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- PDB-4qbl: VRR_NUC domain protein -

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Basic information

Entry
Database: PDB / ID: 4qbl
TitleVRR_NUC domain protein
ComponentsVRR-NUC
KeywordsHYDROLASE / Nuclease
Function / homology
Function and homology information


nuclease activity / nucleic acid binding / metal ion binding
Similarity search - Function
VRR-NUC domain / VRR-NUC domain / VRR_NUC / Trna Endonuclease; Chain: A, domain 1 - #10 / Trna Endonuclease; Chain: A, domain 1 / tRNA endonuclease-like domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesPsychrobacter sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsSmerdon, S.J. / Pennell, S. / Li, J.
CitationJournal: Cell Rep / Year: 2014
Title: FAN1 activity on asymmetric repair intermediates is mediated by an atypical monomeric virus-type replication-repair nuclease domain.
Authors: Pennell, S. / Declais, A.C. / Li, J. / Haire, L.F. / Berg, W. / Saldanha, J.W. / Taylor, I.A. / Rouse, J. / Lilley, D.M. / Smerdon, S.J.
History
DepositionMay 8, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 10, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: VRR-NUC
B: VRR-NUC
D: VRR-NUC
E: VRR-NUC
F: VRR-NUC
C: VRR-NUC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,85212
Polymers97,7066
Non-polymers1466
Water8,881493
1
A: VRR-NUC
E: VRR-NUC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,6174
Polymers32,5692
Non-polymers492
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3830 Å2
ΔGint-26 kcal/mol
Surface area12300 Å2
MethodPISA
2
B: VRR-NUC
F: VRR-NUC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,6174
Polymers32,5692
Non-polymers492
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3690 Å2
ΔGint-26 kcal/mol
Surface area11930 Å2
MethodPISA
3
D: VRR-NUC
C: VRR-NUC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,6174
Polymers32,5692
Non-polymers492
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3770 Å2
ΔGint-29 kcal/mol
Surface area12020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)213.143, 51.180, 127.267
Angle α, β, γ (deg.)90.00, 125.49, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
VRR-NUC


Mass: 16284.306 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Psychrobacter sp. (bacteria) / Strain: PRwf-1 / Gene: PsycPRwf_1331 / Production host: Escherichia coli (E. coli) / References: UniProt: A5WF35
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 493 / 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: 2.89 Å3/Da / Density % sol: 57.47 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 12.5 % w/v PEG 1000, 12.5% w/v PEG 3350, 12.5% v/v MPD, 0.02 M sodium L-glutamate, 0.02 M DL-alanine, 0.02 M glycine, 0.02 M DL-lysine, 0.2 M DL-serine, 0.1 M MES/imidazole pH 6.5, VAPOR ...Details: 12.5 % w/v PEG 1000, 12.5% w/v PEG 3350, 12.5% v/v MPD, 0.02 M sodium L-glutamate, 0.02 M DL-alanine, 0.02 M glycine, 0.02 M DL-lysine, 0.2 M DL-serine, 0.1 M MES/imidazole pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9804 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 27, 2010
RadiationMonochromator: 0.98 / Protocol: SAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9804 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. all: 147916 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0

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Processing

Software
NameVersionClassification
PHENIXmodel building
PHENIX(phenix.refine: 1.8.4_1496)refinement
XDSdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2→29.673 Å / SU ML: 0.2 / σ(F): 1.34 / Phase error: 20.28 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2025 3823 5.02 %5%
Rwork0.1752 ---
obs0.1766 76117 99.97 %-
all-76140 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→29.673 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5815 0 6 493 6314
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085917
X-RAY DIFFRACTIONf_angle_d0.9747934
X-RAY DIFFRACTIONf_dihedral_angle_d12.0132250
X-RAY DIFFRACTIONf_chiral_restr0.043858
X-RAY DIFFRACTIONf_plane_restr0.0051009
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.02530.31051350.25462660X-RAY DIFFRACTION100
2.0253-2.0520.25721530.23222692X-RAY DIFFRACTION100
2.052-2.08010.25721320.212606X-RAY DIFFRACTION100
2.0801-2.10980.19451180.19382716X-RAY DIFFRACTION100
2.1098-2.14120.22131480.1982646X-RAY DIFFRACTION100
2.1412-2.17470.23121380.19232621X-RAY DIFFRACTION100
2.1747-2.21030.22571240.18592674X-RAY DIFFRACTION100
2.2103-2.24840.16511340.18662670X-RAY DIFFRACTION100
2.2484-2.28930.19731230.19052691X-RAY DIFFRACTION100
2.2893-2.33330.25971480.18622677X-RAY DIFFRACTION100
2.3333-2.38090.21161380.18522635X-RAY DIFFRACTION100
2.3809-2.43270.22761510.18352685X-RAY DIFFRACTION100
2.4327-2.48920.20551360.17592626X-RAY DIFFRACTION100
2.4892-2.55150.21011350.18382727X-RAY DIFFRACTION100
2.5515-2.62040.1761490.17992603X-RAY DIFFRACTION100
2.6204-2.69750.20311410.17312674X-RAY DIFFRACTION100
2.6975-2.78450.1991370.1772663X-RAY DIFFRACTION100
2.7845-2.88390.21341610.17872671X-RAY DIFFRACTION100
2.8839-2.99930.22031560.18242647X-RAY DIFFRACTION100
2.9993-3.13560.22041330.18932700X-RAY DIFFRACTION100
3.1356-3.30070.1981520.182662X-RAY DIFFRACTION100
3.3007-3.50720.21851510.17072687X-RAY DIFFRACTION100
3.5072-3.77750.21791360.16452698X-RAY DIFFRACTION100
3.7775-4.15680.17131470.14742704X-RAY DIFFRACTION100
4.1568-4.75610.15071600.13772705X-RAY DIFFRACTION100
4.7561-5.98420.18991490.17112725X-RAY DIFFRACTION100
5.9842-29.6760.23281380.19592829X-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)
18.38-7.2459-6.15247.40143.60247.0179-0.3372-0.99810.21780.04250.6763-0.6547-1.32611.8585-0.41380.4276-0.10480.09580.8823-0.18820.4033109.816725.7332-20.179
26.82446.38632.50159.50810.13553.5152-0.08371.17180.1879-0.02890.41140.3652-0.0489-0.2228-0.2470.39260.07790.05580.7079-0.05920.289895.214818.9711-20.9584
39.44322.4492.45028.108-2.44841.92510.11831.6248-0.927-1.068-0.24790.22071.1901-0.81990.02860.6151-0.0482-0.12790.6756-0.25050.491282.92079.2063-20.8798
42.0678-1.24961.94012.0769-0.06397.7094-0.07610.69330.1025-0.31520.30310.1144-0.55580.269-0.20620.24540.00040.03730.425-0.02070.321586.716918.903-14.9001
52.00029.7128-2.15872.0463-1.63587.41830.5721-0.46892.5357-0.3016-0.18450.6054-1.8037-0.2912-0.19420.746-0.00220.13920.4287-0.12610.925587.949836.2090.0002
64.7918-0.38820.03543.37710.54543.0085-0.04910.3901-0.0084-0.08020.1796-0.03290.20480.6214-0.08990.20610.0703-0.01550.3025-0.02690.217795.204316.9622-7.1725
72.08065.6106-2.10366.6601-0.61262.93380.2177-0.72250.00060.79730.0496-0.05810.19110.4727-0.15320.31220.1567-0.04520.41290.00130.40396.052217.3562.6656
85.04893.056-1.52223.1286-1.55243.8241-0.28630.5178-0.9442-0.34220.2145-0.59690.7090.61430.00530.3450.15180.01650.4026-0.11070.44496.66989.6155-11.8767
96.2275-2.2564-3.16885.1432-1.14244.90680.01370.0271-1.80910.16070.2286-0.1310.89170.295-0.0840.4770.08940.0440.2775-0.04210.64488.83760.3146-4.9167
102.4427-0.0273-0.22344.3067-0.78395.6099-0.4037-1.0933-0.88351.06010.2030.0461.01260.50930.49960.69250.08120.23190.80330.30730.6089117.14517.486225.4316
112.1972-8.0473-2.10589.70962.40517.1659-0.1639-0.5205-0.38720.39520.28260.3403-0.56790.0139-0.03330.418-0.03560.07720.81310.21990.5619103.638322.930230.4442
125.78423.6036-0.23298.50443.77596.82410.0918-1.4916-0.67111.23250.40910.0191-0.4595-0.3209-0.55590.40010.01430.07640.79940.14970.441299.637720.701937.1231
132.0048-1.97793.72736.68772.79312.0025-0.1656-0.5452-0.52190.2347-0.0369-0.29580.22770.69020.00940.9891-0.2260.09491.74510.0850.911699.68144.208352.9051
143.7081-0.8470.87535.9694-0.88982.3853-0.19870.0544-0.1931-0.1490.0802-0.50740.478-0.79240.1280.4663-0.0840.09930.82580.1220.356996.61910.314833.4989
158.2433-1.0892-4.5871.6136-0.59573.6021-0.56080.0519-0.7287-0.34520.290.14291.7744-1.5980.3440.7795-0.4110.09121.2006-0.02860.433592.04515.253232.835
165.2209-1.6236-0.66081.5792-0.52920.5390.32741.3384-0.5894-0.73930.1832-0.2535-0.0661-1.0527-0.1540.4491-0.18820.20041.52760.3204-0.002796.721217.802823.0317
177.24332.6419-6.62472.539-4.00467.7899-0.77040.4583-0.3853-0.30260.10730.07530.1752-0.26290.23420.35140.04250.22942.17840.50660.27682.312917.706425.0202
187.939-2.1698-5.6624.80883.44767.8272-0.7016-0.9804-0.62781.66610.3591-1.0740.18020.6550.17640.4030.0661-0.03810.27870.08960.373375.1602-25.074515.8979
196.9233-4.17234.44769.6721-6.1278.4555-0.0129-0.62220.37490.42410.41270.142-0.237-0.063-0.14770.29070.0370.00450.2037-0.04870.295371.5176-9.819411.8709
209.81871.25216.54022.0175-6.34829.3064-0.42560.08631.1377-0.21290.0756-0.4075-0.7267-0.09660.24780.3703-0.04420.03240.13260.01330.380265.96482.75364.8254
212.17650.3532-4.72612.0761.06832.03590.0896-0.6451-0.13180.7943-0.2778-0.2839-0.21640.76250.20020.318-0.0353-0.06360.31380.02370.317466.3657-2.131816.0652
229.7377-3.3562-1.1019.2752-5.69969.94-1.3291-0.66540.6820.7333-0.5708-0.0612-0.1377-0.71661.71361.04610.1217-0.10391.5313-0.22340.706262.3483-4.488837.8768
234.3993-1.06120.17924.77270.51554.1014-0.1753-0.2195-0.31940.4924-0.11310.06540.554-0.01990.29480.299-0.02610.03990.1811-0.02590.205658.6063-10.767817.6601
249.47631.91114.1622.0163-4.3447.8421-0.3879-1.9822-0.451.53520.06721.14460.7589-1.04960.08330.5939-0.17950.17470.5351-0.0460.457550.9604-12.848923.6894
256.7618-6.2743-1.36966.71772.37482.1481-0.1159-0.1968-0.50980.148-0.13220.46620.3447-0.31940.26470.2954-0.07910.00350.2357-0.02740.286554.4542-11.303115.4559
262.2162-9.2072.26349.8077-3.3614.78070.45720.5233-0.7825-0.8648-0.49170.8140.559-0.2369-0.03330.2563-0.0225-0.03860.2217-0.05850.274560.0631-10.66925.676
272.0415-6.8598-1.64118.7102-0.36135.7018-0.12060.0944-0.1938-0.3903-0.14480.58850.0885-0.58580.21480.24560.0302-0.11160.3554-0.10210.323547.9767-4.35535.6057
285.48442.2399-05.9476-2.01264.6380.3308-0.8215-0.00230.4073-0.5881-0.15890.59560.52760.24710.5311-0.10990.08640.798-0.12680.304457.32215.031139.2602
299.4136-3.48431.09879.80910.09169.57020.1961-0.8223-0.34540.3428-0.11830.80180.5925-0.3832-0.04670.4206-0.16750.07040.4395-0.06920.29249.9779-2.914530.5776
302.0049-7.60887.22992.0011.52596.3429-0.0981-0.9523-0.27720.83330.251-0.19110.32611.47710.02420.76690.11560.05050.989-0.0240.708676.5051-5.620820.7495
312.96611.57990.28983.73910.7613.92630.2697-0.5321-0.05210.388-0.1122-0.2683-0.16420.4757-0.15610.3107-0.083-0.00990.3704-0.11780.237759.876.303624.9556
322.05016.19092.06077.33177.89372.0581-0.02781.28260.326-0.86380.0382-0.3826-0.02291.71120.20290.5024-0.04130.10220.396-0.01130.37364.332810.054917.3561
332.9508-0.926-0.70513.69311.74653.98290.2702-0.32630.2593-0.0716-0.39620.0891-0.8264-0.14990.2610.3117-0.05250.04010.2345-0.07540.299856.874310.073822.3482
344.93580.42475.85911.41061.15358.2739-0.0883-0.71120.83870.1643-0.58610.6663-0.725-0.99120.66610.3429-0.00670.04660.4145-0.1820.432946.829310.316825.2404
355.58576.7432-3.92389.0808-0.31082.046-0.47340.29871.0665-0.7545-0.05140.4999-1.0967-1.16050.29520.37470.2012-0.1310.2899-0.06350.298167.029743.1971-0.8955
369.3622-6.32644.77745.7957-5.81338.1543-0.0025-0.24060.3438-0.0287-0.0494-0.4189-0.02350.34460.04440.2468-0.0446-0.04590.1944-0.02770.242282.039327.89057.9611
377.10011.3937-3.82029.61922.96656.55720.19250.03070.3935-0.4157-0.1003-0.4275-0.39980.2611-0.05420.17880.0059-0.0360.14310.01110.267686.315624.80651.8776
387.2457-5.97425.24162.0349-6.18332.01450.2430.14560.1816-0.73730.3976-0.8061-1.4555-0.559-0.52630.81750.09290.13050.98470.11540.527790.321927.7081-19.9243
394.2541-0.64880.78152.7736-0.54613.148-0.02260.15450.07780.0415-0.0362-0.0977-0.04460.02280.0430.1411-0.0171-0.0250.130.00460.216476.822.2905-4.2563
408.8012-6.99512.59542.1178-8.31679.81830.29121.4767-0.9514-1.95140.25580.07430.8027-0.0497-0.52510.325-0.0855-0.05070.41-0.10290.379674.36718.0006-12.71
412.7286-1.18230.20685.2962-0.18770.85740.01470.136-0.3565-0.2055-0.00510.20830.28710.0040.00460.2419-0.0145-0.0120.1633-0.00150.287474.087618.3162-3.8461
426.5083-6.15312.68939.9556-1.80444.4625-0.1016-0.6002-0.54510.50080.32290.8510.2544-0.4021-0.19470.2217-0.01220.0310.17170.05920.248773.2320.67157.1068
435.73483.5457-3.07098.85894.88378.4763-0.08120.2481-0.0975-0.36280.07220.6395-0.0623-0.61550.08770.35660.0063-0.00810.210.10980.348172.33958.22162.6022
449.86895.10361.33415.60282.71057.48970.24870.52260.41530.4991-0.0211-0.26090.18020.2538-0.01270.7382-0.02610.02470.61790.20810.421191.650510.360859.582
454.2145-1.24953.83236.06813.40322.1044-0.18550.6732-0.3266-0.102-0.01940.26180.9245-0.54780.27770.7072-0.32030.04260.94480.15850.401986.77564.877446.6907
466.5042-0.18954.99159.32982.81032.01120.4777-1.4175-0.17110.8786-0.0686-0.12480.80810.5248-0.29850.9360.10150.0161.82580.14110.8429110.18519.285839.9702
474.09511.47691.75096.28120.0635.05950.59110.4620.37280.8216-0.1942-0.281-0.3329-0.5584-0.27650.5164-0.03320.10480.80120.23440.347590.142719.268748.5445
484.73971.42026.20470.99812.31248.42910.33991.31531.3362-0.3805-0.2985-0.3167-1.78360.19730.02770.98910.14350.2830.90210.28450.570991.981827.75443.954
492.0843-1.91522.29893.5697-1.11143.410.16240.39570.08280.75550.29540.5499-0.8214-1.7326-0.34730.53620.04150.11840.87890.21530.395482.050216.750951.4807
508.31752.69963.41288.4918-3.08693.73820.1423-0.06210.87480.0605-0.22290.8459-0.0678-1.17770.01880.52190.04560.10581.48360.14310.590474.358419.252641.2886
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 5 through 9 )
2X-RAY DIFFRACTION2chain 'A' and (resid 10 through 23 )
3X-RAY DIFFRACTION3chain 'A' and (resid 24 through 30 )
4X-RAY DIFFRACTION4chain 'A' and (resid 31 through 39 )
5X-RAY DIFFRACTION5chain 'A' and (resid 58 through 65 )
6X-RAY DIFFRACTION6chain 'A' and (resid 66 through 99 )
7X-RAY DIFFRACTION7chain 'A' and (resid 100 through 112 )
8X-RAY DIFFRACTION8chain 'A' and (resid 113 through 135 )
9X-RAY DIFFRACTION9chain 'A' and (resid 136 through 144 )
10X-RAY DIFFRACTION10chain 'B' and (resid 5 through 9 )
11X-RAY DIFFRACTION11chain 'B' and (resid 10 through 30 )
12X-RAY DIFFRACTION12chain 'B' and (resid 31 through 39 )
13X-RAY DIFFRACTION13chain 'B' and (resid 59 through 64 )
14X-RAY DIFFRACTION14chain 'B' and (resid 65 through 99 )
15X-RAY DIFFRACTION15chain 'B' and (resid 100 through 121 )
16X-RAY DIFFRACTION16chain 'B' and (resid 122 through 135 )
17X-RAY DIFFRACTION17chain 'B' and (resid 136 through 144 )
18X-RAY DIFFRACTION18chain 'C' and (resid 5 through 9 )
19X-RAY DIFFRACTION19chain 'C' and (resid 10 through 23 )
20X-RAY DIFFRACTION20chain 'C' and (resid 24 through 30 )
21X-RAY DIFFRACTION21chain 'C' and (resid 31 through 39 )
22X-RAY DIFFRACTION22chain 'C' and (resid 59 through 65 )
23X-RAY DIFFRACTION23chain 'C' and (resid 66 through 99 )
24X-RAY DIFFRACTION24chain 'C' and (resid 100 through 111 )
25X-RAY DIFFRACTION25chain 'C' and (resid 112 through 121 )
26X-RAY DIFFRACTION26chain 'C' and (resid 122 through 135 )
27X-RAY DIFFRACTION27chain 'C' and (resid 136 through 145 )
28X-RAY DIFFRACTION28chain 'D' and (resid 6 through 23 )
29X-RAY DIFFRACTION29chain 'D' and (resid 24 through 39 )
30X-RAY DIFFRACTION30chain 'D' and (resid 59 through 64 )
31X-RAY DIFFRACTION31chain 'D' and (resid 65 through 99 )
32X-RAY DIFFRACTION32chain 'D' and (resid 100 through 111 )
33X-RAY DIFFRACTION33chain 'D' and (resid 112 through 121 )
34X-RAY DIFFRACTION34chain 'D' and (resid 122 through 145 )
35X-RAY DIFFRACTION35chain 'E' and (resid 4 through 9 )
36X-RAY DIFFRACTION36chain 'E' and (resid 10 through 30 )
37X-RAY DIFFRACTION37chain 'E' and (resid 31 through 39 )
38X-RAY DIFFRACTION38chain 'E' and (resid 59 through 65 )
39X-RAY DIFFRACTION39chain 'E' and (resid 66 through 99 )
40X-RAY DIFFRACTION40chain 'E' and (resid 100 through 111 )
41X-RAY DIFFRACTION41chain 'E' and (resid 112 through 121 )
42X-RAY DIFFRACTION42chain 'E' and (resid 122 through 135 )
43X-RAY DIFFRACTION43chain 'E' and (resid 136 through 148 )
44X-RAY DIFFRACTION44chain 'F' and (resid 5 through 22 )
45X-RAY DIFFRACTION45chain 'F' and (resid 23 through 39 )
46X-RAY DIFFRACTION46chain 'F' and (resid 59 through 65 )
47X-RAY DIFFRACTION47chain 'F' and (resid 66 through 99 )
48X-RAY DIFFRACTION48chain 'F' and (resid 100 through 112 )
49X-RAY DIFFRACTION49chain 'F' and (resid 113 through 135 )
50X-RAY DIFFRACTION50chain 'F' and (resid 136 through 145 )

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