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- PDB-5mpv: Crystal structure of a Mycobacterium tuberculosis chorismate muta... -

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Basic information

Entry
Database: PDB / ID: 5mpv
TitleCrystal structure of a Mycobacterium tuberculosis chorismate mutase optimized for high autonomous activity by directed evolution
ComponentsIntracellular chorismate mutase
KeywordsISOMERASE / chorismate mutase / directed evolution / Mycobacterium tuberculosis
Function / homology
Function and homology information


aromatic amino acid family biosynthetic process, prephenate pathway / salicylic acid biosynthetic process / chorismate metabolic process / chorismate mutase / chorismate mutase activity / amino acid biosynthetic process / plasma membrane / cytoplasm
Similarity search - Function
Chorismate mutase, high GC Gram-positive bacteria/archaeal / Chorismate mutase / Chorismate Mutase Domain, subunit A / Chorismate mutase domain superfamily / Chorismate mutase II, prokaryotic-type / Chorismate mutase type II / Chorismate mutase domain profile. / Chorismate mutase type II / Chorismate mutase type II superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Intracellular chorismate mutase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.49 Å
AuthorsThorbjornsrud, H.V. / Kamarauskaite, J. / Kast, P. / Krengel, U.
CitationJournal: J.Biol.Chem. / Year: 2020
Title: Evolving the naturally compromised chorismate mutase from Mycobacterium tuberculosis to top performance.
Authors: Fahrig-Kamarauskait, J. / Wurth-Roderer, K. / Thorbjornsrud, H.V. / Mailand, S. / Krengel, U. / Kast, P.
History
DepositionDec 19, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 1, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 1, 2023Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
D: Intracellular chorismate mutase


Theoretical massNumber of molelcules
Total (without water)10,0641
Polymers10,0641
Non-polymers00
Water1,27971
1
D: Intracellular chorismate mutase

D: Intracellular chorismate mutase


Theoretical massNumber of molelcules
Total (without water)20,1282
Polymers20,1282
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_875-x+3,-y+2,z1
Buried area4180 Å2
ΔGint-32 kcal/mol
Surface area9240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.587, 54.587, 63.217
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number172
Space group name H-MP64

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Components

#1: Protein Intracellular chorismate mutase / CM


Mass: 10063.795 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Strain: ATCC 25618 / H37Rv / Gene: Rv0948c, MTCY10D7.26 / Plasmid: pKTCMM / Production host: Escherichia coli (E. coli) / Variant (production host): KA13 / References: UniProt: P9WIC1, chorismate mutase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 71 / 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: 2.7 Å3/Da / Density % sol: 54.47 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 25% PEG MME 2000, 0.2 M trimehylamino-N-oxide, 0.1 M Tris. Microseeding.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.953723 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 1, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.953723 Å / Relative weight: 1
ReflectionResolution: 1.488→47.27 Å / Num. obs: 16797 / % possible obs: 95.5 % / Redundancy: 6.2 % / CC1/2: 0.999 / Rrim(I) all: 0.056 / Net I/σ(I): 15.01
Reflection shellResolution: 1.488→1.496 Å / Redundancy: 2.2 % / Mean I/σ(I) obs: 0.33 / CC1/2: 0.332 / Rrim(I) all: 2.806 / % possible all: 82.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0151refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2W1A

2w1a


Resolution: 1.49→47.27 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.969 / SU B: 3.36 / SU ML: 0.1 / Cross valid method: THROUGHOUT / ESU R: 0.068 / ESU R Free: 0.071 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21875 831 5 %RANDOM
Rwork0.18954 ---
obs0.1911 15948 95.38 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 49.423 Å2
Baniso -1Baniso -2Baniso -3
1-1.34 Å20.67 Å20 Å2
2--1.34 Å20 Å2
3----4.35 Å2
Refinement stepCycle: 1 / Resolution: 1.49→47.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms607 0 0 71 678
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.019645
X-RAY DIFFRACTIONr_bond_other_d0.0020.02679
X-RAY DIFFRACTIONr_angle_refined_deg1.8922.034872
X-RAY DIFFRACTIONr_angle_other_deg1.08631566
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.007586
X-RAY DIFFRACTIONr_dihedral_angle_2_deg23.57821.42928
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.92315133
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.9991511
X-RAY DIFFRACTIONr_chiral_restr0.1080.2101
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021716
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02133
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_it4.9454.582324
X-RAY DIFFRACTIONr_mcbond_other4.9424.558323
X-RAY DIFFRACTIONr_mcangle_it7.1816.807407
X-RAY DIFFRACTIONr_mcangle_other7.1766.832408
X-RAY DIFFRACTIONr_scbond_it5.7315.049321
X-RAY DIFFRACTIONr_scbond_other5.6755.025319
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other8.2657.384461
X-RAY DIFFRACTIONr_long_range_B_refined11.12556.344782
X-RAY DIFFRACTIONr_long_range_B_other11.03354.961745
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.488→1.527 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.562 28 -
Rwork0.595 891 -
obs--71.91 %

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