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- PDB-3zo8: Wild-type chorismate mutase of Bacillus subtilis at 1.6 A resolution -

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Basic information

Entry
Database: PDB / ID: 3zo8
TitleWild-type chorismate mutase of Bacillus subtilis at 1.6 A resolution
ComponentsCHORISMATE MUTASE AROH
KeywordsISOMERASE / PSEUDO-ALPHA BETA-BARREL
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 REPLACEMENT / Resolution: 1.59 Å
AuthorsBurschowsky, D. / vanEerde, A. / Okvist, M. / Kienhofer, A. / Kast, P. / Hilvert, D. / Krengel, U.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2014
Title: Electrostatic Transition State Stabilization Rather Than Reactant Destabilization Provides the Chemical Basis for Efficient Chorismate Mutase Catalysis.
Authors: Burschowsky, D. / Van Eerde, A. / Okvist, M. / Kienhofer, A. / Kast, P. / Hilvert, D. / Krengel, U.
History
DepositionFeb 20, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 16, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 26, 2014Group: Database references
Revision 1.2Dec 3, 2014Group: Database references
Revision 1.3Dec 10, 2014Group: Database references
Revision 1.4Dec 24, 2014Group: Database references
Revision 1.5Dec 20, 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 AROH
B: CHORISMATE MUTASE AROH
C: CHORISMATE MUTASE AROH
D: CHORISMATE MUTASE AROH
E: CHORISMATE MUTASE AROH
F: CHORISMATE MUTASE AROH


Theoretical massNumber of molelcules
Total (without water)87,0476
Polymers87,0476
Non-polymers00
Water4,089227
1
D: CHORISMATE MUTASE AROH
E: CHORISMATE MUTASE AROH
F: CHORISMATE MUTASE AROH


Theoretical massNumber of molelcules
Total (without water)43,5243
Polymers43,5243
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6080 Å2
ΔGint-37.5 kcal/mol
Surface area15050 Å2
MethodPISA
2
A: CHORISMATE MUTASE AROH
B: CHORISMATE MUTASE AROH
C: CHORISMATE MUTASE AROH


Theoretical massNumber of molelcules
Total (without water)43,5243
Polymers43,5243
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6060 Å2
ΔGint-38.7 kcal/mol
Surface area15010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.498, 165.174, 49.586
Angle α, β, γ (deg.)90.00, 118.67, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given / Matrix: (1), (1), (1))

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Components

#1: Protein
CHORISMATE MUTASE AROH / CM


Mass: 14507.915 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BACILLUS SUBTILIS (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P19080, chorismate mutase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 227 / 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: 2.12 Å3/Da / Density % sol: 41.9 % / Description: NONE
Crystal growpH: 6
Details: 100 MM MMT BUFFER ---MALIC ACID, MES, TRIS, IN MOLAR RATIOS OF 1:2:2, RESPECTIVELY--- PH 6.0, 100 MM MAGNESIUM CHLORIDE, 25% W/V PEG 1000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54187
DetectorType: RIGAKU IMAGE PLATE / Detector: IMAGE PLATE / Date: Nov 2, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54187 Å / Relative weight: 1
ReflectionResolution: 1.59→82.58 Å / Num. obs: 93148 / % possible obs: 85 % / Redundancy: 2.9 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 14.4
Reflection shellResolution: 1.59→1.69 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.18 / Mean I/σ(I) obs: 4.4 / % possible all: 59.4

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
XDSdata reduction
XDSdata scaling
PHASERFOR MRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1DBF

1dbf


Resolution: 1.59→82.6 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.958 / SU B: 3.465 / SU ML: 0.051 / Cross valid method: THROUGHOUT / ESU R: 0.022 / ESU R Free: 0.016 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES 118-127 ARE DISORDERED.
RfactorNum. reflection% reflectionSelection details
Rfree0.16975 4383 5 %RANDOM
Rwork0.14386 ---
obs0.1452 82445 93.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.774 Å2
Baniso -1Baniso -2Baniso -3
1--0.1 Å20 Å20.26 Å2
2--0.22 Å20 Å2
3----0.12 Å2
Refinement stepCycle: LAST / Resolution: 1.59→82.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5586 0 0 227 5813
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.025687
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1711.9837695
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.775704
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.78524.75240
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.135151135
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.7971542
X-RAY DIFFRACTIONr_chiral_restr0.0740.2926
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0214084
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr7.95935687
X-RAY DIFFRACTIONr_sphericity_free17.943590
X-RAY DIFFRACTIONr_sphericity_bonded5.72455742
LS refinement shellResolution: 1.59→1.632 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.224 1 -
Rwork0.167 4054 -
obs--58.84 %

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