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- PDB-5f2g: Tagatose-1,6-bisphosphate aldolase from Streptococcus pyogenes Gl... -

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Open data


ID or keywords:

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Basic information

Entry
Database: PDB / ID: 5f2g
TitleTagatose-1,6-bisphosphate aldolase from Streptococcus pyogenes Glu164Gln mutant in complex with FBP
ComponentsTagatose 1,6-diphosphate aldolase 2
KeywordsLYASE / Covalent intermediate / Substrate / Aldolase / Class I
Function / homology
Function and homology information


6-deoxy-6-sulfofructose-1-phosphate aldolase activity / tagatose-bisphosphate aldolase / 6-sulfoquinovose(1-) catabolic process / lactose catabolic process via tagatose-6-phosphate / D-tagatose 6-phosphate catabolic process / tagatose-6-phosphate kinase activity / tagatose-bisphosphate aldolase activity
Similarity search - Function
Tagatose 1,6-diphosphate aldolase / DeoC/LacD family aldolase / DeoC/FbaB/LacD aldolase / DeoC/LacD family aldolase / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
1,3-DIHYDROXYACETONEPHOSPHATE / 1,6-di-O-phosphono-D-fructose / Tagatose 1,6-diphosphate aldolase 2
Similarity search - Component
Biological speciesStreptococcus pyogenes serotype M1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.918 Å
AuthorsLowKam, C.
CitationJournal: To Be Published
Title: NON-STEREOSPECIFIC SUBSTRATE CLEAVAGE BY TAGATOSE-BISPHOSPHATE CLASS I ALDOLASE
Authors: LowKam, C. / Liotard, B. / Sygusch, J.
History
DepositionDec 1, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 7, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Author supporting evidence / Category: pdbx_audit_support

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tagatose 1,6-diphosphate aldolase 2
B: Tagatose 1,6-diphosphate aldolase 2
C: Tagatose 1,6-diphosphate aldolase 2
D: Tagatose 1,6-diphosphate aldolase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)147,18811
Polymers146,4784
Non-polymers7117
Water26,1761453
1
A: Tagatose 1,6-diphosphate aldolase 2
C: Tagatose 1,6-diphosphate aldolase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,6595
Polymers73,2392
Non-polymers4203
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Tagatose 1,6-diphosphate aldolase 2
D: Tagatose 1,6-diphosphate aldolase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,5296
Polymers73,2392
Non-polymers2904
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.712, 106.858, 238.445
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Tagatose 1,6-diphosphate aldolase 2 / D-tagatose-1 / 6-bisphosphate aldolase 2 / Tagatose-bisphosphate aldolase 2


Mass: 36619.477 Da / Num. of mol.: 4 / Mutation: E163Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pyogenes serotype M1 (bacteria)
Gene: lacD2, lacD.2, SPy_1919, M5005_Spy1635 / Production host: Escherichia coli (E. coli) / References: UniProt: P63705, tagatose-bisphosphate aldolase
#2: Chemical ChemComp-P6F / 1,6-di-O-phosphono-D-fructose


Mass: 340.116 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H14O12P2
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-13P / 1,3-DIHYDROXYACETONEPHOSPHATE


Mass: 170.058 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C3H7O6P
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1453 / 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: 2.8 Å3/Da / Density % sol: 56.03 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Tris Acetate, Calcium Acetate, PEG 4000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 296K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 16, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.918→50 Å / Num. obs: 125051 / % possible obs: 99.66 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.082 / Net I/σ(I): 16.53
Reflection shellResolution: 1.918→1.94 Å / Redundancy: 2.3 % / Mean I/σ(I) obs: 2.18 / Num. unique all: 6292 / % possible all: 67.8

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementResolution: 1.918→49.734 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 21.72 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1957 1936 1.6 %
Rwork0.1553 --
obs0.1559 121233 96.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.918→49.734 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10191 0 33 1453 11677
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00410584
X-RAY DIFFRACTIONf_angle_d0.83814319
X-RAY DIFFRACTIONf_dihedral_angle_d12.4313967
X-RAY DIFFRACTIONf_chiral_restr0.031589
X-RAY DIFFRACTIONf_plane_restr0.0041863
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9181-1.9660.24111220.21277408X-RAY DIFFRACTION85
1.966-2.01920.22381310.19188052X-RAY DIFFRACTION92
2.0192-2.07860.21951310.17568229X-RAY DIFFRACTION94
2.0786-2.14570.21051340.16758319X-RAY DIFFRACTION95
2.1457-2.22240.20741400.16298417X-RAY DIFFRACTION97
2.2224-2.31140.22691390.16258507X-RAY DIFFRACTION97
2.3114-2.41660.21991340.15518507X-RAY DIFFRACTION97
2.4166-2.5440.21421390.15798653X-RAY DIFFRACTION98
2.544-2.70340.22081410.15528628X-RAY DIFFRACTION99
2.7034-2.91210.22441430.1668750X-RAY DIFFRACTION99
2.9121-3.20510.20231420.15558787X-RAY DIFFRACTION99
3.2051-3.66870.18681430.14438845X-RAY DIFFRACTION100
3.6687-4.62170.1551460.12398946X-RAY DIFFRACTION100
4.6217-49.75120.18031510.16559249X-RAY DIFFRACTION99
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
14.0866-0.13381.61234.6681-2.59954.95150.07-0.0199-0.12930.0074-0.0339-0.18190.0901-0.0157-0.04010.05750.02530.05990.234-0.03680.137961.927556.285834.9322
25.5214-2.93311.88864.3381-0.15484.0048-0.47860.22381.3347-1.0203-0.39930.6764-1.0378-0.12710.3830.93520.2383-0.35520.3953-0.08480.853461.268784.534528.4763
33.95190.31780.89321.6525-0.59242.8455-0.05140.31960.4569-0.0429-0.0258-0.2187-0.34050.22240.09220.2009-0.01410.03390.26140.04080.257265.988168.13328.4799
43.0225-0.8213-0.39511.98260.67612.38320.04680.22490.1753-0.1217-0.00880.0509-0.1038-0.0768-0.04110.11990.0020.00470.21920.05190.175547.587261.796827.5098
55.7883-3.4495.89914.3876-3.06618.275-0.067-0.30350.9664-0.0437-0.16970.2013-0.6989-0.54330.21550.22260.06550.02590.3077-0.08160.490640.898277.550442.4098
62.6477-0.2354-0.42153.04362.82975.3820.0814-0.08910.24240.0236-0.13150.0647-0.0115-0.15410.03690.10460.01990.01580.1850.02040.162544.593660.720340.461
76.2299-2.5838-2.22133.50040.39596.11940.0779-0.89940.91010.5521-0.32230.0639-0.6855-0.7322-0.11420.28650.05520.00250.5175-0.20850.38146.823773.406156.0373
84.0392.4620.03363.63230.48682.61110.1085-0.33680.37110.0744-0.14880.14-0.1253-0.10770.01650.12780.03650.00490.2017-0.02110.201655.318864.603946.8913
95.2631.2052-0.95433.5155-3.97934.9428-0.0990.17810.87670.3877-0.2942-0.4035-1.50710.6960.38290.5913-0.1377-0.08120.32140.04550.471473.646679.542437.1621
105.9618-4.03810.57513.73841.60546.072-0.1191-0.27510.1280.10520.1025-0.1594-0.06820.02470.01940.11570.00680.00520.24740.00180.088364.488260.447948.5269
113.80571.1326-2.22634.5697-1.6394.81680.14080.03840.1533-0.1151-0.1386-0.1886-0.22670.1866-0.00010.0612-0.0217-0.03110.2333-0.00010.162530.42252.267147.9563
120.7417-1.52630.47713.1475-0.97870.3039-0.4821-0.2183-1.4623-0.1384-0.1832-0.09911.26920.12410.26770.71960.03250.35080.37310.10830.853833.49225.583958.1546
132.5195-0.1318-0.0490.7623-0.35031.9748-0.0379-0.286-0.37570.0079-0.0648-0.08310.13640.29380.13070.17390.03420.0150.18030.05080.256429.267440.364755.316
143.65521.30130.64042.14541.15042.8694-0.0321-0.1213-0.08740.0801-0.00180.05350.0580.03210.02750.1179-0.00230.01560.11840.060.157916.434447.336455.2108
150.2571-0.29850.53816.92824.49145.1147-0.48150.3147-0.66810.3491-0.00550.43290.5059-0.50630.4050.3442-0.10040.14380.2252-0.06620.52638.302430.023641.8162
162.70630.93440.15673.71642.40534.4308-0.05660.1723-0.1817-0.1528-0.03250.03860.0123-0.17820.08630.1133-0.02210.01250.13970.01880.161912.676246.111442.6541
173.81010.57441.74175.97442.40233.8447-0.05270.6579-0.7032-0.5243-0.18070.12810.7135-0.50850.1470.3838-0.10050.09360.3578-0.16980.372314.80334.070526.7907
183.42330.4183-1.38693.69551.25844.4672-0.14770.2107-0.41210.0086-0.0922-0.01730.46390.02530.13630.1663-0.00980.03990.15030.00080.184322.871842.825436.0362
192.8801-2.13471.2163.786-2.17981.6052-0.8048-0.1931-0.4051-0.271-0.2703-0.4091.32440.5176-0.70970.71760.17430.34380.26330.08730.631441.817828.78946.7784
206.62234.26680.04512.8381-0.70626.9488-0.14620.5755-0.0855-0.2660.0187-0.1380.17820.34140.13060.0992-0.00350.01290.29660.02210.114632.499347.527334.6837
218.442-3.11563.64499.047-0.2435.85430.23090.0385-0.6529-0.02390.2394-0.20980.8338-0.2373-0.45640.3311-0.06030.03650.3649-0.03560.182140.165137.63299.3514
224.57541.8077-1.73142.7033-3.83065.6471-0.3559-0.13211.4804-0.4346-0.34340.9633-0.8983-1.44080.57650.8020.3099-0.26651.1975-0.11490.810119.870559.33915.9009
235.00061.7971.74083.89382.05752.75610.1288-0.16540.1012-0.0807-0.28340.51370.0366-1.19760.19310.297-0.0668-0.02930.74320.02230.241525.496244.98419.8308
242.1106-2.24670.75552.4076-0.98555.0920.03880.03840.09650.05940.03250.2944-0.0692-0.3578-0.01660.14430.0295-0.02990.5030.0220.229935.022451.526610.2734
252.75352.6617-2.15074.0819-2.67586.199-0.15370.38710.1786-0.23150.17360.0511-0.2557-0.1201-0.04470.17950.0299-0.04310.38710.05060.211243.009757.807210.5534
264.27234.4235-1.19738.8023-5.08315.915-0.04050.2422-0.0967-0.15450.0639-0.02420.13460.20360.05220.1520.02340.00380.3508-0.01170.182449.543653.187214.7015
270.39250.5845-0.18172.3782-0.77045.6983-0.22260.55660.1645-0.47170.32110.0625-0.26640.2775-0.03910.3229-0.1118-0.02590.63990.05220.242548.058854.9519-2.0846
280.08530.2519-0.42031.1155-0.63264.5008-0.22250.54880.0537-0.31170.28030.0254-0.05810.3817-0.07640.4283-0.1255-0.06970.852-0.01680.25943.05346.4846-11.8392
293.3541.35040.93833.9333-0.37832.7259-0.2908-0.16010.4793-0.708-0.19420.9834-0.559-1.28750.34330.67310.2154-0.20011.3996-0.03760.442516.717148.0233-0.3622
307.08682.45583.68416.07572.56555.6050.49980.4004-0.893-0.3013-0.0135-0.08810.768-0.5886-0.49990.5034-0.0813-0.05940.63060.00510.230634.949935.8643-4.3194
316.19221.5844-1.06067.09660.95995.852-0.0365-0.21280.4813-0.24630.1765-0.2991-0.84730.0961-0.17170.38850.00610.03060.2206-0.060.22897.555269.236774.0263
325.91682.7236-2.73847.3104-6.08915.1205-0.304-0.3806-1.13970.3033-0.16060.82081.1821-1.30310.35030.973-0.3660.31590.8234-0.12140.7464-12.014547.314577.3838
335.0337-2.9259-0.52923.92691.1133.31730.1886-0.0893-0.1023-0.0321-0.18760.4245-0.2356-0.686-0.01030.2014-0.01520.05630.3468-0.00260.191-3.502559.274173.3407
342.4633-0.91171.19252.7951-1.46514.9641-0.0239-0.2825-0.24470.2054-0.0223-0.01390.18460.17630.0370.1405-0.0240.04890.26520.0430.20410.776749.398972.7211
355.3712-3.96240.8164.8466-1.32385.10430.0284-0.2040.0125-0.03020.0372-0.0839-0.15770.36710.00490.1255-0.060.02420.2278-0.00470.174316.910454.243469.5454
360.1740.3962-0.78094.6869-2.16663.6912-0.0029-0.725-0.34810.60590.064-0.00780.10730.3769-0.0330.35050.04190.01860.6260.09160.243715.995349.051788.4638
370.1206-0.3540.09061.47691.12084.7109-0.1065-0.6812-0.01990.39420.19760.07310.22530.0879-0.01210.3170.02720.03330.70120.06520.21212.265955.743292.6162
380.1681-0.4258-0.27931.19820.03294.59010.0194-0.77390.10080.22050.0327-0.04620.09690.1551-0.07050.4392-0.08860.06150.6227-0.04520.23178.821462.031191.6074
396.06690.6616-1.33511.3849-0.43022.53510.0064-0.53850.25330.3941-0.22280.58120.6938-1.0260.11980.5768-0.14950.18130.7605-0.10430.3794-10.969864.063486.1008
404.8917-1.48663.70134.38925.21521.9999-0.16640.04841.1661-0.620.6078-1.7015-2.2582.3321-0.62230.7444-0.19320.06840.404-0.12620.550415.458773.632680.6919
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 3:30)
2X-RAY DIFFRACTION2(chain A and resid 31:44)
3X-RAY DIFFRACTION3(chain A and resid 45:97)
4X-RAY DIFFRACTION4(chain A and resid 98:169)
5X-RAY DIFFRACTION5(chain A and resid 170:180)
6X-RAY DIFFRACTION6(chain A and resid 181:210)
7X-RAY DIFFRACTION7(chain A and resid 211:233)
8X-RAY DIFFRACTION8(chain A and resid 234:284)
9X-RAY DIFFRACTION9(chain A and resid 285:306)
10X-RAY DIFFRACTION10(chain A and resid 307:324)
11X-RAY DIFFRACTION11(chain B and resid 3:29)
12X-RAY DIFFRACTION12(chain B and resid 30:52)
13X-RAY DIFFRACTION13(chain B and resid 53:110)
14X-RAY DIFFRACTION14(chain B and resid 111:168)
15X-RAY DIFFRACTION15(chain B and resid 169:179)
16X-RAY DIFFRACTION16(chain B and resid 180:211)
17X-RAY DIFFRACTION17(chain B and resid 212:233)
18X-RAY DIFFRACTION18(chain B and resid 234:280)
19X-RAY DIFFRACTION19(chain B and resid 281:307)
20X-RAY DIFFRACTION20(chain B and resid 308:324)
21X-RAY DIFFRACTION21(chain C and resid 3:27)
22X-RAY DIFFRACTION22(chain C and resid 28:51)
23X-RAY DIFFRACTION23(chain C and resid 52:82)
24X-RAY DIFFRACTION24(chain C and resid 83:97)
25X-RAY DIFFRACTION25(chain C and resid 98:138)
26X-RAY DIFFRACTION26(chain C and resid 139:159)
27X-RAY DIFFRACTION27(chain C and resid 160:210)
28X-RAY DIFFRACTION28(chain C and resid 211:276)
29X-RAY DIFFRACTION29(chain C and resid 277:303)
30X-RAY DIFFRACTION30(chain C and resid 304:325)
31X-RAY DIFFRACTION31(chain D and resid 3:27)
32X-RAY DIFFRACTION32(chain D and resid 28:51)
33X-RAY DIFFRACTION33(chain D and resid 52:97)
34X-RAY DIFFRACTION34(chain D and resid 98:137)
35X-RAY DIFFRACTION35(chain D and resid 138:161)
36X-RAY DIFFRACTION36(chain D and resid 162:196)
37X-RAY DIFFRACTION37(chain D and resid 197:225)
38X-RAY DIFFRACTION38(chain D and resid 226:284)
39X-RAY DIFFRACTION39(chain D and resid 285:320)
40X-RAY DIFFRACTION40(chain D and resid 321:326)

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