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- PDB-5vl1: Crystal Structure of Lysyl-tRNA Synthetase from Mycobacterium ulc... -

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Basic information

Entry
Database: PDB / ID: 5vl1
TitleCrystal Structure of Lysyl-tRNA Synthetase from Mycobacterium ulcerans complexed with L-lysine
ComponentsLysine--tRNA ligase
KeywordsLIGASE / SSGCID / synthetase / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


lysine-tRNA ligase / lysine-tRNA ligase activity / lysyl-tRNA aminoacylation / nucleic acid binding / magnesium ion binding / ATP binding / cytoplasm
Similarity search - Function
Lysine-tRNA ligase, class II / Lysine-tRNA ligase, class II, N-terminal / Lysyl-tRNA synthetase, class II, C-terminal / Aminoacyl-tRNA synthetase, class II (D/K/N) / tRNA synthetases class II (D, K and N) / OB-fold nucleic acid binding domain, AA-tRNA synthetase-type / OB-fold nucleic acid binding domain / Bira Bifunctional Protein; Domain 2 / BirA Bifunctional Protein; domain 2 / Aminoacyl-tRNA synthetase, class II ...Lysine-tRNA ligase, class II / Lysine-tRNA ligase, class II, N-terminal / Lysyl-tRNA synthetase, class II, C-terminal / Aminoacyl-tRNA synthetase, class II (D/K/N) / tRNA synthetases class II (D, K and N) / OB-fold nucleic acid binding domain, AA-tRNA synthetase-type / OB-fold nucleic acid binding domain / Bira Bifunctional Protein; Domain 2 / BirA Bifunctional Protein; domain 2 / Aminoacyl-tRNA synthetase, class II / Aminoacyl-transfer RNA synthetases class-II family profile. / Class II Aminoacyl-tRNA synthetase/Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL) / Nucleic acid-binding proteins / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Nucleic acid-binding, OB-fold / Beta Barrel / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
LYSINE / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Lysine--tRNA ligase
Similarity search - Component
Biological speciesMycobacterium ulcerans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.7 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: to be published
Title: Crystal Structure of Lysyl-tRNA Synthetase from Mycobacterium ulcerans complexed with L-lysine
Authors: Dranow, D.M. / Lorimer, D.D. / Edwards, T.E.
History
DepositionApr 24, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 10, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 4, 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.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Lysine--tRNA ligase
B: Lysine--tRNA ligase
C: Lysine--tRNA ligase
D: Lysine--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)227,83415
Polymers226,3264
Non-polymers1,50811
Water5,855325
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A: Lysine--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,0915
Polymers56,5821
Non-polymers5104
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Lysine--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,9854
Polymers56,5821
Non-polymers4033
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Lysine--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,8793
Polymers56,5821
Non-polymers2972
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Lysine--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,8793
Polymers56,5821
Non-polymers2972
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
A: Lysine--tRNA ligase
B: Lysine--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,0769
Polymers113,1632
Non-polymers9137
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10070 Å2
ΔGint-15 kcal/mol
Surface area38060 Å2
MethodPISA
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C: Lysine--tRNA ligase
D: Lysine--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,7586
Polymers113,1632
Non-polymers5954
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9810 Å2
ΔGint-19 kcal/mol
Surface area38140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.040, 96.690, 105.560
Angle α, β, γ (deg.)90.380, 104.840, 117.150
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 9 through 15 or (resid 16...
21(chain B and (resid 9 or (resid 10 through 13...
31(chain C and (resid 9 through 10 or (resid 11...
41(chain D and (resid 9 or (resid 10 through 13...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11PROPROARGARG(chain A and (resid 9 through 15 or (resid 16...AA9 - 1517 - 23
12ARGARGARGARG(chain A and (resid 9 through 15 or (resid 16...AA1624
13PROPROARGARG(chain A and (resid 9 through 15 or (resid 16...AA9 - 49417 - 502
14PROPROARGARG(chain A and (resid 9 through 15 or (resid 16...AA9 - 49417 - 502
15PROPROARGARG(chain A and (resid 9 through 15 or (resid 16...AA9 - 49417 - 502
16PROPROARGARG(chain A and (resid 9 through 15 or (resid 16...AA9 - 49417 - 502
21PROPROPROPRO(chain B and (resid 9 or (resid 10 through 13...BB917
22GLUGLUARGARG(chain B and (resid 9 or (resid 10 through 13...BB10 - 1318 - 21
23ILEILEARGARG(chain B and (resid 9 or (resid 10 through 13...BB8 - 49416 - 502
24ILEILEARGARG(chain B and (resid 9 or (resid 10 through 13...BB8 - 49416 - 502
25ILEILEARGARG(chain B and (resid 9 or (resid 10 through 13...BB8 - 49416 - 502
26ILEILEARGARG(chain B and (resid 9 or (resid 10 through 13...BB8 - 49416 - 502
31PROPROGLUGLU(chain C and (resid 9 through 10 or (resid 11...CC9 - 1017 - 18
32GLNGLNARGARG(chain C and (resid 9 through 10 or (resid 11...CC11 - 1319 - 21
33ILEILEARGARG(chain C and (resid 9 through 10 or (resid 11...CC8 - 49416 - 502
34ILEILEARGARG(chain C and (resid 9 through 10 or (resid 11...CC8 - 49416 - 502
35ILEILEARGARG(chain C and (resid 9 through 10 or (resid 11...CC8 - 49416 - 502
36ILEILEARGARG(chain C and (resid 9 through 10 or (resid 11...CC8 - 49416 - 502
41PROPROPROPRO(chain D and (resid 9 or (resid 10 through 13...DD917
42GLUGLUARGARG(chain D and (resid 9 or (resid 10 through 13...DD10 - 1318 - 21
43ASNASNARGARG(chain D and (resid 9 or (resid 10 through 13...DD7 - 49415 - 502
44ASNASNARGARG(chain D and (resid 9 or (resid 10 through 13...DD7 - 49415 - 502
45ASNASNARGARG(chain D and (resid 9 or (resid 10 through 13...DD7 - 49415 - 502
46ASNASNARGARG(chain D and (resid 9 or (resid 10 through 13...DD7 - 49415 - 502

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Components

#1: Protein
Lysine--tRNA ligase / Lysyl-tRNA synthetase / LysRS


Mass: 56581.621 Da / Num. of mol.: 4 / Fragment: MyulA.00612.a.B1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium ulcerans (strain Agy99) (bacteria)
Strain: Agy99 / Gene: lysS, MUL_4181 / Plasmid: MyulA.00612.a.B1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0PV47, lysine-tRNA ligase
#2: Chemical
ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H14O4
#3: Chemical
ChemComp-LYS / LYSINE


Type: L-peptide linking / Mass: 147.195 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H15N2O2
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 325 / 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: 3.65 Å3/Da / Density % sol: 66.29 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop
Details: MyulA.00612.a.B1.PW37993 at 28 mg/ml was incubated with 3 mM MgCl2, AMPPNP, and L-Lysine, then mixed 1:1 with Morpheus(e9): 10% (w/v) PEG-20,000, 20% (v/v) PEG MME 550, 0.1 M bicine/ Trisma ...Details: MyulA.00612.a.B1.PW37993 at 28 mg/ml was incubated with 3 mM MgCl2, AMPPNP, and L-Lysine, then mixed 1:1 with Morpheus(e9): 10% (w/v) PEG-20,000, 20% (v/v) PEG MME 550, 0.1 M bicine/ Trisma base, pH = 8.5, and 0.03 M each diethyleneglycol, triethyleneglycol, tetraethyleneglycol, pentaethylene glycol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 12, 2017 / Details: Beryllium Lenses
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.7→46.455 Å / Num. obs: 86858 / % possible obs: 98.8 % / Observed criterion σ(I): -3 / Redundancy: 3.945 % / Biso Wilson estimate: 52.3 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.082 / Rrim(I) all: 0.096 / Χ2: 1.021 / Net I/σ(I): 12.14 / Num. measured all: 342637 / Scaling rejects: 4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.7-2.773.9860.5992.3663960.8050.69298.2
2.77-2.853.9860.4732.9362140.880.54798.4
2.85-2.933.9830.3763.6861070.9160.43598.2
2.93-3.023.9820.3064.4358770.9420.35498.7
3.02-3.123.9790.245.657230.960.27798.4
3.12-3.233.9710.1876.9255540.9740.21798.7
3.23-3.353.9660.1488.5253120.9830.17298.7
3.35-3.493.960.11510.5651670.9890.13498.7
3.49-3.643.9470.09612.6349340.9910.11199
3.64-3.823.9460.07815.147380.9930.09198.8
3.82-4.023.9270.0716.6644820.9950.08199.1
4.02-4.273.9140.05819.3942640.9960.06799.2
4.27-4.563.9140.05221.3940190.9960.06198.8
4.56-4.933.9020.0521.9937090.9960.05899.5
4.93-5.43.9040.05121.7834290.9960.0699.3
5.4-6.043.8940.05521.6931190.9950.06399.3
6.04-6.973.8760.05122.0627360.9970.05999.3
6.97-8.543.8820.04226.1623190.9970.04899.5
8.54-12.073.8560.03629.0918010.9970.04299.4
12.07-46.4553.6940.03629.349580.9980.04297.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
MoRDaphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3A74

3a74


Resolution: 2.7→46.455 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 24.55
RfactorNum. reflection% reflection
Rfree0.2043 2193 2.53 %
Rwork0.177 --
obs0.1777 86835 98.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 218.31 Å2 / Biso mean: 63.6092 Å2 / Biso min: 5.35 Å2
Refinement stepCycle: final / Resolution: 2.7→46.455 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14866 0 101 326 15293
Biso mean--78.95 50.74 -
Num. residues----1941
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00215380
X-RAY DIFFRACTIONf_angle_d0.520882
X-RAY DIFFRACTIONf_chiral_restr0.042379
X-RAY DIFFRACTIONf_plane_restr0.0032756
X-RAY DIFFRACTIONf_dihedral_angle_d16.4979364
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A8542X-RAY DIFFRACTION8.803TORSIONAL
12B8542X-RAY DIFFRACTION8.803TORSIONAL
13C8542X-RAY DIFFRACTION8.803TORSIONAL
14D8542X-RAY DIFFRACTION8.803TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 16

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.6999-2.75860.30691190.28465243536298
2.7586-2.82270.3241240.25415247537198
2.8227-2.89330.26591170.24495295541298
2.8933-2.97150.2611270.2365304543198
2.9715-3.05890.30031260.24735284541099
3.0589-3.15770.27221340.24285292542699
3.1577-3.27050.25571300.22355298542899
3.2705-3.40140.25141330.21265313544699
3.4014-3.55610.25261550.19755249540499
3.5561-3.74350.21461590.19015265542499
3.7435-3.9780.20751360.1635302543899
3.978-4.28490.17951450.14025297544299
4.2849-4.71580.15441230.12135323544699
4.7158-5.39730.16491530.13815307546099
5.3973-6.79660.19331380.16575349548799
6.7966-46.46210.14751740.14815274544899
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.16-0.2450.5711.2637-1.29882.6743-0.1783-0.2737-0.06920.32860.0027-0.2962-0.28560.23190.15360.44420.0467-0.00390.37660.0050.42297.5002-11.00315.7467
25.7287-2.1687-2.86891.01990.84827.7693-0.22610.0071-0.156-0.04440.44060.19790.5417-0.598-0.16080.3547-0.0099-0.01220.3191-0.04460.4247-10.5642-5.8726-7.46
31.1044-0.3063-0.02681.12320.21951.4967-0.01060.0689-0.0631-0.03260.05650.18370.1214-0.3031-0.06040.3401-0.02070.03760.37430.06090.374-13.932-12.1899-15.9063
43.92130.8064-0.76112.5478-1.08234.05450.10350.1862-0.0092-0.2767-0.1002-0.1468-0.1355-0.074-0.00430.49810.0115-0.00740.30590.08250.3639-2.359615.1972-35.6676
51.4855-0.10751.59881.0426-1.6643.9829-0.0436-0.16230.28050.31520.01380.0565-0.8263-0.18150.11440.6852-0.0040.00620.2847-0.03670.4519-1.890816.4806-10.8263
61.689-0.30480.30671.9327-1.39622.9124-0.1698-0.2230.18550.4130.22450.0374-0.2034-0.2018-0.04580.50980.07850.07390.299-0.00920.3181-4.5208-1.088311.2542
77.6966-0.91810.30060.2725-0.54522.8848-0.4299-0.24230.63650.41260.3315-0.3164-0.73120.04080.09350.80380.0204-0.0910.3338-0.07360.5169-0.9788.43411.8676
80.95880.29450.1922.00080.51891.4193-0.331-0.46470.6810.6868-0.1774-0.1998-1.21240.63740.01851.231-0.1328-0.23950.5887-0.19150.77748.354220.786319.7361
90.6575-0.1880.0211.20840.03052.3458-0.22-0.20630.19510.55920.1051-0.162-0.92230.00270.11170.85950.0401-0.08740.4332-0.03680.4721.19949.433319.4257
103.49941.1591-0.89665.1435-0.1223.5075-0.22020.4325-0.7297-0.6946-0.3581-0.16990.3927-0.34360.53410.78960.0361-0.00170.5277-0.13660.6042-37.69599.375812.2221
110.8186-0.4179-0.38331.50180.83252.06480.10060.1168-0.092-0.2592-0.1230.0432-0.0378-0.15290.03860.3330.07060.01350.3430.06940.3485-33.433531.10435.3807
120.74550.52591.91916.7382-1.58356.26850.16010.0336-0.0963-0.39250.0253-0.347-0.01780.6088-0.07090.24740.01180.00330.3057-0.00890.3316-28.414339.24747.6548
130.9286-0.09160.17281.8115-0.26831.95630.067-0.05990.13170.0997-0.0259-0.1708-0.31270.263-0.06150.3309-0.0580.04610.32850.0280.3546-21.04538.449255.765
143.19390.8945-0.93018.98890.38643.25470.2286-0.31220.53220.621-0.06610.0048-0.83420.1738-0.21330.60120.02020.13540.481-0.09440.3411-40.063252.746272.6247
153-0.3154-0.71332.89080.06275.1463-0.18570.1777-0.24470.17880.0280.37690.0487-0.6440.1870.32820.07840.1860.53610.01770.4867-55.361338.718574.6253
162.0238-0.1612-0.92811.72660.29824.22930.1566-0.0070.13140.1476-0.10410.2697-0.619-0.3059-0.06590.46130.1620.12790.43580.03080.4737-50.826347.361271.8604
170.1958-0.7092-0.29434.2113.57325.1791-0.167-0.2544-0.23140.22510.0990.37880.1916-0.4970.15640.22920.02260.02770.60740.03830.4881-52.222532.625744.8371
181.0511-0.2322-0.14092.38910.43962.51630.16040.20770.1028-0.4273-0.07410.1128-0.2417-0.0701-0.05230.46470.12370.02070.42610.08520.3362-35.643737.442228.7153
191.8973.1134-0.40356.78242.14864.67970.2010.00870.2606-0.5189-0.14070.5904-0.6277-0.74660.05510.44030.1602-0.08290.6680.07020.4402-46.281139.340428.8708
200.7999-0.34310.98950.7932-0.35171.6010.130.49510.0331-0.6214-0.42290.9665-0.3955-1.3536-0.21040.77830.344-0.31661.2723-0.02460.7663-62.108938.654921.7346
211.779-0.3733-0.62011.23420.18352.32230.09740.28950.1476-0.5944-0.15340.3988-0.3485-0.73210.03580.72950.2495-0.1720.8804-0.05320.5143-51.407336.2315.8636
220.7003-0.3978-0.12540.81610.31412.25260.20120.2555-0.0151-0.3198-0.2450.1493-0.3748-0.6-0.01560.53580.1563-0.07080.55620.06670.4469-44.844139.779427.9209
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 9 through 254 )A9 - 254
2X-RAY DIFFRACTION2chain 'A' and (resid 255 through 278 )A255 - 278
3X-RAY DIFFRACTION3chain 'A' and (resid 279 through 502 )A279 - 502
4X-RAY DIFFRACTION4chain 'B' and (resid 8 through 140 )B8 - 140
5X-RAY DIFFRACTION5chain 'B' and (resid 141 through 191 )B141 - 191
6X-RAY DIFFRACTION6chain 'B' and (resid 192 through 254 )B192 - 254
7X-RAY DIFFRACTION7chain 'B' and (resid 255 through 278 )B255 - 278
8X-RAY DIFFRACTION8chain 'B' and (resid 279 through 372 )B279 - 372
9X-RAY DIFFRACTION9chain 'B' and (resid 373 through 502 )B373 - 502
10X-RAY DIFFRACTION10chain 'C' and (resid 8 through 123 )C8 - 123
11X-RAY DIFFRACTION11chain 'C' and (resid 124 through 254 )C124 - 254
12X-RAY DIFFRACTION12chain 'C' and (resid 255 through 278 )C255 - 278
13X-RAY DIFFRACTION13chain 'C' and (resid 279 through 502 )C279 - 502
14X-RAY DIFFRACTION14chain 'D' and (resid 7 through 39 )D7 - 39
15X-RAY DIFFRACTION15chain 'D' and (resid 40 through 86 )D40 - 86
16X-RAY DIFFRACTION16chain 'D' and (resid 87 through 169 )D87 - 169
17X-RAY DIFFRACTION17chain 'D' and (resid 170 through 193 )D170 - 193
18X-RAY DIFFRACTION18chain 'D' and (resid 194 through 254 )D194 - 254
19X-RAY DIFFRACTION19chain 'D' and (resid 255 through 278 )D255 - 278
20X-RAY DIFFRACTION20chain 'D' and (resid 279 through 372 )D279 - 372
21X-RAY DIFFRACTION21chain 'D' and (resid 373 through 441 )D373 - 441
22X-RAY DIFFRACTION22chain 'D' and (resid 442 through 502 )D442 - 502

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