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- PDB-3rrl: Complex structure of 3-oxoadipate coA-transferase subunit A and B... -

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Basic information

Entry
Database: PDB / ID: 3rrl
TitleComplex structure of 3-oxoadipate coA-transferase subunit A and B from Helicobacter pylori 26695
Components
  • Succinyl-CoA:3-ketoacid-coenzyme A transferase subunit A
  • Succinyl-CoA:3-ketoacid-coenzyme A transferase subunit B
KeywordsTRANSFERASE / MCSG / PSI-biology / Structural Genomics / Midwest Center for Structural Genomics / 3-oxoadipate coA-transferase subunit A and B
Function / homology
Function and homology information


3-oxoacid CoA-transferase / succinyl-CoA:3-oxo-acid CoA-transferase activity / CoA-transferase activity
Similarity search - Function
3-oxoacid CoA-transferase, subunit A / Coenzyme A transferase active site / Coenzyme A transferases signature 2. / Coenzyme A transferase binding site / 3-oxoacid CoA-transferase, subunit B / Coenzyme A transferases signature 1. / Glutaconate Coenzyme A-transferase / Glutaconate Coenzyme A-transferase / Coenzyme A transferase family I / Coenzyme A transferase ...3-oxoacid CoA-transferase, subunit A / Coenzyme A transferase active site / Coenzyme A transferases signature 2. / Coenzyme A transferase binding site / 3-oxoacid CoA-transferase, subunit B / Coenzyme A transferases signature 1. / Glutaconate Coenzyme A-transferase / Glutaconate Coenzyme A-transferase / Coenzyme A transferase family I / Coenzyme A transferase / Coenzyme A transferase / NagB/RpiA transferase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Succinyl-CoA:3-ketoacid coenzyme A transferase subunit A / Succinyl-CoA:3-ketoacid coenzyme A transferase subunit B
Similarity search - Component
Biological speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.29 Å
AuthorsNocek, B. / Stein, A. / Marshall, N. / Jedrzejczak, R. / Babnigg, G. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: TO BE PUBLISHED
Title: Complex structure of 3-oxoadipate coA-transferase subunit A and B from Helicobacter pylori 26695
Authors: Nocek, B. / Stein, A. / Marshall, N. / Jedrzejczak, R. / Babnigg, G. / Joachimiak, A.
History
DepositionApr 29, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 29, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jan 11, 2012Group: Structure summary
Revision 1.3Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Succinyl-CoA:3-ketoacid-coenzyme A transferase subunit A
B: Succinyl-CoA:3-ketoacid-coenzyme A transferase subunit B
C: Succinyl-CoA:3-ketoacid-coenzyme A transferase subunit A
D: Succinyl-CoA:3-ketoacid-coenzyme A transferase subunit B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,2185
Polymers97,1264
Non-polymers921
Water4,414245
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12500 Å2
ΔGint-76 kcal/mol
Surface area31640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)156.392, 65.705, 104.740
Angle α, β, γ (deg.)90.00, 109.81, 90.00
Int Tables number5
Space group name H-MC121
Detailsheterotetramer

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Components

#1: Protein Succinyl-CoA:3-ketoacid-coenzyme A transferase subunit A / Succinyl CoA:3-oxoacid CoA-transferase / OXCT A


Mass: 25806.244 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (bacteria) / Strain: 2669 / Gene: scoA, HP_0691 / Production host: Escherichia coli (E. coli) / References: UniProt: P56006, 3-oxoacid CoA-transferase
#2: Protein Succinyl-CoA:3-ketoacid-coenzyme A transferase subunit B / OXCT B / Succinyl CoA:3-oxoacid CoA-transferase


Mass: 22756.857 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (bacteria) / Strain: 2669 / Gene: scoB, HP_0692 / Production host: Escherichia coli (E. coli) / References: UniProt: P56007, 3-oxoacid CoA-transferase
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 245 / Source method: isolated from a natural source / Formula: H2O
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: 2.61 Å3/Da / Density % sol: 52.81 %
Crystal growpH: 5.5
Details: Sodium Citrate 20 % Peg 3000, pH 5.5, VAPOR DIFFUSION, SITTING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 20, 2010 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.288→40 Å / Num. obs: 44755 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Rmerge(I) obs: 0.124 / Net I/σ(I): 13
Reflection shellResolution: 2.3→2.34 Å / % possible all: 100

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
PHENIXmodel building
MOLREPphasing
HKL-3000phasing
PHENIX(phenix.refine: 1.7_650)refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.29→39.3 Å / SU ML: 0.3 / σ(F): 1.34 / Phase error: 22.53 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.217 2260 5.05 %
Rwork0.176 --
obs0.178 44743 98.5 %
all-47003 -
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40 Å2 / ksol: 0.33 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--3.7338 Å20 Å21.6836 Å2
2--9.5011 Å2-0 Å2
3----5.9389 Å2
Refinement stepCycle: LAST / Resolution: 2.29→39.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6453 0 6 245 6704
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0056557
X-RAY DIFFRACTIONf_angle_d1.0198858
X-RAY DIFFRACTIONf_dihedral_angle_d12.5142381
X-RAY DIFFRACTIONf_chiral_restr0.0781037
X-RAY DIFFRACTIONf_plane_restr0.0041137
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2876-2.36940.30722140.25393695X-RAY DIFFRACTION87
2.3694-2.46420.26472120.22114261X-RAY DIFFRACTION100
2.4642-2.57640.25082160.21384290X-RAY DIFFRACTION100
2.5764-2.71220.29062240.2094297X-RAY DIFFRACTION100
2.7122-2.88210.2682240.20084294X-RAY DIFFRACTION100
2.8821-3.10450.25592470.19994300X-RAY DIFFRACTION100
3.1045-3.41680.24562360.1934303X-RAY DIFFRACTION100
3.4168-3.91080.19412360.16674304X-RAY DIFFRACTION100
3.9108-4.92570.16222240.12184322X-RAY DIFFRACTION100
4.9257-39.30870.18162270.16744417X-RAY DIFFRACTION99
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)
10.16930.0214-0.05430.8331-0.17030.05330.0710.1408-0.0355-0.3175-0.12370.00870.32460.46010.05960.4063-0.03040.02410.5597-0.12390.223435.6651-3.4685-2.2507
21.42060.71960.19750.8317-0.06470.09340.01710.1587-0.0021-0.2012-0.04190.19210.1854-0.27740.0030.2954-0.0715-0.0270.2597-0.06610.236622.4503-4.90339.3897
31.32071.65411.16682.78950.93261.4819-0.1339-0.0620.27910.0231-0.040.43730.163-0.76390.18620.2992-0.1002-0.01470.4262-0.03820.380714.7443-3.190214.4561
43.1872.7331-2.05012.7725-1.43222.89320.02310.30640.78280.00950.57480.63370.0997-1.334-0.57830.5606-0.19020.22851.2747-0.18190.70288.7985-6.299320.379
50.6905-0.4388-0.12730.3409-0.12820.7423-0.08640.01630.16880.11570.113-0.21610.0007-0.03770.00530.2297-0.00480.02440.1767-0.00650.210825.95630.798925.2189
60.28520.26910.06720.25550.06830.01450.0127-0.0571-0.14050.0729-0.0147-0.05470.2537-0.00020.01470.26210.04710.02550.17520.03230.162230.81420.88932.5901
71.35810.5244-0.56641.911-0.18470.43040.28-0.65890.05170.3118-0.13370.07440.24490.2048-0.15730.3797-0.05860.04050.3456-0.00310.236932.13521.844741.2779
80.6042-0.0841-0.26960.15990.54091.82540.10990.0515-0.17220.03630.0747-0.040.2715-0.0963-0.17120.2826-0.0261-0.02290.206-0.06220.277330.9204-0.389314.2088
90.51880.1307-0.24670.4827-0.02790.63140.15690.1776-0.0334-0.0678-0.11160.09360.18630.0069-0.01260.20540.04380.00060.2278-0.04610.146832.90445.61248.9202
100.1533-0.10070.24290.2622-0.14340.40340.2290.12410.0891-0.1229-0.2462-0.08360.0607-0.12830.01460.31040.02240.03460.53570.0680.19441.015513.12260.9309
111.07560.18970.0050.20.24050.3433-0.04250.0945-0.1041-0.1322-0.13540.0924-0.095-0.11990.17730.27190.0253-0.00230.342-0.04020.216336.18553.28694.9836
120.2202-0.1909-0.05610.23740.03790.0372-0.0072-0.0884-0.1065-0.0554-0.01530.11810.0277-0.014-0.02010.27660.2317-0.08820.5585-0.0550.283914.555315.01936.398
131.51720.1563-0.30775.03570.37110.62260.07840.175-0.0837-0.012-0.1374-0.1534-0.2714-0.31480.01070.3340.1357-0.00680.3799-0.1050.29189.722428.157633.181
140.861-0.3498-0.26530.2265-0.26561.83380.03320.07080.1543-0.3774-0.0862-0.3721-0.5644-0.15640.04130.28460.04390.05550.1938-0.02520.283618.283725.403327.4387
151.73820.74510.40081.5952-0.16211.96180.17850.0509-0.22460.09270.1832-0.1184-0.2774-0.2097-0.31980.24210.07580.01340.21870.01520.217723.435424.594922.3408
160.2223-0.10090.13160.1127-0.04640.09690.09920.263-0.0578-0.0977-0.08480.008-0.00180.0243-0.01470.45160.3683-0.10580.6538-0.01810.301615.949325.21048.6093
170.30180.25570.18510.81160.21720.4450.12750.1379-0.0797-0.0215-0.12720.1094-0.0644-0.2286-0.00120.18790.0837-0.00770.2122-0.01780.182925.890917.692820.0822
180.0912-0.06780.07660.0551-0.06140.0722-0.13870.0035-0.00120.1087-0.08830.16090.26390.04030.16720.3463-0.00410.09130.2452-0.09820.315913.204211.683838.5498
190.26620.07110.42882.20230.71241.1977-0.08390.19050.0645-0.1243-0.12050.1010.0034-0.40060.20640.2348-0.00420.08130.3383-0.06850.282915.995710.803333.0853
201.91161.12270.98620.84180.41820.7823-0.0914-0.48560.7337-0.0942-0.19270.62420.1203-0.78890.29410.3029-0.10450.04850.4611-0.20150.56741.56613.489141.2458
210.11290.06410.13050.12430.07480.162-0.0914-0.0446-0.0369-0.0349-0.10110.08180.0056-0.17870.07230.23880.00290.09710.3039-0.11270.287413.485616.320841.7436
220.4869-0.50350.99191.3878-0.79542.55630.3658-0.5096-0.3623-0.0543-0.481-0.02470.01040.0590.11470.30320.06560.03790.542-0.01590.466917.406618.94150.5533
231.668-0.72331.11591.8559-0.53791.0002-0.0698-0.07550.1141-0.2039-0.1255-0.1161-0.0445-0.08790.16250.33270.03970.0870.2897-0.11320.35595.639229.633345.4426
240.3837-0.3686-0.18270.44650.20030.0928-0.1766-0.065-0.01580.22570.1221-0.02220.265-0.07660.05740.3909-0.09580.17310.328-0.17050.3315.549421.631851.0281
250.10140.03480.0020.03320.04460.08890.0887-0.00380.09820.07770.03870.1438-0.07880.0266-0.10150.6887-0.1698-0.07030.20960.04620.474142.389236.445325.4415
260.19730.06470.19370.249-0.25760.64020.1188-0.20540.03770.3677-0.2815-0.0851-0.33660.14450.10960.3444-0.1631-0.08910.33760.04850.190852.244125.338430.9402
270.02910.04020.04370.04740.05280.05310.0166-0.06640.0410.0674-0.0045-0.0654-0.0340.035-0.00480.3474-0.3481-0.19130.3670.01720.221656.588326.890235.9885
280.0224-0.00780.01830.0053-0.01140.0122-0.04-0.02120.06160.0052-0.0401-0.0731-0.11610.16720.00530.1358-0.3086-0.34940.7220.15140.104961.291119.386632.6112
290.2078-0.10990.01890.26310.10340.813-0.11510.13010.14740.00650.086-0.0451-0.0445-0.12130.00350.40330.0625-0.06351.07340.40680.855566.478412.484533.2571
300.04550.13370.14470.58520.62220.6806-0.0267-0.0523-0.0348-0.1111-0.2-0.0975-0.1968-0.05370.08360.2431-0.002-0.03170.33750.13460.202551.55088.320832.0017
310.22640.2993-0.00590.42460.11180.4378-0.13530.01870.1326-0.0315-0.05310.1181-0.04950.14890.01890.230.08920.02050.18460.13360.153945.69180.988833.1793
322.563-0.9497-0.50932.5456-1.60721.99020.0131-0.3732-0.3653-0.15770.03430.17850.06630.2064-0.060.32560.11170.01490.27410.07980.253944.2257-4.305435.3966
331.01790.41350.86440.44710.64382.23020.11260.01950.21220.2079-0.2163-0.07-0.09030.24930.13950.2675-0.041-0.00510.20880.05520.236445.682422.054121.5053
340.85-0.16090.36690.0924-0.05640.16190.06330.08390.02260.51340.12330.2989-0.39240.0244-0.15460.3895-0.0979-0.01850.19280.00960.237241.329420.928731.2879
350.8858-0.1693-0.41140.42650.01890.19940.18490.33730.0913-0.0981-0.17860.0647-0.16930.0681-0.05080.3719-0.0353-0.00050.24250.1190.231940.982228.824814.9582
360.26130.1747-0.16550.4691-0.12350.381-0.13610.0059-0.09590.0424-0.0471-0.0201-0.27610.44970.06570.2806-0.12780.00990.39220.09960.263351.701824.237117.6011
370.3205-0.8768-0.09913.00331.61833.03410.2697-0.77410.26110.0361-0.3086-0.5981-0.0130.98160.05210.27320.05230.01720.57540.00950.369468.8904-7.74348.2532
382.3009-0.2348-0.99880.8564-0.22310.5695-0.05570.40460.2173-0.2559-0.155-0.0696-0.0268-0.19080.19250.25260.08460.01360.44860.04940.235559.2085-3.10588.2155
394.64161.9733-0.04881.5586-0.19090.0408-0.0824-0.26820.2273-0.03450.6725-0.10330.3990.091-0.58890.43060.05130.06411.0387-0.04280.288256.3458-2.29960.2667
400.1496-0.01830.02290.02620.01790.02230.07340.06320.1104-0.0746-0.0588-0.0926-0.03110.03710.03660.1340.07010.03990.38390.11850.231956.7959.63348.6757
410.4753-0.266-0.42830.34320.30370.40550.0770.3220.14380.0066-0.3263-0.2102-0.0510.25580.20170.18-0.0195-0.02190.38170.13760.247254.21512.774511.7324
421.1483-0.75510.40740.588-0.21540.4572-0.16180.0473-0.14810.01250.0040.11530.0315-0.01160.13690.21120.04630.03220.20190.04760.211255.0844-4.764120.261
430.0686-0.09420.00990.142-0.02760.01520.00130.0430.01720.03750.0596-0.0483-0.0037-0.0239-0.0123-0.03280.0779-0.13890.57320.16580.219465.0572-0.333430.5856
442.20360.31310.44760.7771-0.75451.37010.02090.0065-0.12280.15920.1025-0.0008-0.211-0.0742-0.13320.35280.14770.06060.40220.10710.335956.5715-5.462720.5127
454.80622.09013.46473.11033.02443.7541-0.26790.5145-0.47780.03290.5279-0.0842-0.10930.6956-0.28390.31550.1694-0.02320.72960.0160.398376.4967-9.501523.1631
460.64970.9714-0.14961.6594-0.00591.2579-0.1677-0.03980.10550.11910.20110.20950.1852-0.1145-0.06410.24760.09340.02170.38840.15520.258763.3842-10.88930.2537
470.2890.1851-0.44310.5324-0.11550.7710.22310.19720.1034-0.1080.00090.25420.1629-0.0457-0.28330.34780.1237-0.00720.4306-0.05020.468466.3555-18.400716.0033
482.5501-1.9197-1.5661.77791.37341.6167-0.3802-0.1467-0.93680.1853-0.24390.41260.58250.13950.52940.63710.2098-0.03380.40480.0340.613169.9778-22.901320.448
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 1:9)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 10:56)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 57:81)
4X-RAY DIFFRACTION4(CHAIN A AND RESID 82:93)
5X-RAY DIFFRACTION5(CHAIN A AND RESID 94:108)
6X-RAY DIFFRACTION6(CHAIN A AND RESID 109:128)
7X-RAY DIFFRACTION7(CHAIN A AND RESID 129:143)
8X-RAY DIFFRACTION8(CHAIN A AND RESID 144:158)
9X-RAY DIFFRACTION9(CHAIN A AND RESID 159:190)
10X-RAY DIFFRACTION10(CHAIN A AND RESID 191:202)
11X-RAY DIFFRACTION11(CHAIN A AND RESID 203:217)
12X-RAY DIFFRACTION12(CHAIN A AND RESID 218:230)
13X-RAY DIFFRACTION13(CHAIN B AND RESID 1:13)
14X-RAY DIFFRACTION14(CHAIN B AND RESID 14:32)
15X-RAY DIFFRACTION15(CHAIN B AND RESID 33:49)
16X-RAY DIFFRACTION16(CHAIN B AND RESID 50:58)
17X-RAY DIFFRACTION17(CHAIN B AND RESID 59:96)
18X-RAY DIFFRACTION18(CHAIN B AND RESID 97:112)
19X-RAY DIFFRACTION19(CHAIN B AND RESID 113:140)
20X-RAY DIFFRACTION20(CHAIN B AND RESID 141:152)
21X-RAY DIFFRACTION21(CHAIN B AND RESID 153:176)
22X-RAY DIFFRACTION22(CHAIN B AND RESID 177:182)
23X-RAY DIFFRACTION23(CHAIN B AND RESID 183:192)
24X-RAY DIFFRACTION24(CHAIN B AND RESID 193:207)
25X-RAY DIFFRACTION25(CHAIN C AND RESID 1:7)
26X-RAY DIFFRACTION26(CHAIN C AND RESID 8:34)
27X-RAY DIFFRACTION27(CHAIN C AND RESID 35:50)
28X-RAY DIFFRACTION28(CHAIN C AND RESID 51:76)
29X-RAY DIFFRACTION29(CHAIN C AND RESID 77:92)
30X-RAY DIFFRACTION30(CHAIN C AND RESID 93:108)
31X-RAY DIFFRACTION31(CHAIN C AND RESID 109:128)
32X-RAY DIFFRACTION32(CHAIN C AND RESID 129:147)
33X-RAY DIFFRACTION33(CHAIN C AND RESID 148:179)
34X-RAY DIFFRACTION34(CHAIN C AND RESID 180:185)
35X-RAY DIFFRACTION35(CHAIN C AND RESID 186:201)
36X-RAY DIFFRACTION36(CHAIN C AND RESID 202:230)
37X-RAY DIFFRACTION37(CHAIN D AND RESID 1:9)
38X-RAY DIFFRACTION38(CHAIN D AND RESID 10:32)
39X-RAY DIFFRACTION39(CHAIN D AND RESID 33:38)
40X-RAY DIFFRACTION40(CHAIN D AND RESID 39:57)
41X-RAY DIFFRACTION41(CHAIN D AND RESID 58:83)
42X-RAY DIFFRACTION42(CHAIN D AND RESID 84:107)
43X-RAY DIFFRACTION43(CHAIN D AND RESID 108:122)
44X-RAY DIFFRACTION44(CHAIN D AND RESID 123:139)
45X-RAY DIFFRACTION45(CHAIN D AND RESID 140:150)
46X-RAY DIFFRACTION46(CHAIN D AND RESID 151:163)
47X-RAY DIFFRACTION47(CHAIN D AND RESID 164:194)
48X-RAY DIFFRACTION48(CHAIN D AND RESID 195:207)

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