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- PDB-5bpi: Structure of TrmBL2, an archaeal chromatin protein, shows a novel... -

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Basic information

Entry
Database: PDB / ID: 5bpi
TitleStructure of TrmBL2, an archaeal chromatin protein, shows a novel mode of DNA binding.
Components
  • DNA (5'-D(P*TP*AP*TP*AP*TP*CP*AP*CP*TP*AP*TP*CP*GP*AP*TP*GP*AP*TP*AP*TP*A)-3')
  • DNA (5'-D(P*TP*AP*TP*AP*TP*CP*AP*TP*CP*GP*AP*TP*AP*GP*TP*GP*AP*TP*AP*TP*A)-3')
  • TrmBL2
KeywordsDNA BINDING PROTEIN / Chromatin binding protein / Archaea
Function / homology
Function and homology information


: / : / Transcription regulator TrmB, C-terminal / Archaeal transcriptional regulator TrmB / Transcription regulator TrmB, N-terminal / Sugar-specific transcriptional regulator TrmB / Endonuclease Chain A / Endonuclease; Chain A / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A ...: / : / Transcription regulator TrmB, C-terminal / Archaeal transcriptional regulator TrmB / Transcription regulator TrmB, N-terminal / Sugar-specific transcriptional regulator TrmB / Endonuclease Chain A / Endonuclease; Chain A / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / Putative HTH-type transcriptional regulator TrmBL2
Similarity search - Component
Biological speciesPyrococcus furiosus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.198 Å
AuthorsAhmad, M.U. / Diederichs, K. / Welte, W.
CitationJournal: J.Mol.Biol. / Year: 2015
Title: Structural Insights into Nonspecific Binding of DNA by TrmBL2, an Archaeal Chromatin Protein.
Authors: Ahmad, M.U. / Waege, I. / Hausner, W. / Thomm, M. / Boos, W. / Diederichs, K. / Welte, W.
History
DepositionMay 28, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Sep 2, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 7, 2015Group: Database references
Revision 1.2Jan 10, 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: TrmBL2
B: TrmBL2
C: TrmBL2
D: TrmBL2
E: DNA (5'-D(P*TP*AP*TP*AP*TP*CP*AP*TP*CP*GP*AP*TP*AP*GP*TP*GP*AP*TP*AP*TP*A)-3')
F: DNA (5'-D(P*TP*AP*TP*AP*TP*CP*AP*CP*TP*AP*TP*CP*GP*AP*TP*GP*AP*TP*AP*TP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)135,0547
Polymers134,9626
Non-polymers921
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area25260 Å2
ΔGint-161 kcal/mol
Surface area52300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.764, 154.379, 176.123
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A and ( resseq 2:264)
21chain B and ( resseq 2:264 )
12chain C and ( resseq 2:115 or resseq 124:264 )
22chain D and ( resseq 2:115 or resseq 124:264 )

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain A and ( resseq 2:264)A2 - 264
211chain B and ( resseq 2:264 )B0
112chain C and ( resseq 2:115 or resseq 124:264 )C2 - 115
122chain C and ( resseq 2:115 or resseq 124:264 )C124 - 264
212chain D and ( resseq 2:115 or resseq 124:264 )D2 - 115
222chain D and ( resseq 2:115 or resseq 124:264 )D124 - 264

NCS ensembles :
ID
1
2

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Components

#1: Protein
TrmBL2


Mass: 30520.393 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus (archaea) / Gene: trmBL2, PF0496 / Plasmid: pET24d / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8U3H1
#2: DNA chain DNA (5'-D(P*TP*AP*TP*AP*TP*CP*AP*TP*CP*GP*AP*TP*AP*GP*TP*GP*AP*TP*AP*TP*A)-3')


Mass: 6460.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: TGM Sequence / Source: (synth.) Pyrococcus furiosus (archaea)
#3: DNA chain DNA (5'-D(P*TP*AP*TP*AP*TP*CP*AP*CP*TP*AP*TP*CP*GP*AP*TP*GP*AP*TP*AP*TP*A)-3')


Mass: 6420.197 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: TGM sequence / Source: (synth.) Pyrococcus furiosus (archaea)
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3

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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: 2.96 Å3/Da / Density % sol: 58.44 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.1M Imidazole HCl, pH 8.0, 30% MPD and 10% PEG4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.06269 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 4, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.06269 Å / Relative weight: 1
ReflectionResolution: 3.198→50 Å / Num. obs: 27256 / % possible obs: 100 % / Redundancy: 13.1 % / Rmerge(I) obs: 0.3819 / Net I/σ(I): 7.8
Reflection shellResolution: 3.198→3.312 Å / Mean I/σ(I) obs: 0.99 / Rsym value: 2.842 / % possible all: 98

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Processing

Software
NameVersionClassification
PHENIXrefinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
XDSdata scaling
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5BPD
Resolution: 3.198→49.394 Å / SU ML: 0.56 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 33.25 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2988 2496 4.9 %
Rwork0.2546 48478 -
obs0.2569 27264 99.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 194.01 Å2 / Biso mean: 87.2403 Å2 / Biso min: 36.99 Å2
Refinement stepCycle: final / Resolution: 3.198→49.394 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8495 861 14 0 9370
Biso mean--106.68 --
Num. residues----1081
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0059661
X-RAY DIFFRACTIONf_angle_d0.51813150
X-RAY DIFFRACTIONf_chiral_restr0.0261485
X-RAY DIFFRACTIONf_plane_restr0.0021518
X-RAY DIFFRACTIONf_dihedral_angle_d14.8143750
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2460X-RAY DIFFRACTION12.281TORSIONAL
12B2460X-RAY DIFFRACTION12.281TORSIONAL
21C2351X-RAY DIFFRACTION12.281TORSIONAL
22D2351X-RAY DIFFRACTION12.281TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 18

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.1981-3.25960.43581290.38822627275695
3.2596-3.32610.3811380.389526312769100
3.3261-3.39850.43261550.372126862841100
3.3985-3.47750.43631450.348227032848100
3.4775-3.56440.34981410.328826902831100
3.5644-3.66080.3381270.329427822909100
3.6608-3.76850.35721310.319926482779100
3.7685-3.890.34971220.290327282850100
3.89-4.0290.29291500.287227012851100
4.029-4.19030.32091630.25827052868100
4.1903-4.38090.28061230.247426612784100
4.3809-4.61170.30371370.224927272864100
4.6117-4.90040.26951360.217327242860100
4.9004-5.27830.26441420.216526722814100
5.2783-5.80880.26621420.242727032845100
5.8088-6.64760.28411500.252426872837100
6.6476-8.36860.25921570.205327082865100
8.3686-49.40030.2021080.17352695280399
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)
14.1408-1.33571.66772.724-0.40365.8577-0.15040.32940.3141-0.10110.06970.0532-0.2178-0.08680.05720.6811-0.0429-0.07670.7214-0.07920.6704-17.8024-3.017412.0389
22.40470.71122.27235.72234.59494.6579-0.06690.4330.23920.3813-0.04470.8842.02510.24520.21941.0015-0.0313-0.05461.05660.03920.8428-15.056-23.5337-13.0901
37.2790.31-5.79724.3976-0.3524.61461.156-0.20760.1194-2.1805-1.3224-0.43490.62912.38460.34111.36520.4504-0.0542.5713-0.44541.1484-16.904-25.1977-38.7104
48.077-2.1686-1.46942.81191.19356.1650.2888-1.82010.07290.0248-0.0293-1.3428-1.04581.6135-0.62160.9333-0.0682-0.14791.84860.06641.3271-18.5856-16.1016-48.8882
56.4569-1.0027-1.34516.888-1.31066.77520.76310.14730.33151.08540.2291-0.696-0.72390.0532-0.74260.83-0.0352-0.01580.60630.20871.1205-20.2181-11.5084-61.3068
62.8609-2.55243.78773.2153-3.30249.4985-0.2649-1.65560.7994-0.9680.2306-2.0523-0.7468-1.66880.08971.022-0.05060.12711.382-0.11181.1118-16.2015-21.0176-65.9342
75.2243-2.42720.36927.5965-2.79965.20880.77470.58110.1734-1.2222-1.3988-0.6584-0.02030.72740.76471.03820.01360.30841.1622-0.15741.2344-11.2711-21.6279-71.8918
82.7924-0.70084.57345.6506-1.35917.56630.95911.30761.6242-0.5162-0.495-0.7601-0.9150.7981-0.00841.3906-0.03960.19612.4497-0.42411.3723-7.0765-19.1024-80.0796
98.10670.14960.24535.1676-0.90634.9116-0.22210.9205-0.9704-0.5920.07080.22940.39950.12520.33420.82880.02010.0220.8996-0.03950.8934-21.6618-24.3449-68.6279
102.3242.31090.99573.8423-1.71464.2785-0.16240.08360.36430.02870.1869-0.02220.05780.16690.05990.68760.13220.10250.80350.07820.6609-40.8646-4.1299-44.1342
115.2503-2.83025.2371.432-2.62124.99251.10670.4982-0.3272-0.3695-0.30460.14651.86651.0659-0.87910.9603-0.0389-0.0710.83370.06450.7766-43.2083-23.7089-17.9653
126.40347.4892-0.38119.25180.40951.48130.2961-0.82611.48621.1314-3.00480.61841.3822-0.25831.98481.8083-0.5424-0.27281.62420.20951.1203-41.8427-24.10817.5488
134.73621.19710.91543.2881-0.84550.566-1.16960.40811.81190.7029-0.05541.76681.0343-1.8817-0.23271.7125-0.18910.35662.40920.01311.021-41.5251-15.138415.7602
142.90432.49950.06375.6151-2.6812.87920.28140.81671.3814-0.0390.17381.0666-0.2595-0.8513-0.24540.72910.0880.1150.9603-0.0940.7691-37.705-10.99827.9016
159.07751.31471.48073.07751.53247.212-0.33020.06451.02741.1464-0.30971.563-0.5971-0.0017-0.14320.79840.1075-0.13091.12960.23631.1028-42.3823-19.59534.0822
164.91451.193-3.20768.8251-0.77252.38330.15240.07151.24381.8246-0.34792.31170.40520.24-0.02520.99130.14490.20951.0851-0.02091.0247-47.0375-20.252639.9483
174.4791-0.186-0.5499.35636.06993.9778-1.2239-0.1923-0.96650.9535-1.14860.73140.3636-0.24512.64151.1650.27970.09461.4660.25190.9303-51.4768-17.562448.1315
184.2106-0.54950.81094.05740.8122.24180.1042-0.6219-0.37640.72330.08690.59540.05060.0589-0.18560.91130.10780.01950.92150.07390.6083-36.7611-22.915136.8732
197.5608-2.36654.42755.8898-1.21628.4394-0.2250.12350.46980.01150.0135-0.5038-0.07080.63120.09850.7633-0.0130.0380.91710.05210.633-20.3528-11.719-30.5562
207.0907-3.4470.75989.29056.98337.30670.69482.26630.7105-2.1592-0.4119-1.4726-2.41221.9954-0.03911.2652-0.21640.18512.41610.28731.3663-12.4949-6.5063-41.8106
212.5741-0.75352.07170.45522.47247.6082-0.12250.53280.3057-0.390.1988-0.3631-0.4111.75460.25240.8439-0.0935-0.01511.1127-0.09310.7981-5.6458-12.2859-7.816
225.2801-0.4168-3.02385.0387-3.58244.6273-0.00180.24070.40470.64570.5363-1.4948-0.99611.1294-0.67120.7362-0.1272-0.23290.7882-0.13960.7474-18.721-12.469121.6782
232.20810.2326-1.5564.4343-1.15611.30130.0525-0.2563-0.98880.8780.7219-1.12891.0340.8272-0.62730.59650.2812-0.22840.7259-0.14560.8939-13.456-19.284218.6195
248.65621.7753-0.89869.05821.62045.3613-0.42780.2949-0.4581-0.32550.2674-1.0753-0.10550.67820.24570.94880.2191-0.08610.8541-0.070.88-8.7211-32.56520.1521
254.44613.19840.96183.1873-1.71648.0165-0.40292.2233-1.1727-0.72931.5281-0.8191-0.0195-0.6774-0.90080.98180.255-0.17481.1389-0.12680.8592-21.8013-32.212321.4418
263.5321-1.4063-3.82427.6435-1.93855.81650.2316-2.17750.3906-0.64160.0826-0.38651.10760.2841-0.4820.69120.0574-0.1141.13010.03670.4206-21.4445-23.061424.4178
275.0382-0.39570.45314.9673-3.48374.7801-0.3528-0.0631-0.8011-0.71340.3012-0.21250.8291-0.39560.04490.8325-0.0194-0.0170.7347-0.12630.6627-23.4324-28.163722.9482
283.92712.96651.6764.59112.02966.8744-0.303-0.17120.25750.38610.1172-0.4603-0.0214-0.6780.15420.69540.2345-0.18640.8876-0.02420.6327-36.3708-13.9623-2.4383
294.3091.6483.47554.1031-0.87359.6539-0.2988-1.35452.0238-0.876-0.4432-1.35420.85090.12160.23581.09730.2060.05950.5991-0.02241.0285-35.7834-3.44540.9837
301.1181.0347-0.23634.78261.350.94370.42270.14640.7630.895-1.06061.4409-0.3604-1.65870.48620.8297-0.1038-0.04971.36950.05550.6929-46.5396-8.8934-3.2665
317.111.58321.86065.28064.51319.0342-0.3508-1.4887-0.52991.7862-2.98352.28410.4201-2.04842.16792.31040.146-0.0231.9474-0.25771.257-49.6904-5.860110.4344
321.1733-0.2550.9003-0.0696-0.14396.8227-0.0789-0.19230.27660.14760.0756-0.0296-0.1527-1.116-0.05070.8307-0.01530.00670.97620.0680.7998-52.3741-12.4418-21.6451
335.3348-1.7566-0.49856.25464.67963.606-0.6136-0.0854-0.03040.11470.38340.02450.3599-0.1045-0.14420.7779-0.1060.17680.80010.09320.6417-38.4195-15.6105-51.9531
347.83462.1376-0.66918.60243.73853.5258-0.0288-0.7979-0.74430.6112-0.41660.54580.8287-0.77310.41761.0051-0.15320.10940.97740.06360.8224-49.3079-32.3685-51.8403
356.7516-0.87290.65322.06161.19112.28440.89940.2054-2.0489-0.0527-0.12830.31861.7047-0.1264-0.74981.0778-0.1643-0.20581.01790.16371.2204-37.9433-32.0869-55.0652
368.33273.8610.85468.25562.45274.76680.2399-0.0392-0.9070.28350.3045-0.71950.9308-0.4652-0.50180.7570.1248-0.03810.76880.15610.675-34.4173-28.0865-54.5674
376.62640.89821.011.95372.05273.48440.0816-1.7972-0.48731.80730.067-2.54760.6813-0.16531.89530.8010.07020.10221.31790.04451.0804-23.02033.9699-42.7677
384.4094-3.16843.9683.4176-0.8857.1911-0.695-1.60490.8761-1.10671.19190.9425-3.308-0.2046-0.44822.23270.0102-0.0861.31840.09581.2671-32.67985.5265-22.1873
396.096-3.06162.82629.5282-0.93198.2407-0.4168-1.55060.24110.83321.27990.7845-2.4391-1.9884-0.76021.5427-0.0227-0.18621.38460.04830.9468-27.0548-0.4033-6.039
404.1244.4042-0.20278.5233-6.68491.9833-0.79570.6901-1.2961-1.5755-0.8962-1.78550.46941.51750.98891.31640.2205-0.47170.38970.00541.2363-34.817911.11637.7989
411.9874-4.25913.93366.131-0.16121.7214-0.55393.3893-1.7635-2.0421.21171.9014-1.33074.88150.80281.2914-0.3790.13171.5496-0.07431.349-35.67135.110810.2929
426.14050.42972.31082.22411.44171.605-0.47431.36420.4671-0.19920.6203-1.2741-1.02020.1676-0.20071.4660.0327-0.01851.49670.01051.302-26.01836.0632-10.2983
437.7861.8328-2.82365.5305-3.42652.5026-0.0839-0.54190.2987-0.96561.0126-0.2685-2.07970.0817-1.18611.54210.1567-0.11091.3004-0.12221.065-31.74490.5332-27.7734
443.283.5840.8388.798-0.13372.00830.7526-0.74340.33752.892-0.91640.0649-0.6257-1.3366-3.13780.6992-0.22080.0543-0.0440.33791.2101-21.967310.4304-41.3684
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 2:85)A2 - 85
2X-RAY DIFFRACTION2(chain A and resid 86:111)A86 - 111
3X-RAY DIFFRACTION3(chain A and resid 112:117)A112 - 117
4X-RAY DIFFRACTION4(chain A and resid 118:125)A118 - 125
5X-RAY DIFFRACTION5(chain A and resid 126:143)A126 - 143
6X-RAY DIFFRACTION6(chain A and resid 144:160)A144 - 160
7X-RAY DIFFRACTION7(chain A and resid 161:187)A161 - 187
8X-RAY DIFFRACTION8(chain A and resid 188:193)A188 - 193
9X-RAY DIFFRACTION9(chain A and resid 194:264)A194 - 264
10X-RAY DIFFRACTION10(chain B and resid 2:85)B2 - 85
11X-RAY DIFFRACTION11(chain B and resid 86:112)B86 - 112
12X-RAY DIFFRACTION12(chain B and resid 113:117)B113 - 117
13X-RAY DIFFRACTION13(chain B and resid 118:123)B118 - 123
14X-RAY DIFFRACTION14(chain B and resid 124:143)B124 - 143
15X-RAY DIFFRACTION15(chain B and resid 144:160)B144 - 160
16X-RAY DIFFRACTION16(chain B and resid 161:187)B161 - 187
17X-RAY DIFFRACTION17(chain B and resid 188:193)B188 - 193
18X-RAY DIFFRACTION18(chain B and resid 194:264)B194 - 264
19X-RAY DIFFRACTION19(chain C and resid 3:66)C3 - 66
20X-RAY DIFFRACTION20(chain C and resid 67:72)C67 - 72
21X-RAY DIFFRACTION21(chain C and resid 73:114)C73 - 114
22X-RAY DIFFRACTION22(chain C and resid 115:133)C115 - 133
23X-RAY DIFFRACTION23(chain C and resid 134:143)C134 - 143
24X-RAY DIFFRACTION24(chain C and resid 144:207)C144 - 207
25X-RAY DIFFRACTION25(chain C and resid 208:217)C208 - 217
26X-RAY DIFFRACTION26(chain C and resid 218:226)C218 - 226
27X-RAY DIFFRACTION27(chain C and resid 227:264)C227 - 264
28X-RAY DIFFRACTION28(chain D and resid 4:42)D4 - 42
29X-RAY DIFFRACTION29(chain D and resid 43:54)D43 - 54
30X-RAY DIFFRACTION30(chain D and resid 55:63)D55 - 63
31X-RAY DIFFRACTION31(chain D and resid 64:69)D64 - 69
32X-RAY DIFFRACTION32(chain D and resid 70:114)D70 - 114
33X-RAY DIFFRACTION33(chain D and resid 115:134)D115 - 134
34X-RAY DIFFRACTION34(chain D and resid 135:207)D135 - 207
35X-RAY DIFFRACTION35(chain D and resid 208:219)D208 - 219
36X-RAY DIFFRACTION36(chain D and resid 220:262)D220 - 262
37X-RAY DIFFRACTION37(chain E and resid 1:6)E1 - 6
38X-RAY DIFFRACTION38(chain E and resid 7:11)E7 - 11
39X-RAY DIFFRACTION39(chain E and resid 12:16)E12 - 16
40X-RAY DIFFRACTION40(chain E and resid 17:21)E17 - 21
41X-RAY DIFFRACTION41(chain F and resid 1:6)F1 - 6
42X-RAY DIFFRACTION42(chain F and resid 7:11)F7 - 11
43X-RAY DIFFRACTION43(chain F and resid 12:17)F12 - 17
44X-RAY DIFFRACTION44(chain F and resid 18:21)F18 - 21

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