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- PDB-2qbv: Crystal Structure of Intracellular Chorismate Mutase from Mycobac... -

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Basic information

Entry
Database: PDB / ID: 2qbv
TitleCrystal Structure of Intracellular Chorismate Mutase from Mycobacterium Tuberculosis
ComponentsCHORISMATE MUTASE
KeywordsISOMERASE / chorismate mutase / tuberculosis / intracellular / helical / dimeric
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 / aromatic amino acid family biosynthetic process / 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 / Intracellular chorismate mutase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsLadner, J.E. / Reddy, P.T. / Kim, S.K. / Reddy, S.-K. / Nelson, B.C.
CitationJournal: Febs J. / Year: 2008
Title: A comparative biochemical and structural analysis of the intracellular chorismate mutase (Rv0948c) from Mycobacterium tuberculosis H(37)R(v) and the secreted chorismate mutase (y2828) from Yersinia pestis.
Authors: Kim, S.K. / Reddy, S.K. / Nelson, B.C. / Robinson, H. / Reddy, P.T. / Ladner, J.E.
History
DepositionJun 18, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 26, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Source and taxonomy / Version format compliance
Revision 1.3Aug 30, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _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
A: CHORISMATE MUTASE


Theoretical massNumber of molelcules
Total (without water)10,1081
Polymers10,1081
Non-polymers00
Water84747
1
A: CHORISMATE MUTASE

A: CHORISMATE MUTASE


Theoretical massNumber of molelcules
Total (without water)20,2162
Polymers20,2162
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area3910 Å2
ΔGint-28 kcal/mol
Surface area8640 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)59.860, 59.860, 47.520
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
DetailsThe molecule is a homodimer. The second chain of the dimer is generated by the symmetry operation y,x,-z and shifted along the c-axis by one c length (47.52).

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Components

#1: Protein CHORISMATE MUTASE


Mass: 10107.812 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: Rv0948c / Plasmid: pG58 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P64767, UniProt: P9WIC1*PLUS, chorismate mutase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 47 / 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: 2.11 Å3/Da / Density % sol: 41.57 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8.6
Details: 20% polyethylene glycol 400, 0.1M tris pH 8.6, 0.2M magnesium chloride, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jan 1, 2007 / Details: msc blue confocal
RadiationMonochromator: confocal mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→19.33 Å / Num. obs: 6192 / % possible obs: 100 % / Redundancy: 14.7 % / Rmerge(I) obs: 0.056 / Χ2: 0.94 / Net I/σ(I): 25.3 / Scaling rejects: 857
Reflection shellResolution: 2→2.07 Å / Redundancy: 14.8 % / Rmerge(I) obs: 0.323 / Mean I/σ(I) obs: 7 / Num. measured all: 10903 / Num. unique all: 594 / Χ2: 1.11 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
d*TREK9.7 W8RSSIdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT2data extraction
CrystalCleardata collection
d*TREKdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1YBZ

1ybz


Resolution: 2→19.33 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.908 / SU B: 5.712 / SU ML: 0.158 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.198 / ESU R Free: 0.202 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.298 295 4.8 %RANDOM
Rwork0.219 ---
obs0.222 6191 99.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 42.997 Å2
Baniso -1Baniso -2Baniso -3
1--2.01 Å20 Å20 Å2
2---2.01 Å20 Å2
3---4.03 Å2
Refinement stepCycle: LAST / Resolution: 2→19.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms573 0 0 47 620
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.022613
X-RAY DIFFRACTIONr_angle_refined_deg1.9852.019823
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.655582
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.2220.34529
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.51515135
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.1451513
X-RAY DIFFRACTIONr_chiral_restr0.1190.295
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02447
X-RAY DIFFRACTIONr_nbd_refined0.2180.2252
X-RAY DIFFRACTIONr_nbtor_refined0.3010.2407
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2060.227
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.250.262
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1630.214
X-RAY DIFFRACTIONr_mcbond_it1.3061.5398
X-RAY DIFFRACTIONr_mcangle_it2.0452601
X-RAY DIFFRACTIONr_scbond_it3.1983243
X-RAY DIFFRACTIONr_scangle_it5.2324.5217
LS refinement shellResolution: 2→2.107 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.361 41 -
Rwork0.241 815 -
obs-856 100 %

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