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- PDB-2g5f: The structure of MbtI from Mycobacterium Tuberculosis, the first ... -

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Basic information

Entry
Database: PDB / ID: 2g5f
TitleThe structure of MbtI from Mycobacterium Tuberculosis, the first enzyme in the synthesis of Mycobactin, reveals it to be a salicylate synthase
ComponentsCOG0147: Anthranilate/para-aminobenzoate synthases component I
KeywordsBIOSYNTHETIC PROTEIN / Beta Sandwhich / Structural Genomics / PSI / Protein Structure Initiative / TB Structural Genomics Consortium / TBSGC
Function / homology
Function and homology information


isochorismate lyase / isochorismate pyruvate lyase activity / catechol-containing siderophore biosynthetic process / isochorismate synthase / isochorismate synthase activity / oxo-acid-lyase activity / salicylic acid biosynthetic process / cellular response to iron ion starvation / chorismate mutase / chorismate mutase activity ...isochorismate lyase / isochorismate pyruvate lyase activity / catechol-containing siderophore biosynthetic process / isochorismate synthase / isochorismate synthase activity / oxo-acid-lyase activity / salicylic acid biosynthetic process / cellular response to iron ion starvation / chorismate mutase / chorismate mutase activity / response to host immune response / tryptophan biosynthetic process / magnesium ion binding / plasma membrane
Similarity search - Function
Salicylate synthase / 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
IMIDAZOLE / PYRUVIC ACID / Salicylate synthase / Salicylate synthase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.8 Å
AuthorsHarrison, A.J. / Lott, J.S. / Yu, M. / Ramsay, R. / Baker, E.N. / TB Structural Genomics Consortium (TBSGC)
CitationJournal: J.Bacteriol. / Year: 2006
Title: The Structure of MbtI from Mycobacterium tuberculosis, the First Enzyme in the Biosynthesis of the Siderophore Mycobactin, Reveals It To Be a Salicylate Synthase
Authors: Harrison, A.J. / Gardenborg, T. / Yu, M. / Middleditch, M. / Ramsay, R.J. / Baker, E.N. / Lott, J.S.
History
DepositionFeb 22, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 5, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: COG0147: Anthranilate/para-aminobenzoate synthases component I
B: COG0147: Anthranilate/para-aminobenzoate synthases component I
C: COG0147: Anthranilate/para-aminobenzoate synthases component I
D: COG0147: Anthranilate/para-aminobenzoate synthases component I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)196,12216
Polymers195,1174
Non-polymers1,00512
Water17,889993
1
A: COG0147: Anthranilate/para-aminobenzoate synthases component I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,0284
Polymers48,7791
Non-polymers2493
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: COG0147: Anthranilate/para-aminobenzoate synthases component I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,9593
Polymers48,7791
Non-polymers1802
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: COG0147: Anthranilate/para-aminobenzoate synthases component I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,1025
Polymers48,7791
Non-polymers3224
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: COG0147: Anthranilate/para-aminobenzoate synthases component I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,0324
Polymers48,7791
Non-polymers2533
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.820, 163.370, 194.930
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe molecule runs as a monomer on size exclusion chromatography.

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Components

#1: Protein
COG0147: Anthranilate/para-aminobenzoate synthases component I / MbtI Salicylate synthase


Mass: 48779.172 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: MbtI / Plasmid: pEt42a / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21 (DE3) pRI/L / References: UniProt: Q7D785, UniProt: P9WFX1*PLUS
#2: Chemical ChemComp-PYR / PYRUVIC ACID / Pyruvic acid


Mass: 88.062 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H4O3
#3: Chemical
ChemComp-IMD / IMIDAZOLE / Imidazole


Mass: 69.085 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H5N2
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 993 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.11 Å3/Da / Density % sol: 41.8 %
Crystal growTemperature: 316 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 15% PEG 4000, 0.2M Immadazole/malate, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 316K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONESRF ID14-410.9393
SYNCHROTRONALS 5.0.220.9796, 0.9797
Detector
TypeIDDetectorDate
ADSC QUANTUM 41CCDJul 4, 2003
ADSC QUANTUM 3152CCDJan 10, 2004
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.93931
20.97961
30.97971
ReflectionResolution: 1.8→50 Å / Num. all: 154253 / Num. obs: 154236 / % possible obs: 26 % / Observed criterion σ(F): 23.06 / Observed criterion σ(I): 4.75
Reflection shellResolution: 1.8→1.9 Å / % possible all: 97.6

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Processing

Software
NameVersionClassificationNB
CNSrefinement
PDB_EXTRACT1.701data extraction
MOSFLMdata reduction
CCP4(SCALA)data scaling
SHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.8→50 Å / FOM work R set: 0.846 / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.24 15321 9.9 %Random
Rwork0.205 ---
all0.208 153352 --
obs0.208 153352 99.4 %-
Solvent computationBsol: 43.448 Å2
Displacement parametersBiso mean: 23.685 Å2
Baniso -1Baniso -2Baniso -3
1--0.133 Å20 Å20 Å2
2---0.294 Å20 Å2
3---0.427 Å2
Refinement stepCycle: LAST / Resolution: 1.8→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13110 0 68 993 14171
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_mcangle_it1.5
X-RAY DIFFRACTIONc_mcbond_it2
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 50

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs
1.8-1.810.3193080.28926032911
1.81-1.820.3142820.2727022984
1.82-1.840.3013130.27626492962
1.84-1.850.2922910.26426572948
1.85-1.860.2932810.25226682949
1.86-1.880.2743310.24526472978
1.88-1.890.2953240.24227103034
1.89-1.910.2692850.24127393024
1.91-1.920.2663030.23627093012
1.92-1.940.283080.22526712979
1.94-1.960.2593010.22527193020
1.96-1.970.2562870.21327873074
1.97-1.990.2423090.21627683077
1.99-2.010.2572770.21527062983
2.01-2.030.2612990.21427603059
2.03-2.050.2593010.2127533054
2.05-2.070.2443150.20227763091
2.07-2.090.2612910.21227353026
2.09-2.110.252970.21127383035
2.11-2.130.2492960.21427393035
2.13-2.160.2342890.19928203109
2.16-2.180.263190.20227073026
2.18-2.210.2522930.20727613054
2.21-2.240.2453200.20527803100
2.24-2.270.2592960.20627543050
2.27-2.30.2532930.20427473040
2.3-2.330.2453040.20127813085
2.33-2.370.2453120.20227693081
2.37-2.40.2482970.19727413038
2.4-2.440.2523140.20627793093
2.44-2.490.2423230.19927433066
2.49-2.530.2572970.21127633060
2.53-2.580.2513160.21327693085
2.58-2.630.2473200.2127513071
2.63-2.690.2552940.21528073101
2.69-2.750.2623150.21627593074
2.75-2.820.2383320.20827503082
2.82-2.90.2543210.21727833104
2.9-2.980.2422930.20927693062
2.98-3.080.253130.21127883101
3.08-3.190.2432940.21528003094
3.19-3.320.2442960.20328053101
3.32-3.470.2313060.18828323138
3.47-3.650.23310.18827823113
3.65-3.880.2153070.18528133120
3.88-4.180.1983170.17528113128
4.18-4.60.1973200.1728423162
4.6-5.260.1973060.18628813187
5.26-6.630.2773240.24928993223
6.63-500.010.2223600.19130093369
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4glyparam.paramion.top
X-RAY DIFFRACTION5cis_peptide.paramglytopology.top
X-RAY DIFFRACTION6imdparam.paramimdtopology.top
X-RAY DIFFRACTION7imdparam.paramimdtopology.top

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