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- PDB-5f2i: Tagatose-1,6-bisphosphate aldolase from Streptococcus pyogenes Gl... -

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Basic information

Entry
Database: PDB / ID: 5f2i
TitleTagatose-1,6-bisphosphate aldolase from Streptococcus pyogenes Glu163Gln mutant
ComponentsTagatose 1,6-diphosphate aldolase 2
KeywordsLYASE / TBP Aldolase / class I / mutant
Function / homology
Function and homology information


tagatose-bisphosphate aldolase / tagatose-bisphosphate aldolase activity / lactose catabolic process via tagatose-6-phosphate / D-tagatose 6-phosphate catabolic process / tagatose-6-phosphate kinase 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
ACETATE ION / Tagatose 1,6-diphosphate aldolase 2
Similarity search - Component
Biological speciesStreptococcus pyogenes serotype M1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 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, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry

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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)147,34620
Polymers146,4784
Non-polymers86816
Water22,5371251
1
A: Tagatose 1,6-diphosphate aldolase 2
C: Tagatose 1,6-diphosphate aldolase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,5909
Polymers73,2392
Non-polymers3527
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)73,75611
Polymers73,2392
Non-polymers5179
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.079, 98.542, 237.969
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-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1251 / 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: 2.54 Å3/Da / Density % sol: 51.63 %
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: Apr 18, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. obs: 94857 / % possible obs: 85.78 % / Redundancy: 5.8 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 20.8
Reflection shellResolution: 1.95→1.98 Å / Rmerge(I) obs: 0.377 / Mean I/σ(I) obs: 3.5 / Num. unique all: 4512 / % possible all: 83.2

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHASESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3MHF
Resolution: 1.95→49.371 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 20.24 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2024 1964 2.11 %
Rwork0.165 --
obs0.1658 93295 84.37 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.95→49.371 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10215 0 39 1251 11505
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00610473
X-RAY DIFFRACTIONf_angle_d0.98214141
X-RAY DIFFRACTIONf_dihedral_angle_d12.213927
X-RAY DIFFRACTIONf_chiral_restr0.0371566
X-RAY DIFFRACTIONf_plane_restr0.0051836
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9408-1.98930.24591180.2065395X-RAY DIFFRACTION71
1.9893-2.04310.20271340.18576103X-RAY DIFFRACTION80
2.0431-2.10320.24221300.18036201X-RAY DIFFRACTION81
2.1032-2.17110.20781290.1716183X-RAY DIFFRACTION81
2.1711-2.24870.19521360.1666167X-RAY DIFFRACTION81
2.2487-2.33880.19071330.16386129X-RAY DIFFRACTION80
2.3388-2.44520.21141300.15986168X-RAY DIFFRACTION81
2.4452-2.57410.23631320.16346179X-RAY DIFFRACTION80
2.5741-2.73540.18761330.16226155X-RAY DIFFRACTION79
2.7354-2.94650.20121340.16576217X-RAY DIFFRACTION81
2.9465-3.2430.19391460.1556785X-RAY DIFFRACTION87
3.243-3.71220.19431650.157664X-RAY DIFFRACTION98
3.7122-4.67640.17671690.14067844X-RAY DIFFRACTION100
4.6764-49.38740.22341750.19728141X-RAY DIFFRACTION100
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)
12.9252-1.40752.01135.1372-1.49874.39560.23180.0766-0.05380.0387-0.2184-0.28520.24230.23710.00810.07750.01590.06230.3765-0.00360.146261.148253.335733.0812
26.83083.2021.2467.6748-2.18366.51460.25410.88111.85450.18060.28740.2678-0.80240.4645-0.36990.6388-0.00490.02910.30860.15150.626461.680982.438525.1246
31.58450.5524-0.52391.6522-0.15072.45990.00230.42340.4867-0.117-0.1032-0.1398-0.25770.42910.09210.2024-0.0610.01190.38010.07790.27365.078365.679626.2542
43.4776-1.1987-0.84171.84711.53432.79780.05840.17440.2434-0.14380.01050.0739-0.13180.0314-0.05730.1387-0.0279-0.00340.18160.05710.148146.591559.155225.2222
51.77131.40362.0048.3547-0.80023.2516-0.06170.02380.8369-0.6027-0.2950.4592-0.2046-0.50280.25610.30820.0667-0.05150.2136-0.04640.571139.033474.96740.1016
62.8489-0.8226-0.57654.43313.61046.66440.0925-0.07640.14990.1127-0.18390.20090.1248-0.25350.05220.1042-0.00590.00650.15930.0350.154543.395857.830737.9349
71.5366-0.87120.10786.22642.35425.1289-0.4607-0.9341.38390.5027-0.0371-0.0408-0.6493-0.25670.35970.29470.0696-0.14950.4153-0.20450.666845.010870.973253.9205
84.22561.2542-0.59571.81560.18163.49-0.0551-0.04350.56660.0320.04420.0977-0.2138-0.0405-0.01710.14720.028-0.03520.16420.02030.253754.245962.429744.8321
90.89831.1206-1.06767.8304-4.89843.2779-0.29670.05460.76480.3032-0.3435-0.4677-1.20881.00050.48960.6464-0.2603-0.1510.46920.07930.601273.271177.028134.6848
102.2499-1.9971.16722.41481.16528.23230.0336-0.47390.20760.278-0.3457-0.2076-0.2831-0.08410.31090.08220.0286-0.00640.3279-0.01080.190663.238658.381946.5524
113.0543-0.2903-0.85723.1277-1.48073.20890.0345-0.01020.41620.03540.069-0.1326-0.31050.1921-0.09180.1199-0.0574-0.00460.2238-0.03950.183629.48150.123246.3046
123.652-0.04671.62286.9474-0.46421.1764-0.0099-0.8559-1.03840.17330.0584-0.17130.4442-0.2065-0.01940.3101-0.02410.09010.36010.11070.419832.548923.05155.611
133.60240.0281-0.26420.73770.1282.6406-0.0086-0.2045-0.37920.0271-0.0261-0.09640.19520.19670.04320.16290.02870.00360.13030.01250.176628.581938.039453.0755
143.36870.970.23032.64390.87123.1758-0.01410.01680.11310.082-0.0060.14820.0338-0.15260.03090.1052-0.00790.01260.15130.03810.111615.621444.981153.158
155.1878-1.376-5.46613.5491.46266.2111-0.75110.603-1.2287-0.36-0.06090.52630.6983-0.62780.66590.4576-0.22690.10270.61-0.14120.44777.219327.597839.5409
162.81491.1110.12024.89182.2013.8803-0.1130.2715-0.1888-0.2126-0.01240.14620.0298-0.30050.11610.1546-0.0392-0.00610.2530.01620.12811.918243.875740.6008
174.89350.86341.25126.56621.82866.5828-0.05110.8649-0.6773-0.6564-0.19360.40051.0304-0.47250.19720.5196-0.19040.05250.6232-0.16010.278513.970532.02324.3721
185.0668-0.03390.15632.30440.64924.6357-0.21160.2806-0.397-0.13360.05540.10430.4819-0.20950.11830.2269-0.06430.05250.2578-0.00780.168222.108540.869933.5363
193.9648-1.33030.85744.6294-3.94753.85040.02930.1674-0.5519-0.6407-0.2288-0.41630.73260.32810.23090.31930.06880.09440.2256-0.02940.364340.842526.504944.4826
205.25190.6116-1.44494.86370.91078.60390.01380.3232-0.2761-0.68740.0711-0.0080.13880.0826-0.04920.091-0.04220.0220.2615-0.02120.127231.574345.121932.5714
215.7152-2.0852.3615.6885-0.76915.25960.0332-0.1123-0.45910.39090.25990.00590.6857-0.1063-0.21180.4675-0.0035-0.02530.3329-0.00430.199340.133534.40037.6165
228.33550.09992.31966.8656-0.46912.75910.16820.22440.9072-0.2067-0.30290.7881-0.9782-1.6498-0.00580.62290.2381-0.0091.158-0.01510.507819.188854.9833.1358
235.9530.60770.79961.65771.40974.92470.2431-0.0716-0.01180.0208-0.0930.37830.4677-1.2968-0.14540.3026-0.128-0.02510.61090.06110.202425.516341.20217.7345
245.4463-0.7541-0.49870.85581.22765.87180.12110.26510.0571-0.0602-0.0662-0.0395-0.0677-0.4277-0.05390.19560.0266-0.04820.36750.03890.095834.83348.21918.1017
253.52042.0249-1.73842.7761-0.69915.0782-0.10970.12860.2051-0.16460.1124-0.0034-0.29110.1181-0.02710.1655-0.0041-0.06590.22880.02750.166742.490254.81478.3561
262.84472.9247-0.74819.3324-2.22814.4728-0.06180.1041-0.0129-0.10470.0763-0.20210.18940.46130.01550.16230.0258-0.01220.3269-0.00860.115549.055350.43612.667
270.9910.58570.14931.9692-0.12654.767-0.12540.30230.159-0.48580.25680.0328-0.18970.6294-0.09850.3171-0.0986-0.02190.45940.0250.185947.709451.727-4.2343
281.55850.76190.79911.5538-0.28795.2253-0.18170.53240.0148-0.33770.2248-0.0720.04820.5253-0.08490.3667-0.0537-0.06030.4935-0.01410.21643.360442.5677-13.6849
292.53591.41220.9761.32560.80992.0724-0.0261-0.01560.4507-0.0586-0.28930.6365-0.3393-1.43640.28190.30610.0724-0.20781.6247-0.00460.172116.662643.2149-2.5899
305.5951-1.8317-0.72094.0940.81512.6830.31240.598-0.2841-0.1773-0.16530.211.0137-0.4021-0.20650.6069-0.1288-0.06930.4779-0.00240.192936.289231.8837-5.402
311.96180.55931.2485.3585-0.16954.91960.16850.36440.3341-0.02510.021-0.1732-0.75090.0962-0.17420.29980.00130.12270.2834-0.04240.27767.604465.452972.3276
327.43941.5822-2.14947.117-0.50754.55860.2012-0.4492-0.72680.0163-0.02990.7570.8017-1.2246-0.05020.4478-0.1667-0.01460.71790.050.5128-12.945944.172675.2758
334.0676-1.4781-0.50583.10650.42742.93780.10970.0169-0.0498-0.0322-0.02810.678-0.3099-0.6634-0.06240.18990.02170.04110.35530.03040.241-4.197156.412171.6075
342.1347-1.7851.42373.174-2.29645.1742-0.0374-0.0035-0.07360.11730.05650.04980.20140.1193-0.04080.1207-0.0360.03110.1818-0.02170.166210.244546.423770.4833
353.4175-2.88150.98655.9745-2.57173.89970.15350.04590.3084-0.0482-0.2516-0.2421-0.08870.39010.1030.1083-0.04480.01780.1996-0.01910.161816.30650.969267.63
362.87160.5258-0.98474.9511-1.2445.42810.0478-0.448-0.29720.6180.0037-0.0290.08410.5728-0.04540.20310.04320.01360.30280.00070.157515.50845.617186.3704
370.9789-0.8147-0.60951.58650.13976.1638-0.0938-0.50650.06310.42520.21220.15210.0383-0.0959-0.0870.2722-0.02220.02830.4322-0.01910.204311.805952.348390.5425
383.1208-0.5268-1.10691.4148-0.8113.70970.0412-0.36310.07280.23880.1675-0.0158-0.34970.2264-0.20210.3587-0.06290.08610.392-0.07670.21398.46258.555389.9567
392.12790.32980.56772.12080.83661.94180.2625-0.33920.32880.4109-0.11970.7618-0.0362-0.8967-0.18070.5348-0.00070.20720.83580.06740.4334-11.552360.476984.583
401.5152-0.0771-1.53282.8983-1.13062.24790.093-0.3486-0.10610.0682-0.4854-0.5811-0.28040.78980.35480.5532-0.30880.51710.38130.04780.482813.600570.606380.1157
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 2:30)
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 304:326)
31X-RAY DIFFRACTION31(chain D and resid 1:27)
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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