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- PDB-2eph: Crystal structure of fructose-bisphosphate aldolase from Plasmodi... -

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Basic information

Entry
Database: PDB / ID: 2eph
TitleCrystal structure of fructose-bisphosphate aldolase from Plasmodium falciparum in complex with TRAP-tail determined at 2.7 angstrom resolution
Components
  • Fructose-bisphosphate aldolase
  • PbTRAP
KeywordsLYASE / Aldolase / Invasion machinery / Plasmodium falciparum / Structural Genomics / PSI / Protein Structure Initiative / Structural Genomics of Pathogenic Protozoa Consortium / SGPP
Function / homology
Function and homology information


fructose-bisphosphate aldolase / fructose-bisphosphate aldolase activity / glycolytic process / actin binding / host cell plasma membrane / membrane / plasma membrane / cytoplasm
Similarity search - Function
Fructose-bisphosphate aldolase class-I active site / Fructose-bisphosphate aldolase class-I active site. / Fructose-bisphosphate aldolase, class-I / Fructose-bisphosphate aldolase class-I / Thrombospondin type 1 domain / Thrombospondin type-1 (TSP1) repeat superfamily / Thrombospondin type-1 (TSP1) repeat profile. / Thrombospondin type 1 repeats / Thrombospondin type-1 (TSP1) repeat / von Willebrand factor type A domain ...Fructose-bisphosphate aldolase class-I active site / Fructose-bisphosphate aldolase class-I active site. / Fructose-bisphosphate aldolase, class-I / Fructose-bisphosphate aldolase class-I / Thrombospondin type 1 domain / Thrombospondin type-1 (TSP1) repeat superfamily / Thrombospondin type-1 (TSP1) repeat profile. / Thrombospondin type 1 repeats / Thrombospondin type-1 (TSP1) repeat / von Willebrand factor type A domain / von Willebrand factor (vWF) type A domain / VWFA domain profile. / von Willebrand factor, type A / von Willebrand factor A-like domain superfamily / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Fructose-bisphosphate aldolase / Thrombospondin-related anonymous protein
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsBosch, J. / Buscaglia, C.A. / Krumm, B. / Cardozo, T. / Nussenzweig, V. / Hol, W.G.J. / Structural Genomics of Pathogenic Protozoa Consortium (SGPP)
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2007
Title: Aldolase provides an unusual binding site for thrombospondin-related anonymous protein in the invasion machinery of the malaria parasite.
Authors: Bosch, J. / Buscaglia, C.A. / Krumm, B. / Ingason, B.P. / Lucas, R. / Roach, C. / Cardozo, T. / Nussenzweig, V. / Hol, W.G.
History
DepositionMar 30, 2007Deposition site: PDBJ / Processing site: RCSB
Revision 1.0Apr 17, 2007Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Aug 23, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Fructose-bisphosphate aldolase
B: Fructose-bisphosphate aldolase
C: Fructose-bisphosphate aldolase
D: Fructose-bisphosphate aldolase
H: PbTRAP


Theoretical massNumber of molelcules
Total (without water)161,4035
Polymers161,4035
Non-polymers00
Water6,053336
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)70.019, 146.162, 148.961
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41
51
61
71
81
91
101
111
121
131
141
151
161
171
181
191
201
211
221
231
241
251
261
271
281
291
301
311
321
331
341
351
361
371
381
391
401
411
421
431
441
451
461
471
481
491
501
511
521
531
541
551
561
571
581
591
601

NCS domain segments:

Ens-ID: 1 / Refine code: 3

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASPASPGLNGLNAA16 - 3017 - 31
21ASPASPGLNGLNBB16 - 3017 - 31
31ASPASPGLNGLNCC16 - 3017 - 31
41ASPASPGLNGLNDD16 - 3017 - 31
52GLYGLYALAALAAA32 - 3733 - 38
62GLYGLYALAALABB32 - 3733 - 38
72GLYGLYALAALACC32 - 3733 - 38
82GLYGLYALAALADD32 - 3733 - 38
93THRTHRTHRTHRAA57 - 7158 - 72
103THRTHRTHRTHRBB57 - 7158 - 72
113THRTHRTHRTHRCC57 - 7158 - 72
123THRTHRTHRTHRDD57 - 7158 - 72
134LYSLYSALAALAAA76 - 8177 - 82
144LYSLYSALAALABB76 - 8177 - 82
154LYSLYSALAALACC76 - 8177 - 82
164LYSLYSALAALADD76 - 8177 - 82
175GLUGLULEULEUAA85 - 8886 - 89
185GLUGLULEULEUBB85 - 8886 - 89
195GLUGLULEULEUCC85 - 8886 - 89
205GLUGLULEULEUDD85 - 8886 - 89
216ILEILEASPASPAA108 - 159109 - 160
226ILEILEASPASPBB108 - 159109 - 160
236ILEILEASPASPCC108 - 159109 - 160
246ILEILEASPASPDD108 - 159109 - 160
257SERSERTYRTYRAA169 - 180170 - 181
267SERSERTYRTYRBB169 - 180170 - 181
277SERSERTYRTYRCC169 - 180170 - 181
287SERSERTYRTYRDD169 - 180170 - 181
298GLNGLNGLYGLYAA185 - 201186 - 202
308GLNGLNGLYGLYBB185 - 201186 - 202
318GLNGLNGLYGLYCC185 - 201186 - 202
328GLNGLNGLYGLYDD185 - 201186 - 202
339HISHISALAALAAA203 - 222204 - 223
349HISHISALAALABB203 - 222204 - 223
359HISHISALAALACC203 - 222204 - 223
369HISHISALAALADD203 - 222204 - 223
3710ASNASNTHRTHRAA226 - 241227 - 242
3810ASNASNTHRTHRBB226 - 241227 - 242
3910ASNASNTHRTHRCC226 - 241227 - 242
4010ASNASNTHRTHRDD226 - 241227 - 242
4111GLYGLYPHEPHEAA256 - 276257 - 277
4211GLYGLYPHEPHEBB256 - 276257 - 277
4311GLYGLYPHEPHECC256 - 276257 - 277
4411GLYGLYPHEPHEDD256 - 276257 - 277
4512ALAALAALAALAAA286 - 295287 - 296
4612ALAALAALAALABB286 - 295287 - 296
4712ALAALAALAALACC286 - 295287 - 296
4812ALAALAALAALADD286 - 295287 - 296
4913PROPROTYRTYRAA300 - 307301 - 308
5013PROPROTYRTYRBB300 - 307301 - 308
5113PROPROTYRTYRCC300 - 307301 - 308
5213PROPROTYRTYRDD300 - 307301 - 308
5314ALAALAALAALAAA310 - 313311 - 314
5414ALAALAALAALABB310 - 313311 - 314
5514ALAALAALAALACC310 - 313311 - 314
5614ALAALAALAALADD310 - 313311 - 314
5715GLNGLNLEULEUAA335 - 342336 - 343
5815GLNGLNLEULEUBB335 - 342336 - 343
5915GLNGLNLEULEUCC335 - 342336 - 343
6015GLNGLNLEULEUDD335 - 342336 - 343

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Components

#1: Protein
Fructose-bisphosphate aldolase / 41 kDa antigen


Mass: 40152.906 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Plasmid: pET14B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21STAR(DE3) / References: UniProt: P14223, fructose-bisphosphate aldolase
#2: Protein/peptide PbTRAP


Mass: 791.720 Da / Num. of mol.: 1 / Fragment: C-terminus: Residues 601-606 / Source method: obtained synthetically
Details: Synthetic peptide with the sequence based on PbTRAP protein from Plasmodium berghei, UNP entry P90573, P90573_PLABE, residues 601-606
References: UniProt: P90573
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 336 / 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: 2.36 Å3/Da / Density % sol: 47.89 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 2.5 mM TRAP-tail, 0.5% n-dodecyl-beta-D-maltoside, 50 mM cacodylic acid pH 6.0, 20% PEG 2000, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.9796 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Dec 16, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 2.68→19.97 Å / Num. all: 40459 / Num. obs: 40459 / % possible obs: 98.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Biso Wilson estimate: 65.2 Å2 / Rsym value: 0.07 / Net I/σ(I): 12.4
Reflection shellResolution: 2.68→2.822 Å / Redundancy: 2.3 % / Mean I/σ(I) obs: 2.8 / Rsym value: 0.55 / % possible all: 90.49

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
ADSCQUANTUMdata collection
MOSFLMdata reduction
CCP4(SCALA)data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1A5C
Resolution: 2.7→19.97 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.924 / SU B: 30.585 / SU ML: 0.295 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.369 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2504 2117 5.1 %RANDOM
Rwork0.19154 ---
obs0.19445 39693 98 %-
all-39693 --
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 mean: 59.195 Å2
Baniso -1Baniso -2Baniso -3
1-8.36 Å20 Å20 Å2
2---2.21 Å20 Å2
3----6.15 Å2
Refinement stepCycle: LAST / Resolution: 2.7→19.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10887 0 0 336 11223
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.02211091
X-RAY DIFFRACTIONr_bond_other_d0.0010.027504
X-RAY DIFFRACTIONr_angle_refined_deg1.0481.97315031
X-RAY DIFFRACTIONr_angle_other_deg0.877318455
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.37551424
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.77125.066456
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.503151962
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.0751556
X-RAY DIFFRACTIONr_chiral_restr0.0750.21741
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0212307
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022060
X-RAY DIFFRACTIONr_nbd_refined0.1950.22866
X-RAY DIFFRACTIONr_nbd_other0.1750.27900
X-RAY DIFFRACTIONr_nbtor_refined0.1720.25530
X-RAY DIFFRACTIONr_nbtor_other0.0830.25858
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1570.2401
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0980.23
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1640.228
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1960.2104
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1350.211
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.21949155
X-RAY DIFFRACTIONr_mcbond_other0.16942903
X-RAY DIFFRACTIONr_mcangle_it1.654611352
X-RAY DIFFRACTIONr_scbond_it2.20564672
X-RAY DIFFRACTIONr_scangle_it3.33103676
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A1256tight positional0.020.05
2B1256tight positional0.020.05
3C1256tight positional0.020.05
4D1256tight positional0.020.05
1A1484loose positional0.225
2B1484loose positional0.245
3C1484loose positional0.235
4D1484loose positional0.235
1A1256tight thermal0.040.5
2B1256tight thermal0.040.5
3C1256tight thermal0.050.5
4D1256tight thermal0.050.5
1A1484loose thermal1.2710
2B1484loose thermal1.2910
3C1484loose thermal1.4710
4D1484loose thermal1.4210
LS refinement shellResolution: 2.7→2.82 Å / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.347 557 -
Rwork0.284 10553 -
obs--94.44 %
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)
13.1920.831-2.4792.79143.71849.32-0.12570.06530.07970.71740.3429-0.80010.23261.1775-0.2172-0.1778-0.1367-0.06010.10660.00210.05827.368710.9237-13.4095
22.2145-3.71211.894710.1517-5.18896.4923-0.1529-0.00980.64550.2465-0.0968-0.2648-1.1468-0.42630.24970.0994-0.01290.1593-0.1551-0.0101-0.0687-17.453633.8103-12.094
33.94040.2023-0.20813.7085-1.05144.13890.11590.06050.4244-0.17840.08520.2327-1.22350.1977-0.20110.3885-0.060.1006-0.3565-0.043-0.1394-11.723937.7964-9.0825
40.86911.07920.24783.2450.87682.81840.02090.06170.1925-0.3558-0.01860.0579-0.93020.1528-0.00230.0445-0.04950.0859-0.1614-0.0061-0.0299-9.795525.5985-19.2659
52.23180.4892-0.26472.3589-0.37653.45440.1306-0.0272-0.0416-0.0481-0.03060.0215-0.4541-0.0463-0.1-0.2927-0.00450.0458-0.164-0.023-0.091-12.662712.6096-16.2391
61.56071.91841.89675.3244-1.35856.89430.3831-0.2119-0.30410.1975-0.32060.8671-0.4245-1.3832-0.0625-0.20840.03190.12120.0084-0.0652-0.0873-25.46238.5513-5.0585
71.21730.0305-0.35144.0431.11321.68670.1556-0.20450.4176-0.0324-0.10780.2986-0.709-0.3424-0.0478-0.00890.06590.1029-0.1153-0.0287-0.1062-19.266926.5133-1.5851
822.13498.25293.158418.51941.9270.4870.8835-0.1444-0.8130.9909-1.2427-0.8194-1.73740.68520.35920.0207-0.0116-0.05240.01460.05130.1991-37.302816.654221.7964
94.1625-0.2577-2.17830.91170.86666.2376-0.22620.30780.1086-0.92020.07410.4820.0094-0.81710.15220.12380.0395-0.0731-0.16640.0282-0.0733-17.16398.7548-48.1805
100.7616-0.58012.15341.73290.02258.23050.4569-0.73580.98920.5045-0.2897-0.3884-0.52911.3535-0.16710.4547-0.50650.24740.32680.00010.222113.555826.2592-49.6459
113.6667-0.6043-0.26271.9698-1.23410.8913-0.0437-0.07830.55-0.46180.0510.0416-0.87340.4586-0.00720.848-0.40220.2841-0.1268-0.0035-0.19892.068224.6878-57.4896
120.3578-0.14850.36482.152-0.05073.3079-0.01280.00070.0152-0.42750.1388-0.1642-0.71080.4176-0.1261-0.0245-0.14730.1233-0.0818-0.0223-0.0658-2.486312.4022-41.9505
134.05330.499-0.16442.88460.01783.61810.2483-0.2185-0.1768-0.4309-0.1153-0.4989-0.29871.0146-0.133-0.0874-0.14430.15180.0626-0.0727-0.13526.3755-1.3872-49.2442
145.2662-0.0782-1.27050.8234-1.29032.39090.03160.2098-0.0427-0.4047-0.0394-0.2576-0.59030.90040.00780.2311-0.22370.2105-0.0022-0.0682-0.17093.77233.2039-56.0916
157.93587.93074.1037.92574.10032.12130.44040.38630.6333-1.1855-0.8242-0.55830.37850.55320.38380.8067-0.38110.42880.42360.01460.143812.767824.2479-64.9806
163.51724.0723-1.141814.02793.2333.44660.45060.40930.2084-0.0614-0.0051-0.2765-0.11871.1702-0.44550.3176-0.21710.23930.1485-0.0212-0.21576.63284.2433-65.3525
1770.4486-86.567518.4859112.3436-14.854715.20291.3632-0.2346-1.88-0.6421-0.5717-1.6640.9782.1566-0.79150.1584-0.01410.30790.4356-0.16890.319614.0712-8.0779-31.4778
182.26570.47110.49951.33631.3334.07980.020.2238-0.3961-0.49180.403-0.54840.51890.9547-0.4230.02730.116-0.0132-0.1015-0.02330.0212-3.3556-21.6084-43.2812
1920.5654.4528-4.24783.7653-2.16121.4276-0.1772-0.64560.20380.3940.32080.4290.7259-0.7876-0.14360.5617-0.48180.10340.1165-0.0122-0.0049-32.1135-35.8875-34.8964
202.8852-0.59361.68625.6252-0.55340.99320.1565-0.3293-0.36210.2291-0.13390.35251.3651-0.1328-0.02250.557-0.2849-0.1765-0.2308-0.007-0.1299-21.5553-37.904-43.0924
211.0235-0.26730.24742.66681.05832.99110.09480.0309-0.07310.2446-0.04780.061.0517-0.3108-0.0470.0359-0.1687-0.0569-0.1440.0414-0.0818-16.6055-26.6702-32.8734
222.8873-0.53241.30872.0273-0.40953.87840.2193-0.22270.0188-0.2159-0.0631-0.02690.4648-0.1699-0.1562-0.2813-0.0705-0.0279-0.13770.0178-0.113-15.5054-13.3609-35.784
230.92710.430.00494.36330.26771.91230.0914-0.01530.0056-0.282-0.12350.58860.466-0.59270.0321-0.0342-0.1604-0.1089-0.06120.0068-0.1401-26.0403-20.6948-49.7833
246.9513-1.39698.31778.0995-8.070718.80220.311-0.84980.15650.4342-0.2540.2471-0.4263-1.0404-0.0570.49080.0603-0.06460.5609-0.07170.7279-39.0269-11.8467-70.1708
251.0361-0.54830.51242.3533-0.45023.236-0.0541-0.0165-0.06640.32970.0150.06120.4538-0.2090.0392-0.0699-0.08640.0394-0.2008-0.0042-0.1016-10.6665-17.5181-3.116
262.7336-1.75670.21635.7234-0.51242.1122-0.0537-0.109-0.47390.78850.08130.11270.9477-0.1005-0.02760.2232-0.0018-0.0618-0.2530.0334-0.2652-6.4647-30.15195.9122
2720.080718.92811.345918.02890.09417.46130.2349-0.54850.06451.6252-0.4814-0.241.4298-1.30320.24650.46990.02680.03780.0340.09820.0011-13.7029-27.854110.3449
281.57420.4322-1.01791.5372-0.2823.9253-0.183-0.0347-0.11040.01120.1348-0.10460.9330.29710.0482-0.16990.0342-0.0137-0.1697-0.0109-0.0477-6.2717-19.4021-13.1635
291.1605-0.1565-1.01922.8026-0.35053.29810.0610.12270.0630.25360.0971-0.06420.33840.2398-0.1581-0.3536-0.0146-0.0373-0.134-0.0275-0.083-5.5643-9.0369-11.5562
301.5283-4.65581.723716.28670.614818.30450.21530.14270.62010.11631.5657-1.47240.73092.8495-1.781-0.2217-0.049-0.17240.5636-0.29310.242616.953-6.0714-3.6518
311.52990.143-0.37323.5953-1.10661.3675-0.019-0.18570.0610.3881-0.0729-0.56960.49750.44320.0919-0.08920.0958-0.127-0.0753-0.079-0.16552.3979-13.06284.4201
329.4671-2.662-2.47218.88377.97149.64520.3262-0.53980.43330.9381-0.501-1.18340.03261.39140.17490.2158-0.0525-0.2323-0.04440.0397-0.14824.5556-9.734713.5099
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA4 - 265 - 27
2X-RAY DIFFRACTION2AA27 - 5528 - 56
3X-RAY DIFFRACTION3AA56 - 8857 - 89
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