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- PDB-6xnq: Crystal Structure of Argininosuccinate synthase from Legionella p... -

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Basic information

Entry
Database: PDB / ID: 6xnq
TitleCrystal Structure of Argininosuccinate synthase from Legionella pneumophila Philadelphia 1
ComponentsArgininosuccinate synthase
KeywordsLIGASE / SSGCID / Argininosuccinate synthase / argG / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


argininosuccinate synthase / argininosuccinate metabolic process / argininosuccinate synthase activity / urea cycle / L-arginine biosynthetic process / ATP binding / cytoplasm
Similarity search - Function
Argininosuccinate synthase / Argininosuccinate synthase, conserved site / Argininosuccinate synthase, type 1 subfamily / Argininosuccinate synthetase, catalytic/multimerisation domain body / : / : / Arginosuccinate synthase N-terminal HUP domain / Arginosuccinate synthase C-terminal domain / Argininosuccinate synthase signature 1. / Argininosuccinate synthase signature 2. / Rossmann-like alpha/beta/alpha sandwich fold
Similarity search - Domain/homology
Argininosuccinate synthase
Similarity search - Component
Biological speciesLegionella pneumophila subsp. pneumophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: to be published
Title: Crystal Structure of Argininosuccinate synthase from Legionella pneumophila Philadelphia 1
Authors: Abendroth, J. / Dranow, D.M. / Lorimer, D.D. / Horanyi, P.S. / Edwards, T.E.
History
DepositionJul 3, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 22, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 18, 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
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: Argininosuccinate synthase
B: Argininosuccinate synthase
C: Argininosuccinate synthase
D: Argininosuccinate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)185,88126
Polymers184,2784
Non-polymers1,60322
Water23,9781331
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)122.990, 102.660, 147.660
Angle α, β, γ (deg.)90.000, 95.930, 90.000
Int Tables number5
Space group name H-MC121
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 4 through 6 or resid 8...
21(chain B and (resid 4 through 6 or resid 8...
31(chain C and (resid 4 through 6 or resid 8...
41(chain D and (resid 4 through 6 or resid 8...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 4 through 6 or resid 8...A4 - 6
121(chain A and (resid 4 through 6 or resid 8...A8 - 12
131(chain A and (resid 4 through 6 or resid 8...A14 - 26
141(chain A and (resid 4 through 6 or resid 8...A28 - 55
151(chain A and (resid 4 through 6 or resid 8...A4 - 505
161(chain A and (resid 4 through 6 or resid 8...A4 - 505
171(chain A and (resid 4 through 6 or resid 8...A4 - 505
181(chain A and (resid 4 through 6 or resid 8...A4 - 505
191(chain A and (resid 4 through 6 or resid 8...A4 - 505
211(chain B and (resid 4 through 6 or resid 8...B4 - 6
221(chain B and (resid 4 through 6 or resid 8...B8 - 12
231(chain B and (resid 4 through 6 or resid 8...B0
241(chain B and (resid 4 through 6 or resid 8...B6
251(chain B and (resid 4 through 6 or resid 8...B70 - 7352
261(chain B and (resid 4 through 6 or resid 8...B4 - 507
271(chain B and (resid 4 through 6 or resid 8...B4 - 507
281(chain B and (resid 4 through 6 or resid 8...B4 - 507
291(chain B and (resid 4 through 6 or resid 8...B4 - 507
2101(chain B and (resid 4 through 6 or resid 8...B4 - 507
2111(chain B and (resid 4 through 6 or resid 8...B4 - 507
311(chain C and (resid 4 through 6 or resid 8...C4 - 6
321(chain C and (resid 4 through 6 or resid 8...C8 - 12
331(chain C and (resid 4 through 6 or resid 8...C14 - 26
341(chain C and (resid 4 through 6 or resid 8...C28 - 64
351(chain C and (resid 4 through 6 or resid 8...C66 - 68
361(chain C and (resid 4 through 6 or resid 8...C70 - 73
371(chain C and (resid 4 through 6 or resid 8...C75 - 111
381(chain C and (resid 4 through 6 or resid 8...C112
391(chain C and (resid 4 through 6 or resid 8...C4 - 506
3101(chain C and (resid 4 through 6 or resid 8...C4 - 506
3111(chain C and (resid 4 through 6 or resid 8...C4 - 506
3121(chain C and (resid 4 through 6 or resid 8...C4 - 506
411(chain D and (resid 4 through 6 or resid 8...D4 - 6
421(chain D and (resid 4 through 6 or resid 8...D8 - 12
431(chain D and (resid 4 through 6 or resid 8...D14 - 26
441(chain D and (resid 4 through 6 or resid 8...D28 - 55
451(chain D and (resid 4 through 6 or resid 8...D56
461(chain D and (resid 4 through 6 or resid 8...D4 - 505
471(chain D and (resid 4 through 6 or resid 8...D4 - 505
481(chain D and (resid 4 through 6 or resid 8...D4 - 505
491(chain D and (resid 4 through 6 or resid 8...D4 - 505

NCS oper:
IDCodeMatrixVector
1given(-0.977865462018, 0.00198881398353, -0.209225196406), (0.00440025939366, -0.999538202391, -0.030066919984), (-0.209188374221, -0.0303220477375, 0.977405134789)57.6719459079, 0.793186082281, 6.11334425233
2given(-0.999956118486, -0.00157479208072, -0.0092347783973), (-0.00186376882644, 0.999506178796, 0.0313675774324), (0.00918082065538, 0.0313834124677, -0.999465254)50.9217523581, -1.20731656235, 72.7349553465
3given(0.979015550788, -0.00150491672676, 0.203779995441), (-0.00110180625375, -0.999997205604, -0.00209160405626), (0.203782573689, 0.0018231868238, -0.979014473157)-6.95373975342, -0.155099772468, 67.0543355624

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Components

#1: Protein
Argininosuccinate synthase / Citrulline--aspartate ligase / LepnA.00809.a


Mass: 46069.465 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila subsp. pneumophila (strain Philadelphia 1 / ATCC 33152 / DSM 7513) (bacteria)
Strain: Philadelphia 1 / ATCC 33152 / DSM 7513 / Gene: argG, lpg0494 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q5ZY78, argininosuccinate synthase
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1331 / 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: 2.52 Å3/Da / Density % sol: 51.2 %
Crystal growTemperature: 287 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: Rigaku Reagents JCSG+ screen, G8: 25% (w/V) PEG 3350, 200mM NaCl, 100mM BisTris / HCl pH 5.5: LepnA.00809.a.B1.PS38414 at 17.3mg/ml: tray 299030 g8: cryo 15%EG, puck rjp0-8

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Aug 8, 2018 / 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: 1.95→42.86 Å / Num. obs: 132663 / % possible obs: 99.9 % / Redundancy: 4.223 % / Biso Wilson estimate: 31.112 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.084 / Rrim(I) all: 0.096 / Χ2: 0.971 / Net I/σ(I): 10.52 / Num. measured all: 560249 / Scaling rejects: 23
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.95-24.2380.5062.741605982898160.8490.5899.9
2-2.064.2330.4043.3540371954695380.8940.46399.9
2.06-2.124.2310.3214.1639109924392430.9340.367100
2.12-2.184.2280.2615.0337981899589840.9540.29999.9
2.18-2.254.2190.2175.9136802872687220.9680.248100
2.25-2.334.2230.1846.9135640845284400.9760.2199.9
2.33-2.424.2280.167.8134608819281850.9820.18399.9
2.42-2.524.2170.1359.0733023784078300.9860.15599.9
2.52-2.634.220.11710.1831791754675330.9890.13499.8
2.63-2.764.2240.10311.4530511722572230.9910.118100
2.76-2.914.210.0912.7428765683968320.9920.10399.9
2.91-3.084.2180.07714.3527488652665170.9940.08999.9
3.08-3.34.2090.06915.9625438604960440.9950.07999.9
3.3-3.564.2180.05918.324022570456950.9960.06899.8
3.56-3.94.2380.05620.0122238524852470.9950.064100
3.9-4.364.2480.05221.4420227476947610.9960.05999.8
4.36-5.034.2510.0522.0717871420742040.9960.05899.9
5.03-6.174.2310.05220.7515050355935570.9960.05999.9
6.17-8.724.1960.0521.311599276727640.9960.05799.9
8.72-42.863.9990.0523.26110155115280.9960.05898.5

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Processing

Software
NameVersionClassification
PHENIX1.18.2refinement
XDSdata reduction
XSCALEdata scaling
PDB_EXTRACT3.25data extraction
MoRDaphasing
Cootmodel building
PHENIXmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1j20 as per Morda

1j20


Resolution: 1.95→42.86 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 21.39 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1937 1986 1.5 %0
Rwork0.1633 130596 --
obs0.1638 132582 99.84 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 104.04 Å2 / Biso mean: 28.3543 Å2 / Biso min: 12.11 Å2
Refinement stepCycle: final / Resolution: 1.95→42.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11926 0 95 1356 13377
Biso mean--40.01 34.55 -
Num. residues----1556
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00712530
X-RAY DIFFRACTIONf_angle_d0.81717094
X-RAY DIFFRACTIONf_chiral_restr0.0541959
X-RAY DIFFRACTIONf_plane_restr0.0052183
X-RAY DIFFRACTIONf_dihedral_angle_d15.4954565
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A3283X-RAY DIFFRACTION4.418TORSIONAL
12B3283X-RAY DIFFRACTION4.418TORSIONAL
13C3283X-RAY DIFFRACTION4.418TORSIONAL
14D3283X-RAY DIFFRACTION4.418TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.95-20.30141510.225293079458100
2-2.050.2781330.205893119444100
2.05-2.110.24941360.193992919427100
2.11-2.180.22361220.18992719393100
2.18-2.260.20761230.184793009423100
2.26-2.350.19291200.174993519471100
2.35-2.460.21631600.177192849444100
2.46-2.590.21761550.169793499504100
2.59-2.750.20151580.168892659423100
2.75-2.960.21881350.167693459480100
2.96-3.260.19241430.167493209463100
3.26-3.730.1741510.145693399490100
3.73-4.70.15051430.129194169559100
4.7-42.860.17011560.15699447960399
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)
14.82160.8827-1.20394.3421-0.21254.8049-0.0578-0.36010.40860.00820.03740.0982-0.60980.23680.01050.2670.05-0.03770.2014-0.06910.25833.787934.754352.8558
20.9926-0.8907-0.0933.1098-0.1881.2949-0.0653-0.08020.08120.00150.04870.022-0.1673-0.00690.0250.1590.0344-0.01750.1778-0.01740.16628.243721.319746.4005
30.4443-0.73890.54871.2703-0.81560.6116-0.2503-0.06060.17020.16210.1802-0.2322-0.44580.14110.07650.40530.0213-0.02730.2775-0.06580.245116.254230.574960.7274
41.14750.1165-0.01950.80260.16091.102-0.0219-0.15570.08410.20090.04520.0944-0.0614-0.0681-0.01670.21630.07250.02110.19830.00610.176414.1387.268263.3431
50.29650.15960.06150.74810.07880.7217-0.0199-0.012-0.0206-0.00320.03520.0446-0.0097-0.0433-0.03510.14950.03470.0020.19960.00890.182713.9191.310844.8585
61.090.35990.64791.28040.51532.05890.0992-0.1191-0.16420.15160.04660.02450.341-0.257-0.0350.21830.01620.0070.18960.02160.220510.0029-10.778556.8838
78.0252.1717-5.04985.1746-1.23987.13930.052-0.6312-0.34330.1605-0.1116-0.29280.28180.44930.06770.26630.0835-0.0530.1854-0.01180.16436.9136-23.270334.9714
84.52171.11120.79634.6702-1.18482.6372-0.03970.0629-0.5044-0.37060.02630.03450.5286-0.057-0.00460.35340.0478-0.00340.20350.0210.2542.1058-37.732252.206
91.7515-1.85060.45994.3129-0.61390.7841-0.0683-0.1542-0.12340.11950.1052-0.06660.08310.0072-0.03910.16510.0327-0.00910.1891-0.00470.155341.4845-21.533854.0322
100.6271.9509-1.65596.3057-5.25876.6053-0.0684-0.0518-0.0086-0.27630.24150.29570.6064-0.3884-0.17870.2629-0.0026-0.0360.25040.01140.229233.9984-34.243548.9629
111.0407-0.09930.13760.828-0.23730.78930.0208-0.1187-0.19540.18350.0411-0.03820.16280.0333-0.05520.2410.06-0.02220.18550.01250.164230.2357-12.664764.4664
120.1252-0.0290.0820.3662-0.16920.4881-0.0149-0.00540.0060.06850.0508-0.0262-0.0171-0.0087-0.03560.15770.0312-0.010.2015-0.00770.188934.6969-1.868246.9504
131.58671.0879-1.23391.8592-0.94582.79990.0836-0.22130.17210.16860.01620.0494-0.32130.3005-0.06990.19690.024-0.03150.189-0.02910.189736.20799.959359.8781
147.9523.1275.40635.1682.39633.75140.2481-0.57350.47690.0663-0.41060.341-0.1609-0.52030.26210.27420.04740.06140.24540.02110.234814.137123.058333.4294
153.1162-0.3993-0.31564.1606-0.52651.8483-0-0.03060.5040.21530.0804-0.0478-0.6067-0.0562-0.03980.3841-0.0440.03010.21990.00030.280245.110337.190124.5332
161.66480.0989-0.52015.7308-0.82641.3455-0.12140.44140.1838-0.28310.0137-0.4342-0.23320.14890.02440.3093-0.10370.03010.33140.03190.270250.877129.439216.1075
172.39810.2705-0.18413.5194-0.46091.3022-0.04640.0659-0.2109-0.11870.119-0.1118-0.04150.1028-0.02950.169-0.04320.02420.1686-0.02450.129540.1238.807922.5193
181.8239-0.6079-0.62064.8093-0.86383.7876-0.0228-0.02990.19990.11290.08170.0672-0.32550.06780.03610.2142-0.01610.0380.17380.0120.178744.320725.923428.4671
191.0869-0.7586-0.43064.4965-2.15013.6550.02890.23680.10480.08430.14650.257-0.6161-0.4152-0.19640.3416-0.00720.0220.25810.00250.226236.527733.867126.1578
200.55180.40520.22170.34990.25940.30750.06060.33260.4923-0.15280.02130.1147-0.37970.1299-0.04050.384-0.06180.05980.23880.06190.337934.097824.516811.1939
211.34520.0971-0.80550.89640.24141.63810.0230.38940.1712-0.28350.05090.0466-0.084-0.1618-0.09020.3291-0.05550.00060.31350.08050.20329.173411.59791.7305
221.9249-0.1781-0.12831.0936-0.30660.98920.03350.02650.1786-0.2240.045-0.2155-0.08420.13-0.07490.2094-0.05680.0310.1876-0.01580.159639.22726.653412.9948
230.18560.0519-0.13151.04470.20911.1725-0.01860.00530.0108-0.02720.0523-0.0434-0.00760.018-0.03260.1325-0.016-0.0010.185-0.00790.172736.56961.554928.1157
241.1367-0.36880.52341.6235-0.39742.42510.02090.1365-0.026-0.2757-0.0194-0.17570.38720.2909-0.01890.1937-0.00370.03780.2063-0.02860.187840.6302-10.294515.7546
253.1197-2.2322-4.31054.91162.07056.3730.10320.5933-0.2424-0.1118-0.18540.18980.2019-0.45330.08040.2783-0.081-0.0440.23710.01530.210113.7665-23.382337.3777
261.79041.68180.19834.55240.66321.3126-0.09220.1297-0.2415-0.03270.0977-0.0220.2301-0.0415-0.00090.189-0.02650.00940.2188-0.01520.17538.5987-26.062918.8963
270.707-1.4343-1.5943.28812.57964.2989-0.12020.1053-0.16870.0820.1452-0.2490.50480.5516-0.06240.27110.02680.010.3675-0.04320.306616.1634-33.61323.4939
280.65310.0453-0.26680.77740.11220.9344-0.02960.12520.0011-0.15770.05380.03120.0268-0.062-0.0190.1706-0.0298-0.02390.19260.00810.150517.9731-5.254214.31
294.1262-2.24446.03444.204-3.10859.36440.15020.38590.4892-0.0192-0.2564-0.3403-0.12040.41220.13490.2652-0.05760.04720.184-0.03630.241736.400122.94140.325
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 57 )A4 - 57
2X-RAY DIFFRACTION2chain 'A' and (resid 58 through 148 )A58 - 148
3X-RAY DIFFRACTION3chain 'A' and (resid 149 through 194 )A149 - 194
4X-RAY DIFFRACTION4chain 'A' and (resid 195 through 277 )A195 - 277
5X-RAY DIFFRACTION5chain 'A' and (resid 278 through 334 )A278 - 334
6X-RAY DIFFRACTION6chain 'A' and (resid 335 through 377 )A335 - 377
7X-RAY DIFFRACTION7chain 'A' and (resid 378 through 404 )A378 - 404
8X-RAY DIFFRACTION8chain 'B' and (resid 4 through 40 )B4 - 40
9X-RAY DIFFRACTION9chain 'B' and (resid 41 through 125 )B41 - 125
10X-RAY DIFFRACTION10chain 'B' and (resid 126 through 165 )B126 - 165
11X-RAY DIFFRACTION11chain 'B' and (resid 166 through 277 )B166 - 277
12X-RAY DIFFRACTION12chain 'B' and (resid 278 through 334 )B278 - 334
13X-RAY DIFFRACTION13chain 'B' and (resid 335 through 377 )B335 - 377
14X-RAY DIFFRACTION14chain 'B' and (resid 378 through 404 )B378 - 404
15X-RAY DIFFRACTION15chain 'C' and (resid 4 through 40 )C4 - 40
16X-RAY DIFFRACTION16chain 'C' and (resid 41 through 67 )C41 - 67
17X-RAY DIFFRACTION17chain 'C' and (resid 68 through 92 )C68 - 92
18X-RAY DIFFRACTION18chain 'C' and (resid 93 through 125 )C93 - 125
19X-RAY DIFFRACTION19chain 'C' and (resid 126 through 165 )C126 - 165
20X-RAY DIFFRACTION20chain 'C' and (resid 166 through 194 )C166 - 194
21X-RAY DIFFRACTION21chain 'C' and (resid 195 through 218 )C195 - 218
22X-RAY DIFFRACTION22chain 'C' and (resid 219 through 277 )C219 - 277
23X-RAY DIFFRACTION23chain 'C' and (resid 278 through 334 )C278 - 334
24X-RAY DIFFRACTION24chain 'C' and (resid 335 through 377 )C335 - 377
25X-RAY DIFFRACTION25chain 'C' and (resid 378 through 404 )C378 - 404
26X-RAY DIFFRACTION26chain 'D' and (resid 4 through 125 )D4 - 125
27X-RAY DIFFRACTION27chain 'D' and (resid 126 through 165 )D126 - 165
28X-RAY DIFFRACTION28chain 'D' and (resid 166 through 377 )D166 - 377
29X-RAY DIFFRACTION29chain 'D' and (resid 378 through 404 )D378 - 404

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