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- PDB-6yre: Transaldolase variant T30C/D211C from T. acidophilum -

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Basic information

Entry
Database: PDB / ID: 6yre
TitleTransaldolase variant T30C/D211C from T. acidophilum
ComponentsProbable transaldolase
KeywordsTRANSFERASE / ALPHA-BETA BARREL / CONFORMATIONAL SELECTION / DOMAIN SWAPPING / TIM BARREL / SCHIFF BASE / Large-scale motions / Substrate binding / rate-determining product release
Function / homology
Function and homology information


transaldolase / transaldolase activity / aldehyde-lyase activity / pentose-phosphate shunt / carbohydrate metabolic process / cytoplasm
Similarity search - Function
Transaldolase type 3B, putative / Transaldolase type 3B/Fructose-6-phosphate aldolase / Transaldolase/Fructose-6-phosphate aldolase, archaeal/bacterial / Transaldolase active site. / Transaldolase, active site / Transaldolase signature 1. / Transaldolase/Fructose-6-phosphate aldolase / Transaldolase/Fructose-6-phosphate aldolase / Aldolase-type TIM barrel
Similarity search - Domain/homology
ACETATE ION / Probable transaldolase
Similarity search - Component
Biological speciesThermoplasma acidophilum DSM 1728 (acidophilic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.96 Å
AuthorsSautner, V. / Lietzow, T.H. / Tittmann, K.
CitationJournal: To Be Published
Title: Large-scale motions underlie physical but not chemical steps in transaldolase mechanism: Substrate binding by conformational selection and rate-determining product release
Authors: Sautner, V. / Lietzow, T.H. / Klaus, M. / Funk, L.M. / Tittmann, K.
History
DepositionApr 20, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 12, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Probable transaldolase
B: Probable transaldolase
C: Probable transaldolase
D: Probable transaldolase
E: Probable transaldolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,27116
Polymers122,4235
Non-polymers84811
Water8,287460
1
A: Probable transaldolase
B: Probable transaldolase
C: Probable transaldolase
D: Probable transaldolase
E: Probable transaldolase
hetero molecules

A: Probable transaldolase
B: Probable transaldolase
C: Probable transaldolase
D: Probable transaldolase
E: Probable transaldolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)246,54232
Polymers244,84610
Non-polymers1,69622
Water18010
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area44000 Å2
ΔGint-362 kcal/mol
Surface area75810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)147.790, 171.440, 100.450
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11C-302-

GOL

21C-303-

ACT

31C-303-

ACT

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Components

#1: Protein
Probable transaldolase


Mass: 24484.639 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermoplasma acidophilum DSM 1728 (acidophilic)
Gene: tal, Ta0616 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9HKI3, transaldolase
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 460 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.6 Å3/Da / Density % sol: 52.67 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 188 mM ammonium acetate (pH 4.4), 10% (w/v) PEG 6000, and 25% (v/v) glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.85 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 8, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.85 Å / Relative weight: 1
ReflectionResolution: 1.96→48.892 Å / Num. obs: 91427 / % possible obs: 100 % / Redundancy: 8.077 % / Biso Wilson estimate: 41.23 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.117 / Rrim(I) all: 0.125 / Χ2: 0.979 / Net I/σ(I): 9.73 / Num. measured all: 738420 / Scaling rejects: 47
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.96-2.068.5012.41.03125650.5462.551100
2.06-2.18.431.7691.4444020.6881.882100
2.1-2.28.251.2572.0695530.8051.339100
2.2-2.258.0490.9642.7741910.8841.029100
2.25-2.357.5620.7313.4373400.930.784100
2.35-2.458.2690.5574.7362200.9590.594100
2.45-2.58.4310.4555.7227090.9690.484100
2.5-57.9780.09415.23386680.9980.1100
5-107.6230.04930.3950090.9990.053100
10-207.5770.03838.036690.9990.04199.9
20-504.1880.04626.981010.9990.05298.1

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIX1.13_2998refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3S0C
Resolution: 1.96→48.892 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.93
RfactorNum. reflection% reflection
Rfree0.2143 4572 5 %
Rwork0.1826 --
obs0.1842 91391 99.94 %
Solvent computationShrinkage radii: 1.1 Å / VDW probe radii: 1.3 Å
Displacement parametersBiso max: 189.85 Å2 / Biso mean: 55.9609 Å2 / Biso min: 27.17 Å2
Refinement stepCycle: final / Resolution: 1.96→48.892 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8412 0 56 460 8928
Biso mean--54.41 51.69 -
Num. residues----1093
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
1.96-1.98230.41261520.38122887
1.9823-2.00560.41221500.35142832
2.0056-2.030.3571510.33612877
2.03-2.05570.34251520.31422877
2.0557-2.08280.31411490.29062843
2.0828-2.11130.31341510.29732861
2.1113-2.14150.30491520.26952896
2.1415-2.17340.28051510.24912866
2.1734-2.20740.27021510.24612857
2.2074-2.24360.25861500.2362864
2.2436-2.28230.30861530.22282891
2.2823-2.32380.27351500.2142860
2.3238-2.36850.28711520.20632882
2.3685-2.41680.25071520.19812888
2.4168-2.46940.24681510.19412868
2.4694-2.52680.23351520.19042894
2.5268-2.590.23091520.18492876
2.59-2.660.23911510.18742884
2.66-2.73830.23091520.1932879
2.7383-2.82670.24141520.19022889
2.8267-2.92770.20851520.17792887
2.9277-3.04490.21631540.18012912
3.0449-3.18340.20681510.18012882
3.1834-3.35120.25361540.17872927
3.3512-3.56110.21951530.17612898
3.5611-3.8360.18021530.16272920
3.836-4.22180.18191550.15172934
4.2218-4.83230.1711540.13622936
4.8323-6.08630.20221570.17422978
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)
13.8556-1.62650.43258.68442.61261.0992-0.27230.7413-0.9113-0.1066-0.0965-0.00221.5211-0.4340.17241.1055-0.09810.17870.4481-0.130.57384.4494-72.4205-1.0013
24.2037-0.40191.23193.48232.04684.78270.10570.2349-1.4525-0.1028-0.2146-0.40061.5669-0.04450.19631.00960.01110.13960.4734-0.10540.733412.0337-72.6644-4.4594
34.7402-0.60773.8575.42052.95.82570.12431.0889-1.386-0.9421-0.2761-0.48970.93330.082-0.35361.38-0.23160.32790.7729-0.35150.84739.4295-73.9587-13.1037
43.55121.5539-0.1234.7343-0.09293.184-0.28410.7929-0.6117-0.71170.0789-0.17090.685-0.29080.22740.6719-0.01740.11150.6231-0.18130.427912.0325-59.6713-14.6369
53.48790.98234.55069.67282.50556.3304-0.58781.3866-0.0436-1.42030.396-0.6195-0.46730.18370.14460.5828-0.04580.11980.5768-0.03220.370312.8661-48.9609-14.7239
63.07170.0716-0.63865.54010.08963.00740.02250.4712-0.1814-0.2792-0.07460.19090.1796-0.32520.05390.3657-0.0260.02120.3732-0.06610.24379.5579-51.5969-5.1695
75.111-2.89961.36742.7498-1.97062.1557-0.01220.297-0.32990.1366-0.06160.13180.15940.13110.0710.3887-0.04550.02840.3267-0.05160.30769.8979-51.11768.5724
80.9930.2303-0.55471.8006-2.18583.61280.02180.1734-0.2874-0.0205-0.0485-0.08650.17230.10990.06470.4263-0.05230.01590.3222-0.08730.33934.3739-56.11386.2405
91.61140.538-1.66080.3816-1.42825.3646-0.3889-0.1041-0.6471-0.56260.25070.00221.4980.07180.21750.6729-0.06680.11730.3971-0.09430.49843.3181-68.5458.1236
108.13783.667-2.10263.2197-2.88722.8895-0.02660.263-1.35930.50060.24220.58540.8363-1.0047-0.15711.0784-0.16790.11720.5423-0.04311.0204-12.0702-84.391922.7652
115.8466-0.3757-2.04345.3970.20966.61560.26560.3016-0.1606-0.5023-0.3268-0.59850.18630.60350.08290.49390.07060.06250.45660.08130.366617.7357-32.3079-10.6869
122.1247-1.6131.55734.17330.43143.3940.20320.3910.2839-0.6459-0.3488-1.0251-0.06380.53430.1620.6720.0620.22110.62570.06290.538120.9605-24.5909-10.7726
134.93780.6681-0.49310.9821-0.72133.2382-0.00860.69360.7645-1.3524-0.3189-0.7689-0.74020.4441-0.02750.92830.12810.26020.71910.1810.504417.7552-22.0029-18.834
142.4637-1.1263-0.25192.0324-0.8962.02920.5510.61390.4467-1.0414-0.3070.0539-1.1282-0.2898-0.16880.8680.10130.07610.53430.13470.45365.6829-14.2341-9.5576
152.9431-0.1265-2.10233.30451.42632.30610.25250.2543-0.0462-0.3361-0.09250.2073-0.318-0.3509-0.14670.48260.05350.01930.32660.0410.293.4998-20.16340.3516
162.2126-0.5728-0.14691.14330.28590.50070.11580.12650.149-0.1069-0.0514-0.0626-0.13750.0652-0.05640.4355-0.01170.00910.33630.01680.30077.4945-29.51647.3066
170.12510.39910.14297.5425-2.96584.64110.47510.5202-0.1795-0.9064-0.6308-0.9313-0.00440.44040.18720.40440.03190.04320.5045-0.02160.359517.4094-37.2797-2.1036
187.0983-1.5973-1.3357.01824.65573.14590.01570.2225-1.066-0.17970.1932-0.48150.04420.4072-0.06260.55060.02190.06680.5254-0.04650.654624.9325-62.1727-4.8988
195.40011.2002-0.05034.9877-0.15853.7495-0.15480.44460.7168-0.29330.1874-0.4873-0.54920.1759-0.0380.74550.12270.05880.39680.11990.4925-8.7667-4.9568.7673
205.1556-0.32211.06544.6203-0.57836.1826-0.4747-0.06510.97540.5820.10770.294-0.88690.73760.29710.77330.0456-0.04650.45540.09470.5831-12.95030.101414.0776
211.43870.76120.55843.04840.01320.23490.11880.2790.4914-0.09720.11820.1462-0.9687-0.5337-0.2520.84350.19550.0430.37040.12580.5266-21.3688-1.155912.163
221.34441.5229-1.61863.4534-1.89486.11420.544-0.17430.21990.5251-0.05821.4611-0.8383-0.4706-0.40890.77170.38140.04540.60440.13820.7217-32.756-5.352115.3114
231.19961.5144-2.65623.4946-2.7639.7899-0.00050.3642-0.0671-0.0440.06660.5274-0.5693-0.5813-0.13620.57430.17660.01950.48750.10550.4692-24.6071-9.963115.1773
242.5184-0.1628-0.13914.1089-1.29614.37610.07690.14130.23450.02460.13460.3559-0.3212-0.5705-0.19590.34710.12280.03660.40050.07030.3568-25.9329-17.06319.7685
252.44642.58961.1383.52612.21662.69310.04230.1960.04120.07230.1265-0.1788-0.18970.2325-0.10680.47510.04880.02470.36430.0390.341-11.3211-22.830124.3921
261.64641.1825-0.46761.963-0.14070.9439-0.00780.17380.20780.13510.08870.2026-0.15-0.1329-0.05930.46270.04650.01520.32770.04230.3122-10.0837-20.651717.1414
274.4271-1.1762-0.48584.79281.07040.28980.10660.37360.69050.10970.2269-0.3814-0.3966-0.0238-0.31740.55990.07650.06530.39610.0790.3537-2.5099-11.764812.46
285.43130.259-1.33933.77760.67615.91820.09880.72270.242-0.84430.3174-0.6833-1.160.508-0.40410.8246-0.15880.13910.50490.03970.641419.2647-10.8015-3.8705
296.25110.7255-1.41145.31390.10824.3929-0.14160.67620.9959-0.0714-0.29831.0306-0.7839-1.0630.37190.4810.1379-0.11460.667-0.00390.757-37.7743-26.794830.8939
304.24611.00551.70487.3336-1.40343.13810.0478-1.2050.56771.1169-0.52210.5086-0.2659-0.08210.21610.42430.03660.02750.7046-0.13480.6157-42.9649-33.147437.2218
312.3385-3.59911.36428.5937-0.5738.160.0166-2.10920.7460.75090.26241.3872-0.5825-1.2914-0.29660.33740.1718-0.0680.8398-0.05730.7058-49.9731-32.862231.987
322.2636-0.41450.76168.2023-3.07134.54350.1736-0.2050.205-0.0047-0.33450.33850.265-0.54880.07030.20210.0332-0.00840.8325-0.02040.4992-43.3457-41.924730.1387
333.2345-2.78241.67349.3707-0.65232.9792-0.1052-0.957-0.0973-0.25020.30411.40020.0347-0.9653-0.16190.3139-0.1166-0.04810.82180.01590.5776-48.9682-49.626827.743
344.6088-4.3932.7786.5612-3.51493.80340.07290.1814-0.0189-0.0459-0.2380.53260.1072-0.11940.13160.336-0.0642-0.06920.61480.03880.482-40.8797-44.744827.7303
354.6862-0.07520.87093.13550.12752.244-0.03030.4857-0.3997-0.29980.08310.39210.2786-0.3523-0.07830.3036-0.0852-0.03890.46890.00990.4176-38.0391-51.512626.6454
361.1009-0.3895-0.6960.9977-0.0712.0842-0.0641-0.079-0.04520.05820.01150.0526-0.0709-0.2933-0.01860.2912-0.0284-0.00510.38190.01160.3329-23.9837-45.77829.9222
371.32390.9658-0.57453.51921.02172.31620.11240.03290.1869-0.0035-0.16290.3195-0.3231-0.18930.09230.31840.049-0.02910.37770.02640.3438-25.8387-33.161329.6457
382.66150.2815-0.00922.645-3.42794.83450.21520.14040.7824-0.3196-0.22850.135-1.1117-0.2482-0.04870.86270.18720.04250.4403-0.02490.6071-20.4832-1.629128.5687
393.50052.15241.03012.97510.25122.2137-0.1732-0.4196-0.61470.0224-0.34320.16511.1384-0.94870.32770.8473-0.33230.21560.7243-0.23150.9074-28.0099-73.610624.9468
401.43120.96910.51551.9225-0.05320.53080.1537-0.0543-0.4451-0.07280.17770.42130.285-0.12660.42650.7415-1.05940.47971.2112-0.96911.5645-32.048-80.48818.4984
412.47141.24980.37514.5182-2.19151.8481-0.21920.2158-0.6079-1.025-0.1467-0.09230.8409-0.0149-0.20220.9199-0.43560.17580.5029-0.33551.0008-21.4544-77.470114.2391
421.68281.61791.31942.68150.75181.415-0.151-0.6609-0.5321-0.26510.82890.7201-0.58910.31330.9203-0.3180.11620.6936-0.36111.037-20.0192-79.37688.3558
431.8259-0.92072.54186.5765-0.34687.17220.53651.2724-1.3628-0.8245-0.4646-0.47620.12830.177-0.07040.8381-0.1570.1020.655-0.28670.7003-12.0118-75.84413.9034
442.1823-1.1462-1.57894.3794-1.0632.0379-0.25960.454-0.1773-0.2577-0.06440.34970.2111-0.51930.20490.4184-0.10050.03760.441-0.15030.4799-12.4691-69.119911.6092
450.9986-0.77550.18483.8755-2.89346.7292-0.1586-0.0635-0.20070.34220.07590.27280.1405-0.16830.1540.3936-0.01180.02950.34-0.04710.4692-7.3937-61.235521.6628
462.5383-0.6799-3.04611.48171.33075.3374-0.34370.3774-0.56310.1504-0.06630.10970.4663-0.72390.38250.3646-0.09250.00540.405-0.05240.417-19.4024-60.919524.9578
473.4754-3.4781-0.08553.56270.12418.435-0.1761-0.5291-0.08340.42720.11230.6534-0.7542-0.95030.01040.56840.00080.06870.67520.02590.5315-40.1952-46.503344.1427
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 18 )A1 - 18
2X-RAY DIFFRACTION2chain 'A' and (resid 19 through 41 )A19 - 41
3X-RAY DIFFRACTION3chain 'A' and (resid 42 through 52 )A42 - 52
4X-RAY DIFFRACTION4chain 'A' and (resid 53 through 90 )A53 - 90
5X-RAY DIFFRACTION5chain 'A' and (resid 91 through 102 )A91 - 102
6X-RAY DIFFRACTION6chain 'A' and (resid 103 through 132 )A103 - 132
7X-RAY DIFFRACTION7chain 'A' and (resid 133 through 156 )A133 - 156
8X-RAY DIFFRACTION8chain 'A' and (resid 157 through 180 )A157 - 180
9X-RAY DIFFRACTION9chain 'A' and (resid 181 through 198 )A181 - 198
10X-RAY DIFFRACTION10chain 'A' and (resid 199 through 218 )A199 - 218
11X-RAY DIFFRACTION11chain 'B' and (resid 1 through 18 )B1 - 18
12X-RAY DIFFRACTION12chain 'B' and (resid 19 through 41 )B19 - 41
13X-RAY DIFFRACTION13chain 'B' and (resid 42 through 52 )B42 - 52
14X-RAY DIFFRACTION14chain 'B' and (resid 53 through 103 )B53 - 103
15X-RAY DIFFRACTION15chain 'B' and (resid 104 through 132 )B104 - 132
16X-RAY DIFFRACTION16chain 'B' and (resid 133 through 180 )B133 - 180
17X-RAY DIFFRACTION17chain 'B' and (resid 181 through 198 )B181 - 198
18X-RAY DIFFRACTION18chain 'B' and (resid 199 through 217 )B199 - 217
19X-RAY DIFFRACTION19chain 'C' and (resid 1 through 18 )C1 - 18
20X-RAY DIFFRACTION20chain 'C' and (resid 19 through 41 )C19 - 41
21X-RAY DIFFRACTION21chain 'C' and (resid 42 through 65 )C42 - 65
22X-RAY DIFFRACTION22chain 'C' and (resid 66 through 79 )C66 - 79
23X-RAY DIFFRACTION23chain 'C' and (resid 80 through 90 )C80 - 90
24X-RAY DIFFRACTION24chain 'C' and (resid 91 through 132 )C91 - 132
25X-RAY DIFFRACTION25chain 'C' and (resid 133 through 156 )C133 - 156
26X-RAY DIFFRACTION26chain 'C' and (resid 157 through 180 )C157 - 180
27X-RAY DIFFRACTION27chain 'C' and (resid 181 through 198 )C181 - 198
28X-RAY DIFFRACTION28chain 'C' and (resid 199 through 223 )C199 - 223
29X-RAY DIFFRACTION29chain 'D' and (resid 1 through 19 )D1 - 19
30X-RAY DIFFRACTION30chain 'D' and (resid 20 through 41 )D20 - 41
31X-RAY DIFFRACTION31chain 'D' and (resid 42 through 52 )D42 - 52
32X-RAY DIFFRACTION32chain 'D' and (resid 53 through 65 )D53 - 65
33X-RAY DIFFRACTION33chain 'D' and (resid 66 through 79 )D66 - 79
34X-RAY DIFFRACTION34chain 'D' and (resid 80 through 90 )D80 - 90
35X-RAY DIFFRACTION35chain 'D' and (resid 91 through 114 )D91 - 114
36X-RAY DIFFRACTION36chain 'D' and (resid 115 through 156 )D115 - 156
37X-RAY DIFFRACTION37chain 'D' and (resid 157 through 198 )D157 - 198
38X-RAY DIFFRACTION38chain 'D' and (resid 199 through 218 )D199 - 218
39X-RAY DIFFRACTION39chain 'E' and (resid 1 through 41 )E1 - 41
40X-RAY DIFFRACTION40chain 'E' and (resid 42 through 52 )E42 - 52
41X-RAY DIFFRACTION41chain 'E' and (resid 53 through 65 )E53 - 65
42X-RAY DIFFRACTION42chain 'E' and (resid 66 through 90 )E66 - 90
43X-RAY DIFFRACTION43chain 'E' and (resid 91 through 102 )E91 - 102
44X-RAY DIFFRACTION44chain 'E' and (resid 103 through 132 )E103 - 132
45X-RAY DIFFRACTION45chain 'E' and (resid 133 through 156 )E133 - 156
46X-RAY DIFFRACTION46chain 'E' and (resid 157 through 198 )E157 - 198
47X-RAY DIFFRACTION47chain 'E' and (resid 199 through 217 )E199 - 217

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