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- PDB-3n5m: Crystals structure of a Bacillus anthracis aminotransferase -

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Basic information

Entry
Database: PDB / ID: 3n5m
TitleCrystals structure of a Bacillus anthracis aminotransferase
ComponentsAdenosylmethionine-8-amino-7-oxononanoate aminotransferase
KeywordsTRANSFERASE / Aminotransferase / Bacillus anthracis / CSGID / Structural Genomics / Center for Structural Genomics of Infectious Diseases
Function / homologyAspartate Aminotransferase, domain 1 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Alpha-Beta Complex / 3-Layer(aba) Sandwich / Alpha Beta / :
Function and homology information
Biological speciesBacillus anthracis (anthrax bacterium)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.05 Å
AuthorsAnderson, S.M. / Wawrzak, Z. / DiLeo, R. / Onopriyenko, O. / Savchenko, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: TO BE PUBLISHED
Title: Crystals structure of a Bacillus anthracis aminotransferase
Authors: Anderson, S.M. / Wawrzak, Z. / DiLeo, R. / Onopriyenko, O. / Savchenko, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionMay 25, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 9, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Dec 14, 2011Group: Database references / Structure summary
Revision 1.3Nov 8, 2017Group: Refinement description / Category: software

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Adenosylmethionine-8-amino-7-oxononanoate aminotransferase
B: Adenosylmethionine-8-amino-7-oxononanoate aminotransferase
C: Adenosylmethionine-8-amino-7-oxononanoate aminotransferase
D: Adenosylmethionine-8-amino-7-oxononanoate aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)205,95520
Polymers204,9034
Non-polymers1,05216
Water18,7001038
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area31450 Å2
ΔGint-468 kcal/mol
Surface area53120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.414, 176.176, 80.059
Angle α, β, γ (deg.)90.000, 94.470, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain A and (resseq 5:449 )A5 - 449
211chain B and (resseq 5:449 )B5 - 449
311chain C and (resseq 5:449 )C5 - 449
411chain D and (resseq 5:449 )D5 - 449

NCS oper:
IDCodeMatrixVector
1given(-0.987306, -0.004251, -0.158776), (0.001283, -0.999823, 0.018785), (-0.158828, 0.018343, 0.987136)92.390297, 213.705994, 5.40513
2given(0.894149, 0.422611, 0.147981), (0.422186, -0.9058, 0.035842), (0.149189, 0.030428, -0.98834)-43.5923, 184.498001, 31.882601
3given(-0.908735, -0.417249, 0.01021), (-0.417216, 0.907446, -0.049714), (0.011478, -0.049436, -0.998711)129.595001, 29.581301, 46.846901

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Components

#1: Protein
Adenosylmethionine-8-amino-7-oxononanoate aminotransferase


Mass: 51225.676 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Strain: Sterne / Gene: BAS1519, BA_1636, GBAA1636, GBAA_1636 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIL / References: UniProt: Q6I0U5
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1038 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsCLONING ERROR

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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: 2.14 Å3/Da / Density % sol: 42.57 %
Crystal growTemperature: 298 K / Method: hanging drop / pH: 7
Details: 20% PEG 3350,100mM Na Formate,100mM Li Sulfate, 100mM Bis-Tris, pH 7, hanging drop, temperature 298K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97857 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 12, 2010 / Details: beryllium lens
RadiationMonochromator: C(111) diamond laue monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 2.05→50 Å / Num. all: 108118 / Num. obs: 106929 / % possible obs: 98.9 % / Observed criterion σ(F): 1.5 / Observed criterion σ(I): 2.2 / Redundancy: 6.8 % / Rmerge(I) obs: 0.097 / Χ2: 1.016 / Net I/σ(I): 9.7
Reflection shellResolution: 2.05→2.12 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.604 / Mean I/σ(I) obs: 2.2 / Num. unique all: 10035 / Χ2: 0.984 / % possible all: 93.2

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.6.1_357refinement
PDB_EXTRACT3.1data extraction
BLU-MAXdata collection
HKL-2000data reduction
HKL-2000data scaling
SHELXSphasing
RefinementMethod to determine structure: SAD / Resolution: 2.05→34.85 Å / Occupancy max: 1 / Occupancy min: 0.43 / SU ML: 0.25 / σ(F): 1.44 / σ(I): 2.2 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.193 5314 4.99 %
Rwork0.156 --
obs0.158 106428 98.92 %
all-107612 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 50.827 Å2 / ksol: 0.332 e/Å3
Displacement parametersBiso max: 330.23 Å2 / Biso mean: 36.71 Å2 / Biso min: 6.43 Å2
Baniso -1Baniso -2Baniso -3
1-8.808 Å2-0 Å2-4.238 Å2
2---9.932 Å2-0 Å2
3---1.124 Å2
Refinement stepCycle: LAST / Resolution: 2.05→34.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14124 0 48 1038 15210
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0114663
X-RAY DIFFRACTIONf_angle_d1.22519832
X-RAY DIFFRACTIONf_chiral_restr0.0922122
X-RAY DIFFRACTIONf_plane_restr0.0062581
X-RAY DIFFRACTIONf_dihedral_angle_d14.415540
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A3419X-RAY DIFFRACTIONPOSITIONAL0.411
12B3419X-RAY DIFFRACTIONPOSITIONAL0.411
13C3394X-RAY DIFFRACTIONPOSITIONAL0.321
14D3430X-RAY DIFFRACTIONPOSITIONAL0.432
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection allNum. reflection obs% reflection obs (%)
2.05-2.1230.2965050.244951610021951693.3
2.123-2.2080.2625080.20810007105151000798
2.208-2.3090.2315180.18810217107351021799.9
2.309-2.430.2425060.18102241073010224100
2.43-2.5830.2155510.17101861073710186100
2.583-2.7820.225380.168101711070910171100
2.782-3.0620.2015560.16710199107551019999.9
3.062-3.5040.2015390.15310227107661022799.8
3.504-4.4140.1435590.11710142107011014299.1
4.414-34.8550.1575340.13510225107591022599.2
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)
10.0930.72480.28355.71482.47531.26960.0908-0.204-0.0483-0.40190.0258-0.5654-0.2541-0.0288-0.16950.2294-0.043-0.05870.21560.01970.541760.9128144.185520.0895
20.7428-0.38350.04011.5651-0.1810.342-0.01390.12660.1803-0.1089-0.0377-0.14010.00020.00810.04360.08670.0007-0.01370.1080.05640.16338.5714129.500610.9163
30.5118-0.32620.13121.4313-0.26280.13350.06720.10650.0907-0.3173-0.07110.12770.0261-0.0337-0.00630.21420.0164-0.03610.19690.050.219632.7345124.25174.3721
40.8873-0.75770.01551.27250.17410.27450.18910.22280.5014-0.57-0.1712-0.8284-0.02890.1615-0.00420.38870.03440.22990.29630.20010.548755.9554134.6225-5.865
50.3915-0.6667-0.00951.36290.26060.25780.0248-0.0328-0.084-0.1843-0.01550.5084-0.0594-0.03820.00690.1404-0.0250.01220.1879-0.02530.321228.73970.88518.5846
60.1473-0.22350.06391.0491-0.00520.3026-0.01590.0336-0.095-0.1576-0.0709-0.18920.09320.08240.08560.09460.03060.05540.1315-0.0090.221454.383270.424413.8504
70.4923-0.32960.1031.4014-0.24190.20410.01810.08360.0499-0.2668-0.0766-0.2815-0.02410.07210.04520.12990.00740.06080.15230.02640.180555.826892.10498.3028
80.1998-0.10610.10761.50990.00150.18260.04810.1238-0.1216-0.6332-0.08620.2737-0.057-0.01910.02070.4130.0342-0.06890.2425-0.0680.21937.629579.2132-6.9048
90.01850.0398-0.05310.3672-0.14850.1833-0.1058-0.0754-0.01720.0740.0615-0.35380.00710.09690.06510.18370.0405-0.00280.31010.07170.478975.072379.979125.1952
100.3735-0.18930.00010.7338-0.11970.3013-0.02640.009-0.18150.14490.0026-0.06520.0778-0.00210.01890.11910.03710.01450.12650.01560.225651.077870.322930.1223
110.4744-0.23180.07271.5163-0.03750.2367-0.1111-0.0364-0.03790.33630.07190.0549-0.0481-0.0130.02310.14820.03170.03080.11960.00930.113640.242289.811834.2669
120.2477-0.32860.06751.2514-0.08110.3785-0.2031-0.15090.02080.64190.1358-0.5134-0.07010.09260.03420.44070.0903-0.17320.22450.00430.255961.579985.437850.3893
130.37880.6757-0.11081.54170.17960.45290.04650.30550.26110.14940.08220.42740.0503-0.1506-0.11010.17330.0286-0.00160.28340.11730.431715.9808132.013620.2361
140.6752-0.0879-0.01150.8774-0.50380.2928-0.0312-0.00370.31110.32710.0436-0.2072-0.22750.02150.00210.25440.0332-0.0630.1412-0.00130.371736.779144.094228.4446
150.4689-0.1502-0.00771.6552-0.33510.1056-0.1568-0.07990.12930.46080.0948-0.253-0.09510.03080.06130.27560.0381-0.09940.1262-0.01630.199545.7844119.834237.1856
160.7406-0.3395-0.34471.5681-0.14840.5316-0.1352-0.07120.2310.56350.1603-0.025-0.12090.0135-0.03090.35210.0666-0.03380.1738-0.00960.20933.7729131.953439.4025
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid -1:30)A-1 - 30
2X-RAY DIFFRACTION2(chain A and resid 31:188)A31 - 188
3X-RAY DIFFRACTION3(chain A and resid 189:346)A189 - 346
4X-RAY DIFFRACTION4(chain A and resid 347:449)A347 - 449
5X-RAY DIFFRACTION5(chain B and resid 1:30)B1 - 30
6X-RAY DIFFRACTION6(chain B and resid 31:104)B31 - 104
7X-RAY DIFFRACTION7(chain B and resid 105:347)B105 - 347
8X-RAY DIFFRACTION8(chain B and resid 348:449)B348 - 449
9X-RAY DIFFRACTION9(chain C and resid -1:30)C-1 - 30
10X-RAY DIFFRACTION10(chain C and resid 31:104)C31 - 104
11X-RAY DIFFRACTION11(chain C and resid 105:341)C105 - 341
12X-RAY DIFFRACTION12(chain C and resid 342:449)C342 - 449
13X-RAY DIFFRACTION13(chain D and resid 4:31)D4 - 31
14X-RAY DIFFRACTION14(chain D and resid 32:104)D32 - 104
15X-RAY DIFFRACTION15(chain D and resid 105:270)D105 - 270
16X-RAY DIFFRACTION16(chain D and resid 271:449)D271 - 449

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