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- PDB-6ygt: Crystal structure of variant T52P of the intracellular chorismate... -

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Basic information

Entry
Database: PDB / ID: 6ygt
TitleCrystal structure of variant T52P of the intracellular chorismate mutase from Mycobacterium tuberculosis
ComponentsIntracellular chorismate mutase
KeywordsISOMERASE / functional variant / biosynthetic enzyme / chorismate mutase / 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 domain superfamily / Chorismate mutase domain profile. / Chorismate mutase type II / Chorismate mutase type II superfamily / Chorismate mutase II, prokaryotic-type / Chorismate mutase type II
Similarity search - Domain/homology
Intracellular chorismate mutase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.635 Å
AuthorsKhatanbaatar, T. / Thorbjornsrud, H.V. / Cordara, G. / Krengel, U.
Funding support Norway, 1items
OrganizationGrant numberCountry
Swiss National Science Foundation182648 Norway
CitationJournal: To Be Published
Title: Crystal structure of variant T52P of the intracellular chorismate mutase from Mycobacterium tuberculosis
Authors: Khatanbaatar, T. / Thorbjornsrud, H.V. / Cordara, G. / Krengel, U.
History
DepositionMar 27, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 7, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
AAA: Intracellular chorismate mutase


Theoretical massNumber of molelcules
Total (without water)10,1041
Polymers10,1041
Non-polymers00
Water32418
1
AAA: Intracellular chorismate mutase

AAA: Intracellular chorismate mutase


Theoretical massNumber of molelcules
Total (without water)20,2082
Polymers20,2082
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z+1/21
Buried area3970 Å2
ΔGint-27 kcal/mol
Surface area9570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.590, 59.590, 46.579
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Intracellular chorismate mutase / CM


Mass: 10103.823 Da / Num. of mol.: 1 / Mutation: T52P
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Strain: ATCC 25618 / H37Rv / Cell line: pinnipedii / Gene: Rv0948c, MTCY10D7.26 / Organ: 25618 / Variant: ATCC 25618 / H37Rv / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: P9WIC1, chorismate mutase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 18 / 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: 2.32 Å3/Da / Density % sol: 47 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2 M Sodium malonate, 0.1 M Bis Tris propane pH=8.5, 20% w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.9677 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Oct 22, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 1.635→36.698 Å / Num. obs: 9569 / % possible obs: 88.1 % / Redundancy: 8.7 % / CC1/2: 0.995 / Rmerge(I) obs: 0.075 / Rpim(I) all: 0.029 / Rrim(I) all: 0.081 / Net I/σ(I): 15.7
Reflection shellResolution: 1.635→1.716 Å / Redundancy: 9.8 % / Num. unique obs: 478 / CC1/2: 0.445 / % possible all: 33.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSMar 15, 2019 BUILT=20191211data reduction
Aimless0.7.4data scaling
PHASERPhaser-2.8.3 (svn 8432)phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5MPV

5mpv


Resolution: 1.635→36.698 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.929 / SU B: 2.32 / SU ML: 0.077 / Cross valid method: FREE R-VALUE / ESU R: 0.137 / ESU R Free: 0.126
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2645 445 4.7 %
Rwork0.2402 9124 -
all0.241 --
obs-9124 88.11 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 32.922 Å2
Baniso -1Baniso -2Baniso -3
1-0.207 Å20 Å20 Å2
2--0.207 Å20 Å2
3----0.415 Å2
Refinement stepCycle: LAST / Resolution: 1.635→36.698 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms596 0 0 18 614
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.013686
X-RAY DIFFRACTIONr_bond_other_d0.0020.017728
X-RAY DIFFRACTIONr_angle_refined_deg1.7111.65924
X-RAY DIFFRACTIONr_angle_other_deg1.4011.5981679
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.556595
X-RAY DIFFRACTIONr_dihedral_angle_2_deg23.89516.81844
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.6815150
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2421514
X-RAY DIFFRACTIONr_chiral_restr0.0780.287
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02790
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02164
X-RAY DIFFRACTIONr_nbd_refined0.2330.2164
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1940.2611
X-RAY DIFFRACTIONr_nbtor_refined0.1590.2311
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0810.2342
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2410.219
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.5940.213
X-RAY DIFFRACTIONr_nbd_other0.2470.275
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.4510.212
X-RAY DIFFRACTIONr_mcbond_it3.1143.157345
X-RAY DIFFRACTIONr_mcbond_other3.0743.151344
X-RAY DIFFRACTIONr_mcangle_it4.2744.723438
X-RAY DIFFRACTIONr_mcangle_other4.274.728439
X-RAY DIFFRACTIONr_scbond_it4.4783.662341
X-RAY DIFFRACTIONr_scbond_other4.4723.663342
X-RAY DIFFRACTIONr_scangle_it7.1755.252481
X-RAY DIFFRACTIONr_scangle_other7.1685.253482
X-RAY DIFFRACTIONr_lrange_it9.54336.522771
X-RAY DIFFRACTIONr_lrange_other9.53736.545772
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.635-1.7160.40470.537148X-RAY DIFFRACTION19.6701
1.677-1.7230.438230.429381X-RAY DIFFRACTION52.6042
1.723-1.7730.427300.39562X-RAY DIFFRACTION80.9849
1.773-1.8270.396260.319644X-RAY DIFFRACTION92.7978
1.827-1.8870.25360.246636X-RAY DIFFRACTION96.83
1.887-1.9530.324360.236646X-RAY DIFFRACTION99.4169
1.953-2.0270.324280.234631X-RAY DIFFRACTION99.6974
2.027-2.1090.219240.228613X-RAY DIFFRACTION100
2.109-2.2030.176270.203576X-RAY DIFFRACTION99.8344
2.203-2.310.184210.204565X-RAY DIFFRACTION100
2.31-2.4350.272270.214501X-RAY DIFFRACTION94.2857
2.435-2.5820.266290.212473X-RAY DIFFRACTION94.1839
2.582-2.7590.268190.208483X-RAY DIFFRACTION100
2.759-2.9790.257170.201455X-RAY DIFFRACTION100
2.979-3.2620.25260.228408X-RAY DIFFRACTION100
3.262-3.6440.237140.208383X-RAY DIFFRACTION100
3.644-4.2030.181160.207350X-RAY DIFFRACTION100
4.203-5.1350.224180.214287X-RAY DIFFRACTION99.6732
4.841-36.6980.359110.374145X-RAY DIFFRACTION94.5455
5.135-7.2090.346100.36237X-RAY DIFFRACTION99.5968

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