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- PDB-5cwa: Structure of Anthranilate Synthase Component I (TrpE) from Mycoba... -

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Basic information

Entry
Database: PDB / ID: 5cwa
TitleStructure of Anthranilate Synthase Component I (TrpE) from Mycobacterium tuberculosis with inhibitor bound
ComponentsAnthranilate synthase component 1
KeywordsLyase/Lyase Inhibitor / Lyase / Inhibitor / Lyase-Lyase Inhibitor complex
Function / homology
Function and homology information


anthranilate synthase / anthranilate synthase activity / tryptophan biosynthetic process / metal ion binding
Similarity search - Function
Anthranilate synthase component I, PabB-like / Anthranilate synthase component I, N-terminal / Anthranilate synthase component I, N terminal region / Anthranilate synthase / Anthranilate synthase / Anthranilate synthase component I-like / ADC synthase / Chorismate-utilising enzyme, C-terminal / chorismate binding enzyme / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-0GA / Unknown ligand / Anthranilate synthase component 1
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsJohnston, J.M. / Bashiri, G. / Evans, G.L. / Lott, J.S. / Baker, E.N.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2015
Title: Structure and inhibition of subunit I of the anthranilate synthase complex of Mycobacterium tuberculosis and expression of the active complex.
Authors: Bashiri, G. / Johnston, J.M. / Evans, G.L. / Bulloch, E.M. / Goldstone, D.C. / Jirgis, E.N. / Kleinboelting, S. / Castell, A. / Ramsay, R.J. / Manos-Turvey, A. / Payne, R.J. / Lott, J.S. / Baker, E.N.
History
DepositionJul 28, 2015Deposition site: RCSB / Processing site: RCSB
SupersessionAug 12, 2015ID: 4PEN
Revision 1.0Aug 12, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 18, 2015Group: Database references
Revision 1.2Nov 1, 2017Group: Author supporting evidence / Data collection / Derived calculations
Category: diffrn_source / pdbx_struct_assembly_auth_evidence / pdbx_struct_oper_list
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Sep 27, 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

Downloads & links

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Assembly

Deposited unit
A: Anthranilate synthase component 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,1117
Polymers55,4961
Non-polymers6156
Water3,693205
1
A: Anthranilate synthase component 1
hetero molecules

A: Anthranilate synthase component 1
hetero molecules

A: Anthranilate synthase component 1
hetero molecules

A: Anthranilate synthase component 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)224,44328
Polymers221,9854
Non-polymers2,45824
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_545-x,-y-1,z1
crystal symmetry operation9_554-x,-x+y,-z-1/31
crystal symmetry operation12_544x,x-y-1,-z-1/31
Buried area13940 Å2
ΔGint-154 kcal/mol
Surface area73510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)156.406, 156.406, 128.384
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number181
Space group name H-MP6422
DetailsBiological assembly of TrpE is a dimer. In the structure this dimer is generated by application of crystal symmetry. This is supported by PISA analysis. Also further supported by experimental work - SEC and SEC-MALS analysis.

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Anthranilate synthase component 1 / / ASI


Mass: 55496.258 Da / Num. of mol.: 1 / Mutation: H2D
Source method: isolated from a genetically manipulated source
Details: D TO H MUTATION FROM PUBLISHED SEQUENCE AT POSITION 2 DUE TO CLONING ARTEFACT, ALSO AFTER RTEV CLEAVAGE AN ADDITIONAL GA REMAINS ON CONSTRUCT USED PRIOR TO START M (NOT SHOWN IN SEQUENCE ABOVE)
Source: (gene. exp.) Mycobacterium tuberculosis (strain CDC 1551 / Oshkosh) (bacteria)
Strain: CDC 1551 / Oshkosh / Gene: trpE, MT1644 / Production host: Mycobacterium smegmatis (bacteria) / References: UniProt: P9WFX2, anthranilate synthase

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Non-polymers , 5 types, 211 molecules

#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-0GA / 3-{[(1Z)-1-carboxyprop-1-en-1-yl]oxy}-2-hydroxybenzoic acid


Mass: 238.193 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H10O6
#5: Chemical ChemComp-UNL / UNKNOWN LIGAND


Num. of mol.: 1 / Source method: obtained synthetically
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 205 / 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: 4.09 Å3/Da / Density % sol: 69.95 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.6-1.0 M AMMONIUM SULFATE, 0.1 M BIS -TRIS PROPANE, PH 7, "silver bullet" additive G6, VAPOR DIFFUSION, TEMPERATURE 291K
PH range: 7

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.8983 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 31, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8983 Å / Relative weight: 1
ReflectionResolution: 2.1→135.452 Å / Num. obs: 54312 / % possible obs: 99.9 % / Redundancy: 21.9 % / Rsym value: 0.158 / Net I/σ(I): 14.8
Reflection shellResolution: 2.1→2.21 Å / Redundancy: 22.4 % / Rmerge(I) obs: 3.794 / Mean I/σ(I) obs: 1.1 / Rsym value: 3.794 / % possible all: 99.8

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Processing

Software
NameVersionClassification
XDSdata reduction
SCALA3.3.20data scaling
MOLREP11.0.02phasing
REFMAC5.8.0069refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1QDL

1qdl


Resolution: 2.1→135.45 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.942 / SU B: 5.884 / SU ML: 0.143 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.152 / ESU R Free: 0.153 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING
RfactorNum. reflection% reflectionSelection details
Rfree0.253 2767 5.1 %RANDOM
Rwork0.207 ---
obs0.209 54282 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 56.53 Å2
Baniso -1Baniso -2Baniso -3
1-0.79 Å20.4 Å20 Å2
2--0.79 Å20 Å2
3----2.57 Å2
Refinement stepCycle: LAST / Resolution: 2.1→135.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3825 0 48 205 4078
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0193992
X-RAY DIFFRACTIONr_bond_other_d0.0010.023761
X-RAY DIFFRACTIONr_angle_refined_deg1.5271.9755448
X-RAY DIFFRACTIONr_angle_other_deg0.8238614
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7895513
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.99723.146178
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.51515607
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4221539
X-RAY DIFFRACTIONr_chiral_restr0.0890.2623
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0214583
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02898
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_it3.7715.4792031
X-RAY DIFFRACTIONr_mcbond_other3.775.4772030
X-RAY DIFFRACTIONr_mcangle_it5.3548.2012539
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_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.16 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.366 187 -
Rwork0.361 3748 -
obs--99.57 %

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