20 kcal/mol
Surface area14900 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)71.252, 71.252, 152.360
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-302-

MES

21A-460-

HOH

31A-471-

HOH

41A-522-

HOH

51A-525-

HOH

61A-528-

HOH

DetailsThe biological assembly is a trimer generated from the monomer in the asymmetric unit by the operations: -y+2, x-y+1, z and -x+y+1, -x+1, z.

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Components

#1: Protein Chorismate mutase


Mass: 13666.668 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Plasmid: PET11A / 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-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H2O4
#4: Chemical
ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 132 / 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: 2.71 Å3/Da / Density % sol: 54.7 %
Crystal growTemperature: 291 K / Method: microbatch / pH: 7
Details: SODIUM MALONATE, MES, pH 7.0, MICRO BATCH, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 0.8 / Wavelength: 0.8 Å
DetectorType: RIGAKU RAXIS V / Detector: IMAGE PLATE / Date: Nov 7, 2002 / Details: mirrors
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8 Å / Relative weight: 1
ReflectionResolution: 0.95→50 Å / Num. all: 93458 / Num. obs: 90841 / % possible obs: 97.2 % / Observed criterion σ(I): -1 / Redundancy: 4.7 % / Biso Wilson estimate: 2.7 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 22.2
Reflection shellResolution: 0.95→0.96 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.345 / Mean I/σ(I) obs: 1.5 / % possible all: 59.7

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Processing

Software
NameClassification
HKL-2000data collection
SCALEPACKdata scaling
CNSrefinement
SHELXL-97refinement
HKL-2000data reduction
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PROTOMER A OF PDB ENTRY 1ODE

1ode


Resolution: 0.96→10 Å / Num. parameters: 10275 / Num. restraintsaints: 12599 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
Details: Anisotropic refinement reduced free R (no cutoff) by 0.03. In final 20 cycles of refinement all refrections were included. Free R value is caluculated before including all refrections in the refinement.
RfactorNum. reflection% reflectionSelection details
Rfree0.1274 4471 5 %RANDOM
Rwork0.1099 ---
all0.1099 88990 --
obs0.1099 88990 98.1 %-
Solvent computationSolvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-228
Refine analyzeLuzzati coordinate error obs: 0.11 Å / Luzzati d res low obs: 3.84 Å / Num. disordered residues: 5 / Occupancy sum hydrogen: 963.52 / Occupancy sum non hydrogen: 1043.55
Refinement stepCycle: LAST / Resolution: 0.96→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms941 0 56 132 1129
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.018
X-RAY DIFFRACTIONs_angle_d0.031
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0308
X-RAY DIFFRACTIONs_zero_chiral_vol0.111
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.117
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.049
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.007
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.05
X-RAY DIFFRACTIONs_approx_iso_adps0.097
LS refinement shellResolution: 0.96→1 Å /
RfactorNum. reflection
Rwork0.228 -
obs-8965

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