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- PDB-5f4w: Tagatose-1,6-bisphosphate aldolase from Streptococcus pyogenes in... -

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Basic information

Entry
Database: PDB / ID: 5f4w
TitleTagatose-1,6-bisphosphate aldolase from Streptococcus pyogenes in complex with TBP
ComponentsTagatose 1,6-diphosphate aldolase 2
KeywordsLYASE / Covalent intermediate / Acidic pH / Substrate / Aldolase / Class I
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
1,3-DIHYDROXYACETONEPHOSPHATE / 1,6-di-O-phosphono-D-tagatose / Tagatose 1,6-diphosphate aldolase 2
Similarity search - Component
Biological speciesStreptococcus pyogenes serotype M1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.663 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 3, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 1, 2017Provider: 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_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _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.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_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _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.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

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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)147,29414
Polymers146,4824
Non-polymers81210
Water26,2481457
1
A: Tagatose 1,6-diphosphate aldolase 2
B: Tagatose 1,6-diphosphate aldolase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,9028
Polymers73,2412
Non-polymers6616
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Tagatose 1,6-diphosphate aldolase 2
D: Tagatose 1,6-diphosphate aldolase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,3926
Polymers73,2412
Non-polymers1514
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.955, 107.373, 237.730
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 4 molecules ABCD

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


Mass: 36620.457 Da / Num. of mol.: 4
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

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Non-polymers , 5 types, 1467 molecules

#2: Chemical ChemComp-P6T / 1,6-di-O-phosphono-D-tagatose


Mass: 340.116 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O12P2
#3: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: Cl
#4: Chemical ChemComp-13P / 1,3-DIHYDROXYACETONEPHOSPHATE / Dihydroxyacetone phosphate


Mass: 170.058 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C3H7O6P
#5: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1457 / 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: 2.79 Å3/Da / Density % sol: 55.85 %
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: 1.663→50 Å / Num. obs: 170703 / % possible obs: 92.9 % / Redundancy: 4.3 % / Rmerge(I) obs: 0.4 / Net I/σ(I): 15.98
Reflection shellResolution: 1.94→1.98 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.089 / Mean I/σ(I) obs: 1.88 / % possible all: 88

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3MHF
Resolution: 1.663→49.876 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 28.1 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2056 1764 1.17 %
Rwork0.1733 --
obs0.1737 150379 78.14 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.663→49.876 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10246 0 36 1460 11742
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01210666
X-RAY DIFFRACTIONf_angle_d1.28814428
X-RAY DIFFRACTIONf_dihedral_angle_d14.0074004
X-RAY DIFFRACTIONf_chiral_restr0.0481600
X-RAY DIFFRACTIONf_plane_restr0.0061876
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6634-1.70830.5376290.53442199X-RAY DIFFRACTION15
1.7083-1.75860.4829610.43425498X-RAY DIFFRACTION38
1.7586-1.81540.3777880.3798049X-RAY DIFFRACTION56
1.8154-1.88030.33131220.31259975X-RAY DIFFRACTION69
1.8803-1.95550.3261450.260911496X-RAY DIFFRACTION79
1.9555-2.04450.26241540.220712423X-RAY DIFFRACTION86
2.0445-2.15230.20951510.194412961X-RAY DIFFRACTION89
2.1523-2.28720.20691650.181613479X-RAY DIFFRACTION92
2.2872-2.46380.20691630.172813883X-RAY DIFFRACTION95
2.4638-2.71170.22351640.170914152X-RAY DIFFRACTION97
2.7117-3.1040.18651670.166414478X-RAY DIFFRACTION98
3.104-3.91050.17251750.139714790X-RAY DIFFRACTION100
3.9105-49.89790.1741800.141715232X-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)
13.55680.34561.32628.8983-1.36915.32170.1649-0.0396-0.1632-0.114-0.1605-0.00640.18290.0082-0.05030.11110.03780.04130.2856-0.03130.153861.965755.242935.2684
26.88213.15693.52991.5021.86253.5711-0.03260.8541.7133-1.1143-0.59531.4782-1.23360.13730.55511.10430.2517-0.27370.5953-0.0040.838961.376784.644328.2934
33.63680.21530.93221.8435-0.79482.678-0.04950.34470.3988-0.0115-0.0882-0.2448-0.34650.37520.14970.2771-0.03460.03020.30550.05060.271266.178368.222928.3091
42.8114-0.5678-0.70431.88330.85372.63050.05560.20660.1503-0.11520.02630.0729-0.0985-0.0929-0.08480.19560.00590.0030.27040.05710.196647.739961.771127.4396
54.4071-1.26512.29832.2824-1.86717.7412-0.0408-0.24861.433-0.19980.05220.5313-0.6586-1.02080.04910.31340.0580.01850.2837-0.02360.482341.135677.598342.3395
62.8836-0.357-0.95153.25052.71085.51730.0911-0.04970.18060.0496-0.1220.12360.086-0.23530.03990.14380.03110.01750.18940.03840.14944.760260.552940.1941
76.4127-2.6941-2.11362.53470.98956.09370.0695-1.07040.77530.632-0.192-0.2144-0.508-0.5727-0.01620.29070.05150.00830.5262-0.17970.340647.140873.606655.98
84.77422.89180.68744.10350.65392.99460.065-0.30780.33580.0845-0.10330.1689-0.1007-0.22660.0180.15940.0430.00230.2183-0.01110.18555.713765.050146.8326
94.81291.9716-0.36796.3399-3.60525.2931-0.1334-0.09410.55310.3923-0.1866-0.6329-1.33560.59460.36840.7729-0.1666-0.10120.38590.00980.527873.776679.705336.8961
106.20572.74642.24879.19855.48124.2035-0.1476-0.2920.088-0.23880.0312-0.3161-0.0777-0.09260.05670.19710.0356-0.02230.24690.00660.126464.835160.734548.3822
115.8426-1.68590.92095.22.54896.15470.1950.2247-0.3446-0.03960.1013-0.1460.9745-0.1159-0.28830.3886-0.1001-0.00970.48530.00070.211739.296139.33279.1911
122.2272-0.14723.01998.6479-3.03116.6004-0.2775-0.52880.8552-0.15610.16071.2334-0.8837-1.48320.11320.59040.2219-0.11391.1525-0.01990.659818.810158.9966.1431
132.96111.53550.28382.23690.89272.36920.04580.13150.17440.0378-0.00270.29170.1133-0.6579-0.0350.25990.0082-0.04520.56570.05550.212131.763450.912910.0168
142.07591.1008-0.24192.4725-1.1563.5841-0.0430.26470.091-0.1260.1144-0.0236-0.04960.007-0.0670.23580.0202-0.01320.41760.00980.189446.030454.177110.903
152.98040.74493.16051.53281.78794.1094-0.5590.46620.7101-0.66230.2840.078-1.02680.50990.23440.6633-0.1326-0.08270.66820.14020.364444.049464.4154-9.9272
160.3120.6569-0.25662.1717-0.74526.0088-0.09890.55440.0267-0.33930.2164-0.02310.0540.5033-0.08070.2951-0.04760.00180.58210.00110.212550.347851.676-1.2769
171.3814-0.8436-1.02855.6172-1.06424.5105-0.12540.5148-0.085-0.78910.40.353-0.0930.354-0.29380.5553-0.1757-0.07330.8760.04140.268744.103951.1702-20.3068
182.99771.11852.37562.024-0.26056.3465-0.01640.40860.04-0.18030.1170.04550.0249-0.1341-0.12820.4368-0.026-0.04540.6085-0.0180.220441.662644.1165-7.0345
198.8378-2.1633.83034.0051-1.25622.0522-0.27340.07-0.097-0.4157-0.27280.88220.0976-1.5186-0.19910.50010.0025-0.14391.27440.03570.386616.201146.4675-0.523
206.495-0.74553.64925.22851.92929.47790.00460.512-0.78320.06950.2176-0.00960.7031-0.1991-0.22460.5938-0.1389-0.03990.50770.00320.226137.196835.0757-4.2128
212.41851.0753-1.65398.2250.57095.15770.22080.03380.1739-0.0117-0.1778-0.0563-0.45710.155-0.06250.1073-0.0149-0.02850.29050.01660.183230.503854.765147.4308
223.1994-0.6331.0814.8343-1.18445.0335-0.206-0.3262-0.9306-0.1462-0.0852-0.34721.07760.3480.27670.50850.04220.19140.38350.12370.542132.910626.503858.1812
232.1604-0.37520.2954.2113-3.31936.9304-0.0697-0.2213-0.2687-0.0171-0.1621-0.26630.19650.42120.24230.16790.02370.01550.27680.03770.261437.739840.666253.7444
241.9211-0.08810.12282.8039-0.73354.04710.1151-0.4854-0.37390.0132-0.2983-0.05210.01990.25660.17510.17930.0715-0.010.1650.05180.198626.531842.507155.2741
255.63752.29151.86562.20751.47713.50940.0429-0.2619-0.18040.1511-0.05430.01830.1819-0.10260.03320.19260.02650.01680.14480.03660.211516.530943.364457.0292
264.96985.97271.31828.40712.06523.30750.0001-0.25640.09710.0084-0.1170.174-0.1104-0.1190.12310.16790.00850.00530.16920.03280.145514.902152.184957.4284
272.291.1160.24014.61.57862.7172-0.07370.1738-0.2995-0.02420.00130.13710.1495-0.14990.07150.1439-0.00880.02250.2057-0.00240.195512.363342.311843.6898
283.24020.3085-0.5383.54181.13453.688-0.13310.4717-0.3406-0.2488-0.11380.08240.3491-0.18790.18360.2389-0.01350.0420.2502-0.0270.207619.94840.636432.7079
293.1181-2.85590.69765.4678-1.59362.0178-0.62110.0092-0.4575-0.4198-0.1826-0.27941.02130.44990.30670.53260.13350.19670.23980.05260.440239.567529.348547.4423
302.96841.43521.34574.1263-2.09963.359-0.13760.4175-0.1805-0.0217-0.0742-0.08750.1735-0.0180.19710.20530.00160.040.36280.00490.147633.244146.539235.8678
317.25372.895-2.27937.9877-0.19787.7881-0.0481-0.2170.2747-0.08760.1397-0.4771-0.72970.3232-0.08810.33170.00280.02870.2866-0.06310.2488.620569.564173.8604
324.25321.3296-3.13628.0249-4.47878.28460.0386-0.1692-1.01820.2437-0.0930.98780.5132-0.99460.06690.5592-0.16360.13930.6575-0.01080.6375-12.183747.914277.131
334.6729-2.84530.01794.15480.69272.99620.1471-0.126-0.0947-0.0778-0.12230.4158-0.2185-0.5966-0.01680.226-0.01530.0540.3512-0.00350.1967-3.566459.998973.1084
342.5798-1.48751.60053.2154-2.19195.8687-0.0076-0.2426-0.13340.1802-0.0357-0.04820.16820.21570.01920.1693-0.0320.05070.25320.02190.194110.820349.807372.6693
353.8148-3.91140.44538.3265-1.29324.14480.0551-0.22610.03190.1036-0.0923-0.0548-0.10360.4640.04410.1339-0.06470.01050.2549-0.00040.144616.969754.58669.4593
361.86910.9439-1.2284.9178-2.1416.64990.037-0.572-0.30220.55040.021-0.04430.18980.3868-0.05410.35220.02490.00750.52860.03140.225315.830649.483688.5172
370.2372-0.45520.0251.47611.2563.3239-0.0657-0.6307-0.03850.40290.1380.11950.28090.1311-0.06310.33350.00060.0360.66450.04180.208712.363556.292992.5166
380.4757-0.5179-0.22830.5402-0.19233.75670.1082-0.62520.11670.22130.0068-0.00410.00690.0437-0.0930.4747-0.10810.05620.6095-0.06670.26959.059862.680891.1826
395.03630.0639-0.34431.58320.38013.2460.1622-0.76120.30880.4503-0.31850.61230.2696-0.85650.14840.5019-0.04490.16070.6186-0.04880.325-11.014764.60385.7663
404.4032-1.11053.29123.3341.95665.0101-0.14450.00481.084-0.42420.602-0.7958-2.01042.8437-0.48890.7828-0.35640.05110.6912-0.14480.49515.615973.988280.4307
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 2:27)
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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