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- PDB-7lon: Ornithine Aminotransferase (OAT) cocrystallized with its inactiva... -

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Basic information

Entry
Database: PDB / ID: 7lon
TitleOrnithine Aminotransferase (OAT) cocrystallized with its inactivator - (1S,3S)-3-amino-4-(difluoromethylene)cyclohexene-1-carboxylic acid
ComponentsOrnithine aminotransferase, mitochondrial
KeywordsTRANSFERASE / Ornithine Aminotransferase / OAT / aminotransferase / inactivator / inhibitor
Function / homology
Function and homology information


L-arginine catabolic process to proline via ornithine / ornithine aminotransferase activity / ornithine aminotransferase / L-arginine catabolic process to L-glutamate / L-proline biosynthetic process / Glutamate and glutamine metabolism / visual perception / pyridoxal phosphate binding / mitochondrial matrix / mitochondrion ...L-arginine catabolic process to proline via ornithine / ornithine aminotransferase activity / ornithine aminotransferase / L-arginine catabolic process to L-glutamate / L-proline biosynthetic process / Glutamate and glutamine metabolism / visual perception / pyridoxal phosphate binding / mitochondrial matrix / mitochondrion / nucleoplasm / identical protein binding / cytoplasm
Similarity search - Function
Ornithine aminotransferase / : / : / Aminotransferases class-III pyridoxal-phosphate attachment site. / Aminotransferase class-III / Aminotransferase class-III / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase
Similarity search - Domain/homology
Chem-7QP / THREONINE / Ornithine aminotransferase, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsButrin, A. / Zhu, W. / Liu, D. / Silverman, R.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute on Drug Abuse (NIH/NIDA) United States
CitationJournal: J.Am.Chem.Soc. / Year: 2021
Title: Remarkable and Unexpected Mechanism for ( S )-3-Amino-4-(difluoromethylenyl)cyclohex-1-ene-1-carboxylic Acid as a Selective Inactivator of Human Ornithine Aminotransferase.
Authors: Zhu, W. / Doubleday, P.F. / Butrin, A. / Weerawarna, P.M. / Melani, R.D. / Catlin, D.S. / Dwight, T.A. / Liu, D. / Kelleher, N.L. / Silverman, R.B.
History
DepositionFeb 10, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 25, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._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
Revision 1.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Ornithine aminotransferase, mitochondrial
A: Ornithine aminotransferase, mitochondrial
C: Ornithine aminotransferase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)136,1039
Polymers134,5813
Non-polymers1,5226
Water10,341574
1
B: Ornithine aminotransferase, mitochondrial
hetero molecules

B: Ornithine aminotransferase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,7366
Polymers89,7212
Non-polymers1,0154
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_554-x+y,y,-z-2/31
Buried area10440 Å2
ΔGint-60 kcal/mol
Surface area25660 Å2
MethodPISA
2
A: Ornithine aminotransferase, mitochondrial
hetero molecules

A: Ornithine aminotransferase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,7366
Polymers89,7212
Non-polymers1,0154
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_554-y,-x,-z-1/31
Buried area10460 Å2
ΔGint-57 kcal/mol
Surface area25690 Å2
MethodPISA
3
C: Ornithine aminotransferase, mitochondrial
hetero molecules

C: Ornithine aminotransferase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,7366
Polymers89,7212
Non-polymers1,0154
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_544x,x-y-1,-z-11
Buried area10460 Å2
ΔGint-63 kcal/mol
Surface area25730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)192.024, 192.024, 57.058
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number151
Space group name H-MP3112
Components on special symmetry positions
IDModelComponents
11B-687-

HOH

21B-788-

HOH

31A-687-

HOH

41C-650-

HOH

51C-779-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 38 through 44 or (resid 45...
21(chain B and (resid 38 through 44 or (resid 45...
31(chain C and (resid 38 through 44 or (resid 45...

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
11PROPROPHEPHE(chain A and (resid 38 through 44 or (resid 45...AB38 - 443 - 9
12GLUGLUGLUGLU(chain A and (resid 38 through 44 or (resid 45...AB4510
13PROPROPHEPHE(chain A and (resid 38 through 44 or (resid 45...AB38 - 4393 - 404
14PROPROPHEPHE(chain A and (resid 38 through 44 or (resid 45...AB38 - 4393 - 404
15PROPROPHEPHE(chain A and (resid 38 through 44 or (resid 45...AB38 - 4393 - 404
16PROPROPHEPHE(chain A and (resid 38 through 44 or (resid 45...AB38 - 4393 - 404
21PROPROPHEPHE(chain B and (resid 38 through 44 or (resid 45...BA38 - 443 - 9
22GLUGLUGLUGLU(chain B and (resid 38 through 44 or (resid 45...BA4510
23PROPROPHEPHE(chain B and (resid 38 through 44 or (resid 45...BA38 - 4393 - 404
24PROPROPHEPHE(chain B and (resid 38 through 44 or (resid 45...BA38 - 4393 - 404
25PROPROPHEPHE(chain B and (resid 38 through 44 or (resid 45...BA38 - 4393 - 404
26PROPROPHEPHE(chain B and (resid 38 through 44 or (resid 45...BA38 - 4393 - 404
31PROPROPHEPHE(chain C and (resid 38 through 44 or (resid 45...CC38 - 443 - 9
32GLUGLUGLUGLU(chain C and (resid 38 through 44 or (resid 45...CC4510
33PROPROPHEPHE(chain C and (resid 38 through 44 or (resid 45...CC38 - 4393 - 404
34PROPROPHEPHE(chain C and (resid 38 through 44 or (resid 45...CC38 - 4393 - 404
35PROPROPHEPHE(chain C and (resid 38 through 44 or (resid 45...CC38 - 4393 - 404
36PROPROPHEPHE(chain C and (resid 38 through 44 or (resid 45...CC38 - 4393 - 404

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Components

#1: Protein Ornithine aminotransferase, mitochondrial / Ornithine delta-aminotransferase / Ornithine--oxo-acid aminotransferase


Mass: 44860.320 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: OAT / Production host: Escherichia coli (E. coli) / References: UniProt: P04181, ornithine aminotransferase
#2: Chemical ChemComp-THR / THREONINE


Type: L-peptide linking / Mass: 119.119 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H9NO3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-7QP / (1R,3S,4R)-3-[({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)amino]-4-methylcyclohexane-1-carboxylic acid


Mass: 388.353 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C16H25N2O7P / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 574 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.25 Å3/Da / Density % sol: 45.37 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: The freshly prepared enzyme was buffer exchanged into 50 mM Tricine pH 7.8 and concentrated to a protein concentration of 6 mg/mL. For each hanging drop, 2 ul of protein solution was mixed ...Details: The freshly prepared enzyme was buffer exchanged into 50 mM Tricine pH 7.8 and concentrated to a protein concentration of 6 mg/mL. For each hanging drop, 2 ul of protein solution was mixed with equal volume of well solution and 0.5 ul of 10 mM compound. The crystals with the best morphology and size grew in a final condition containing 12% PEG 6000, 200 mM NaCl, 10% glycerol, 50 mM Tricine pH 7.8.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.127 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Mar 25, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.127 Å / Relative weight: 1
ReflectionResolution: 1.943→49.05 Å / Num. obs: 87426 / % possible obs: 99.5 % / Redundancy: 8.5 % / CC1/2: 0.997 / Rmerge(I) obs: 0.174 / Rpim(I) all: 0.092 / Net I/σ(I): 4.2
Reflection shellResolution: 1.943→1.977 Å / Redundancy: 7 % / Rmerge(I) obs: 1.599 / Num. unique obs: 4085 / CC1/2: 0.745 / Rpim(I) all: 0.925 / % possible all: 93

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
xia2data scaling
PDB_EXTRACT3.27data extraction
xia2data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1OAT

1oat


Resolution: 1.95→49.05 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 37.5 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2784 4075 4.94 %
Rwork0.2434 78457 -
obs0.2452 82532 94.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 137.47 Å2 / Biso mean: 40.4095 Å2 / Biso min: 14.86 Å2
Refinement stepCycle: final / Resolution: 1.95→49.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9510 0 0 574 10084
Biso mean---40.2 -
Num. residues----1203
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A5698X-RAY DIFFRACTION7.989TORSIONAL
12B5698X-RAY DIFFRACTION7.989TORSIONAL
13C5698X-RAY DIFFRACTION7.989TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 29

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.95-1.970.41661280.38752342247082
1.97-1.990.35981300.332428352965100
1.99-2.020.33181360.305228542990100
2.02-2.050.32211340.30152905303999
2.05-2.070.30311340.283827962930100
2.07-2.10.29261280.27722882301099
2.1-2.130.28961630.26652844300799
2.13-2.170.29071760.269627882964100
2.17-2.20.32361430.268928843027100
2.2-2.240.27851460.25462782292899
2.24-2.280.29961420.25652873301599
2.28-2.330.24071260.23982793291998
2.33-2.370.2661140.23592883299799
2.37-2.420.30511670.22652791295899
2.42-2.480.29541260.22412844297098
2.48-2.540.30411550.22362745290097
2.54-2.610.27911360.22182776291297
2.61-2.690.28891640.22342745290996
2.69-2.780.24791260.24052741286796
2.78-2.870.32281550.23822744289996
2.88-2.990.3231490.25862732288194
2.99-3.130.32311420.25872629277193
3.13-3.290.2751200.23922624274491
3.29-3.50.29351730.23752532270590
3.5-3.770.28731190.23342491261086
3.77-4.150.23881440.21712401254584
4.15-4.740.26421280.20952363249182
4.75-5.970.24371330.23522426255984
5.98-49.050.22461380.24762412255082
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)
11.3098-1.58620.62123.43720.74042.02820.07390.433-0.3109-0.19760.1246-0.47260.31510.3483-0.14190.24330.0620.06440.3768-0.11660.299717.2454-37.53-33.7568
23.104-0.8505-0.07811.16160.40421.31310.19350.0163-0.34170.16440.0582-0.18760.31160.2086-0.2150.23040.0745-0.08860.159-0.03930.297714.0777-47.4273-16.4734
31.06010.34250.32560.4110.24820.8587-0.028-0.14760.0196-0.02650.00610.0661-0.0423-0.10220.03540.10820.0105-0.0080.14790.01460.13440.7968-22.773-9.0658
41.62430.45920.8191.08480.53130.89690.0586-0.2529-0.07780.11350.0024-0.03740.0771-0.0961-0.05090.1711-0.0185-0.00480.16510.02430.12145.1036-29.0167-3.3576
54.21510.17241.53534.0363-0.11523.00630.11420.0250.0079-0.29540.0242-0.64040.03190.633-0.05470.1530.061-0.0340.2646-0.12950.388529.834-33.215-6.9721
63.93991.1253-2.5791.4461-0.62534.20120.07320.0344-0.25610.02470.05-0.48350.26950.476-0.07840.13830.0732-0.06680.2757-0.13030.331328.9669-38.9872-14.5827
73.7821-0.4357-0.86741.1716-1.74883.2724-0.12210.6361-0.1703-0.32690.1369-0.21710.17190.0656-0.04050.5374-0.1242-0.08190.27850.01720.667654.9916-51.8579-23.96
83.763.96511.10834.53370.62951.9270.0507-0.0919-0.0207-0.02680.12550.6830.0837-0.4276-0.17160.28620.05610.0180.49520.14770.767947.904-43.931-6.9271
90.1687-0.06280.2061.2242-0.97761.9770.285-0.17510.2930.3285-0.01180.1666-0.47620.2746-0.2420.40480.10130.08550.3683-0.00250.675966.491-29.57962.5599
100.0790.1943-0.35941.5385-0.37161.6194-0.11510.1022-0.0744-0.13210.06-0.10350.03650.01470.05030.28010.0251-0.02760.34280.03740.603280.5923-52.2666-0.6207
115.72540.19183.32074.97191.29086.9530.02950.20670.4440.345-0.2408-0.06590.2980.24120.20910.2716-0.011-0.0030.23220.04160.456374.7712-54.66939.626
120.7530.38290.83713.0164-1.5832.3103-0.00660.0288-0.1521-0.03640.07720.1249-0.0085-0.2531-0.0640.29810.03860.03710.3807-0.01010.578164.9588-40.55224.2384
135.23890.1837-1.73496.4645-0.33172.28210.38890.0749-1.3461-0.1022-0.14560.2560.5587-0.6346-0.2620.519-0.0493-0.15510.44970.08430.859152.1958-64.66732.5507
141.6722-1.6302-0.61499.61074.64775.74860.6685-0.1536-0.2102-0.0737-0.3054-0.04730.59230.2385-0.46950.4899-0.0513-0.14290.51860.10140.794851.4648-62.6606-10.9685
151.3372-1.8505-0.7968.05144.88244.79840.1462-0.4702-0.9003-0.00630.08720.39470.6599-0.82090.10820.4594-0.0914-0.11780.52410.20380.906245.1552-59.8952-0.7255
163.8465-0.8142-1.99760.30411.13685.88130.09770.27870.2734-0.67960.06390.43250.281-0.1129-0.04310.60440.16780.10610.23860.0270.475223.9207-77.3459-43.5796
172.4037-3.3225-0.14355.1143-0.68561.323-0.0249-0.24630.6069-0.0760.0324-0.6686-0.51360.168-0.04390.5715-0.09590.08760.3821-0.14940.650434.0778-74.9706-26.0185
187.0182-0.3007-1.20072.2335-1.20335.3780.1355-0.57820.1440.13220.1719-0.5219-0.00420.552-0.27680.27140.0116-0.03080.3998-0.13780.46237.0837-98.0914-16.2742
194.47670.7068-2.68760.97770.3934.48050.0172-0.1518-0.15-0.2474-0.0573-0.06720.03070.10720.06190.30960.0534-0.00540.3122-0.04250.424914.6085-102.9481-18.3091
200.6566-0.2726-1.04680.49011.22843.5768-0.01840.0482-0.0951-0.1538-0.17890.0936-0.021-0.15810.17990.32020.01560.03830.2606-0.00280.46086.1264-95.0767-21.0269
215.31052.3128-2.1387.0473-1.88625.5765-0.3719-0.2724-0.13920.17580.2633-0.2967-0.1326-0.36220.14690.27380.1043-0.00520.2634-0.02910.287411.3136-92.8389-9.4007
225.31610.4831-4.79034.7445-4.8078.7764-0.10360.10770.25830.04670.28180.21230.0379-0.2914-0.17720.3194-0.0171-0.03980.2954-0.08070.465122.2452-86.5362-9.2492
231.8844-1.26230.8821.9066-1.19941.542-0.02690.1079-0.0249-0.14940.21630.0583-0.4363-0.2727-0.0170.40770.04890.05680.2668-0.10180.473927.4561-94.3918-17.7431
243.68430.1005-1.59862.23760.81822.65840.1174-0.5615-0.0514-0.29230.1008-0.6532-0.26870.4667-0.24940.34320.1022-0.03830.50450.00910.444535.3035-93.3351-17.4262
255.5283-0.48760.62586.95431.57367.42120.12980.12660.69060.08430.25960.7587-0.441-0.4374-0.32720.49670.06770.05320.28420.02450.64613.8464-68.3351-16.594
266.57580.2367-0.64391.35163.51569.3747-0.09870.382-1.0227-0.04880.0847-0.3434-0.0832-0.42770.03930.61280.02780.03420.3027-0.06940.571616.0293-68.6825-30.1245
276.0512-2.27253.71564.3305-2.60246.28610.30230.0258-0.06810.09240.22220.0454-1.23280.0801-0.47220.67620.01790.18690.2801-0.09350.652821.5713-64.639-20.0044
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'B' and (resid 38 through 61 )B38 - 61
2X-RAY DIFFRACTION2chain 'B' and (resid 62 through 105 )B62 - 105
3X-RAY DIFFRACTION3chain 'B' and (resid 106 through 220 )B106 - 220
4X-RAY DIFFRACTION4chain 'B' and (resid 221 through 344 )B221 - 344
5X-RAY DIFFRACTION5chain 'B' and (resid 345 through 389 )B345 - 389
6X-RAY DIFFRACTION6chain 'B' and (resid 390 through 439 )B390 - 439
7X-RAY DIFFRACTION7chain 'A' and (resid 38 through 61 )A38 - 61
8X-RAY DIFFRACTION8chain 'A' and (resid 62 through 105 )A62 - 105
9X-RAY DIFFRACTION9chain 'A' and (resid 106 through 141 )A106 - 141
10X-RAY DIFFRACTION10chain 'A' and (resid 142 through 220 )A142 - 220
11X-RAY DIFFRACTION11chain 'A' and (resid 221 through 263 )A221 - 263
12X-RAY DIFFRACTION12chain 'A' and (resid 264 through 344 )A264 - 344
13X-RAY DIFFRACTION13chain 'A' and (resid 345 through 389 )A345 - 389
14X-RAY DIFFRACTION14chain 'A' and (resid 390 through 410 )A390 - 410
15X-RAY DIFFRACTION15chain 'A' and (resid 411 through 439 )A411 - 439
16X-RAY DIFFRACTION16chain 'C' and (resid 38 through 61 )C38 - 61
17X-RAY DIFFRACTION17chain 'C' and (resid 62 through 105 )C62 - 105
18X-RAY DIFFRACTION18chain 'C' and (resid 106 through 141 )C106 - 141
19X-RAY DIFFRACTION19chain 'C' and (resid 142 through 181 )C142 - 181
20X-RAY DIFFRACTION20chain 'C' and (resid 182 through 220 )C182 - 220
21X-RAY DIFFRACTION21chain 'C' and (resid 221 through 263 )C221 - 263
22X-RAY DIFFRACTION22chain 'C' and (resid 264 through 290 )C264 - 290
23X-RAY DIFFRACTION23chain 'C' and (resid 291 through 313 )C291 - 313
24X-RAY DIFFRACTION24chain 'C' and (resid 314 through 344 )C314 - 344
25X-RAY DIFFRACTION25chain 'C' and (resid 345 through 389 )C345 - 389
26X-RAY DIFFRACTION26chain 'C' and (resid 390 through 410 )C390 - 410
27X-RAY DIFFRACTION27chain 'C' and (resid 411 through 439 )C411 - 439

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