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- PDB-3r74: Crystal structure of 2-amino-2-desoxyisochorismate synthase (ADIC... -

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Basic information

Entry
Database: PDB / ID: 3r74
TitleCrystal structure of 2-amino-2-desoxyisochorismate synthase (ADIC) synthase PhzE from Burkholderia lata 383
ComponentsAnthranilate/para-aminobenzoate synthases component I
KeywordsLYASE / BIOSYNTHETIC PROTEIN / ammonia channel / chorismate / type 1 glutamine amidotransferase / phenazine biosynthesis / SYNTHASE
Function / homology
Function and homology information


anthranilate synthase / anthranilate synthase activity / tryptophan biosynthetic process / glutamine metabolic process / metal ion binding
Similarity search - Function
Anthranilate synthase/para-aminobenzoate synthase like domain / Anthranilate synthase / Anthranilate synthase / Anthranilate synthase component I-like / ADC synthase / Chorismate-utilising enzyme, C-terminal / chorismate binding enzyme / Glutamine amidotransferase class-I / Glutamine amidotransferase / Glutamine amidotransferase type 1 domain profile. ...Anthranilate synthase/para-aminobenzoate synthase like domain / Anthranilate synthase / Anthranilate synthase / Anthranilate synthase component I-like / ADC synthase / Chorismate-utilising enzyme, C-terminal / chorismate binding enzyme / Glutamine amidotransferase class-I / Glutamine amidotransferase / Glutamine amidotransferase type 1 domain profile. / Class I glutamine amidotransferase (GATase) domain / Class I glutamine amidotransferase-like / 4-Layer Sandwich / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
anthranilate synthase
Similarity search - Component
Biological speciesBurkholderia sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.9 Å
AuthorsLi, Q.A. / Mavrodi, D.V. / Thomashow, L.S. / Roessle, M. / Blankenfeldt, W.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Ligand Binding Induces an Ammonia Channel in 2-Amino-2-desoxyisochorismate (ADIC) Synthase PhzE.
Authors: Li, Q.A. / Mavrodi, D.V. / Thomashow, L.S. / Roessle, M. / Blankenfeldt, W.
History
DepositionMar 22, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 30, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Anthranilate/para-aminobenzoate synthases component I
B: Anthranilate/para-aminobenzoate synthases component I


Theoretical massNumber of molelcules
Total (without water)140,3262
Polymers140,3262
Non-polymers00
Water1,44180
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7070 Å2
ΔGint-35 kcal/mol
Surface area49080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)172.360, 172.360, 216.440
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number180
Space group name H-MP6222
Components on special symmetry positions
IDModelComponents
11A-657-

HOH

21A-687-

HOH

31B-664-

HOH

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Components

#1: Protein Anthranilate/para-aminobenzoate synthases component I


Mass: 70163.234 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia sp. (bacteria) / Strain: 383 / Gene: Bcep18194_B1570 / Plasmid: pET19modTEV / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2 pLys S / References: UniProt: Q396C7, anthranilate synthase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 80 / 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: 3.46 Å3/Da / Density % sol: 64.5 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.1 M Bis-TRIS propane, 0.2 M KSCN, 22% (w/v) PEG 3350, 1 mM Mg-chloride, 20 mM chorismate, pH 7.0, vapor diffusion, hanging drop, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.0, 0.97895, 0.97957, 0.97793
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 7, 2007 / Details: SI(111)
RadiationMonochromator: SI(111) MONOCHROMATOR / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
111
20.978951
30.979571
40.977931
ReflectionResolution: 2.9→19.924 Å / Num. obs: 42476 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 60.355 Å2 / Rmerge(I) obs: 0.062 / Net I/σ(I): 20.07
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
2.9-30.473.6819799403099.9
3-3.10.3794.5617367353899.9
3.1-3.20.276.1315210311099.8
3.2-40.10913.89746381528499.9
4-60.0432.06549741146899.7
6-80.0339.0213366286799.3
8-100.02150.454749105099.4
10-120.01952.15210148099
12-140.01952.08106224799.2
14-160.0250.8758314097.2
16-180.01848.173538897.8
18-200.02350.082305898.3
200.0248.0741811664.4

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
SHARPphasing
REFMAC5.6.0077refinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: MAD / Resolution: 2.9→19.92 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.922 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 26.439 / SU ML: 0.237 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.885 / ESU R Free: 0.326 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.2313 2120 5 %RANDOM
Rwork0.1869 ---
obs0.1891 42357 99.77 %-
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 max: 206.44 Å2 / Biso mean: 76.0686 Å2 / Biso min: 23.4 Å2
Refinement stepCycle: LAST / Resolution: 2.9→19.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9088 0 0 80 9168
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0219269
X-RAY DIFFRACTIONr_bond_other_d0.0050.026056
X-RAY DIFFRACTIONr_angle_refined_deg1.7621.95612629
X-RAY DIFFRACTIONr_angle_other_deg1.305314677
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.74451228
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.48222.672393
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.864151347
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.9811585
X-RAY DIFFRACTIONr_chiral_restr0.10.21454
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02110675
X-RAY DIFFRACTIONr_gen_planes_other0.0040.021940
LS refinement shellResolution: 2.9→2.974 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.324 157 -
Rwork0.255 2881 -
all-3038 -
obs--99.87 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.1493-0.39470.35551.241-0.65241.7614-0.03330.11820.1266-0.0016-0.027-0.2568-0.11570.26570.06030.2944-0.08820.05320.22180.01420.0731110.625220.2429101.1909
23.5301-0.62462.56882.3105-1.51379.03080.0455-0.03290.2285-0.1882-0.1065-0.16240.20970.69710.0610.33940.0449-0.16660.59880.06990.141168.034646.593472.6451
32.1081-0.5335-0.31590.56810.44422.921-0.2503-0.78850.24890.17170.14680.2523-0.1949-0.81970.10360.44780.0865-0.13451.56660.13930.4087148.133947.4941103.3023
42.22750.275-0.10112.38120.35413.2203-0.16180.3126-0.0071-0.28210.13890.239-0.0234-0.43720.0230.3876-0.1123-0.00470.36230.09050.055885.949622.969272.7995
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A6 - 395
2X-RAY DIFFRACTION1B401 - 427
3X-RAY DIFFRACTION2A440 - 633
4X-RAY DIFFRACTION3B7 - 395
5X-RAY DIFFRACTION3A401 - 427
6X-RAY DIFFRACTION4B430 - 635

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