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- PDB-36zl: Structure of Bacteroides thetaiotaomicron ATP:cob(I)alamin adenos... -

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Basic information

Entry
Database: PDB / ID: 36zl
TitleStructure of Bacteroides thetaiotaomicron ATP:cob(I)alamin adenosyltransferase (ATR or BtuR, BT2760)bound to cob(II)alamin and ATP
ComponentsCorrinoid adenosyltransferase
KeywordsTRANSFERASE / cobalamin / chaperone / ATP:cob(I)alamin adenosyltransferase
Function / homology
Function and homology information


corrinoid adenosyltransferase / corrinoid adenosyltransferase activity / cobalamin biosynthetic process / ATP binding
Similarity search - Function
Cobalamin adenosyltransferase-like / Corrinoid adenosyltransferase, PduO-type / Cobalamin adenosyltransferase / Cobalamin adenosyltransferase-like superfamily
Similarity search - Domain/homology
TRIPHOSPHATE / ADENOSINE-5'-TRIPHOSPHATE / COBALAMIN / : / Corrinoid adenosyltransferase
Similarity search - Component
Biological speciesBacteroides thetaiotaomicron (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsMascarenhas, R. / Maurya, B.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM143482 United States
CitationJournal: To Be Published
Title: A new role for a B12 chaperone: adenosyltransferase loads cobalamin onto methionine synthase
Authors: Maurya, B. / Mascarenhas, R.
History
DepositionJul 7, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 26, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Corrinoid adenosyltransferase
B: Corrinoid adenosyltransferase
C: Corrinoid adenosyltransferase
D: Corrinoid adenosyltransferase
E: Corrinoid adenosyltransferase
F: Corrinoid adenosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)132,67520
Polymers127,6336
Non-polymers5,04114
Water1,31573
1
A: Corrinoid adenosyltransferase
B: Corrinoid adenosyltransferase
C: Corrinoid adenosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,60311
Polymers63,8173
Non-polymers2,7868
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10980 Å2
ΔGint-71 kcal/mol
Surface area21590 Å2
MethodPISA
2
D: Corrinoid adenosyltransferase
E: Corrinoid adenosyltransferase
F: Corrinoid adenosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,0729
Polymers63,8173
Non-polymers2,2556
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8400 Å2
ΔGint-56 kcal/mol
Surface area20660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.219, 81.857, 111.184
Angle α, β, γ (deg.)90.00, 102.78, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 6 molecules ABCDEF

#1: Protein
Corrinoid adenosyltransferase / Cob(II)alamin adenosyltransferase / Cob(II)yrinic acid a / c-diamide adenosyltransferase / ...Cob(II)alamin adenosyltransferase / Cob(II)yrinic acid a / c-diamide adenosyltransferase / Cobinamide/cobalamin adenosyltransferase


Mass: 21272.240 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides thetaiotaomicron (bacteria)
Gene: BT_2760 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8A443, corrinoid adenosyltransferase

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Non-polymers , 7 types, 87 molecules

#2: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#4: Chemical ChemComp-3PO / TRIPHOSPHATE


Mass: 257.955 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: H5O10P3
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#7: Chemical ChemComp-B12 / COBALAMIN


Mass: 1330.356 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C62H89CoN13O14P / Feature type: SUBJECT OF INVESTIGATION
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 73 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: 2.22 Å3/Da / Density % sol: 44.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 20% PEG 3350, 200 mM Ammonium Chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97872 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 7, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.2→61.65 Å / Num. obs: 55707 / % possible obs: 99 % / Redundancy: 4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.047 / Rpim(I) all: 0.026 / Rrim(I) all: 0.054 / Χ2: 0.83 / Net I/σ(I): 14.6 / Num. measured all: 223730
Reflection shellResolution: 2.2→2.26 Å / % possible obs: 92.1 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.525 / Num. measured all: 12905 / Num. unique obs: 4224 / CC1/2: 0.877 / Rpim(I) all: 0.331 / Rrim(I) all: 0.625 / Χ2: 0.64 / Net I/σ(I) obs: 1.8

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Processing

Software
NameVersionClassification
PHENIX(2.0_5936: ???)refinement
Aimlessdata scaling
PHASERphasing
PDB_EXTRACTdata extraction
autoPROCdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→45.2 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 30.04 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2407 2792 5.02 %
Rwork0.2044 --
obs0.2062 55633 98.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.2→45.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8075 0 163 73 8311
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.018416
X-RAY DIFFRACTIONf_angle_d0.76711467
X-RAY DIFFRACTIONf_dihedral_angle_d16.9983111
X-RAY DIFFRACTIONf_chiral_restr0.0471328
X-RAY DIFFRACTIONf_plane_restr0.0071419
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.240.37061070.36092376X-RAY DIFFRACTION89
2.24-2.280.3431270.31462581X-RAY DIFFRACTION96
2.28-2.320.28051500.29662566X-RAY DIFFRACTION98
2.32-2.370.36961400.30962629X-RAY DIFFRACTION99
2.37-2.420.35751240.28542686X-RAY DIFFRACTION100
2.42-2.480.27231450.25722636X-RAY DIFFRACTION100
2.48-2.540.28321370.23812672X-RAY DIFFRACTION100
2.54-2.610.27361320.23492664X-RAY DIFFRACTION100
2.61-2.690.28971380.23542625X-RAY DIFFRACTION100
2.69-2.770.3011480.23192659X-RAY DIFFRACTION100
2.77-2.870.29431520.23952683X-RAY DIFFRACTION100
2.87-2.990.28551470.24782647X-RAY DIFFRACTION100
2.99-3.120.27771410.22692656X-RAY DIFFRACTION100
3.12-3.290.28121450.22642652X-RAY DIFFRACTION100
3.29-3.490.26491180.22022683X-RAY DIFFRACTION100
3.49-3.760.26891350.19862674X-RAY DIFFRACTION100
3.76-4.140.20031530.16932690X-RAY DIFFRACTION100
4.14-4.740.20451470.16282652X-RAY DIFFRACTION100
4.74-5.970.23541600.19492680X-RAY DIFFRACTION99
5.97-45.20.16981460.16222730X-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)
13.9929-0.6722-0.36194.02280.26763.77220.0970.767-0.123-0.6096-0.14130.56640.64560.14650.04830.71210.0937-0.04010.6924-0.02460.514915.9446.945-13.431
20.9187-0.03270.8090.9433-0.56933.6488-0.1263-0.07410.1376-0.02970.13110.1805-0.0886-0.7171-0.03990.39030.07260.01930.533-0.04020.48717.28612.6365.995
33.3522-4.0246-0.6628.2069-2.05188.83720.2310.7460.84020.3156-0.24531.0392-1.7569-0.765-0.07971.0070.2656-0.09850.74720.09980.79430.81625.48-5.738
40.5943-0.91820.70934.8264-3.32392.47580.3388-0.52370.5082-0.02860.61321.0644-0.2741-1.908-0.78030.53760.22090.02210.9321-0.09560.8133-4.80417.47116.228
55.12161.669-0.43782.33960.04871.96480.3031-0.90680.73360.4844-0.03720.3036-0.3707-0.5757-0.17730.75560.02770.07810.9059-0.15580.63928.26813.26232.433
62.0343-0.28031.00022.3402-1.95894.1382-0.1179-0.48150.2806-0.0056-0.0207-0.3436-0.4585-0.45580.07780.48730.07470.04650.5235-0.11180.529612.83617.65814.669
72.34581.9426-0.96821.9103-1.71153.19310.12330.08790.52470.08880.31720.5414-0.0361-0.8912-0.48171.17150.3533-0.17860.4881-0.03180.98225.54529.9242.902
81.5079-0.37832.03564.1876-3.79155.54670.0643-0.45040.35560.68060.2410.6619-0.9633-0.6882-0.30060.52910.15050.05120.6326-0.1610.60094.38315.08320.989
91.0942-0.1152-0.45330.9237-0.74584.36390.0034-0.69990.13020.46120.0490.07140.0220.47350.13110.49450.01340.03360.6548-0.05370.615114.4310.46921.197
102.0685-0.57211.19643.10160.7242.5782-0.3649-0.8027-0.76721.24120.0688-0.442-1.1652-1.15680.46371.25810.361-0.16351.30330.07251.25498.99428.47419.204
113.0892-2.35240.85095.2491-1.99112.857-0.1456-0.53050.43680.07750.2515-0.1581-0.3093-0.2363-0.13140.49070.02090.01430.5541-0.09570.570421.13115.52720.292
123.0981.3364-0.00840.7217-0.28062.41060.1991-0.65750.04950.1163-0.2082-0.3843-0.1820.67190.03810.4848-0.0834-0.09880.7644-0.03350.491330.86611.50729.117
131.7476-0.10210.78132.4225-0.81212.07560.0618-0.03050.00940.027-0.1845-0.56870.00160.55750.1180.3477-0.01130.00850.54830.00590.550533.23510.46717.706
148.16062.9175-2.54792.8286-4.43038.75581.08881.23870.09890.1964-0.14510.3526-0.13090.5485-0.84020.95690.03290.05451.1036-0.0670.690136.26-5.24410.291
153.8188-2.14132.10436.2645-3.04996.9878-0.3352-0.02480.09130.6884-0.3818-0.5656-0.84651.11430.59070.8341-0.11080.01091.17550.130.942544.16514.75717.208
162.66451.67751.29663.9174-3.40136.8365-0.68160.47450.58850.00370.0705-1.674-1.34221.22640.4630.7529-0.109-0.08160.7550.00211.216839.00723.1957.03
172.46480.18210.78868.0687-1.83372.74760.0480.38-0.07810.2162-0.1135-0.6149-0.04110.37770.10440.42320.03070.03850.5948-0.04770.530727.1298.6796.588
184.046-0.4120.43253.727-0.00715.7860.19040.4161-0.4215-0.3192-0.2106-0.44060.38030.9890.05480.52740.16240.03520.5915-0.08720.569627.887-1.0871.246
196.4701-4.4535-3.00433.08352.14361.7334-0.02550.74271.2786-1.66960.3004-0.7401-0.5358-0.1176-0.08531.37110.020.18851.28050.22781.373542.9516.197-4.881
208.35814.646-4.24392.756-2.07536.8027-0.20470.5809-0.7389-1.1163-0.2518-0.97070.4790.65290.37760.78480.1540.13130.692-0.07720.68225.684-0.001-10.303
212.63771.6722-0.39382.6460.25023.38760.04670.5069-0.2636-0.5582-0.06630.17020.2101-0.45950.02820.5811-0.0198-0.05230.731-0.12780.59265.827-0.444-2.917
222.27891.43480.3652.6037-0.50782.2787-0.09040.36010.0982-0.28220.0285-0.05820.04440.17830.08750.46940.06690.04040.52310.00090.51319.9127.735-1.431
234.47463.77632.59717.2972-2.8227.26720.0892-0.21880.6031-0.64060.17680.76450.1529-0.7026-0.19980.48520.00360.00860.884-0.12120.6787-0.3611.4132.964
243.0518-0.73230.04082.68460.34612.22810.1219-0.1543-0.34310.0449-0.07040.5387-0.0066-0.7919-0.04740.4418-0.0025-0.02320.69090.02030.5072-4.49931.871-27.586
251.6011-0.05940.52932.77620.33812.91320.109-0.0407-0.37610.11110.231-0.05630.54260.0222-0.30520.5566-0.0106-0.03320.6195-0.04370.572912.26916.509-30.379
262.4312-2.21870.05835.62672.41692.35190.05060.24340.20790.07360.3039-0.86560.19040.7469-0.35590.45680.02260.00630.8625-0.07570.590421.41825.782-29.081
273.8046-2.27044.74191.5295-2.24887.80620.76721.7499-0.5517-0.1253-0.5228-0.17190.75561.5489-0.26431.14850.2163-0.13621.34-0.33691.097924.9575.273-45.977
281.7630.41031.24224.36920.0662.78880.11170.488-0.01-0.41550.0923-0.16860.20270.2203-0.10810.56820.00160.03240.8513-0.03970.500713.05621.731-40.673
294.1467-0.50050.08225.93242.46484.8297-0.07690.8911-0.7206-0.6081.0827-0.83440.68670.821-0.95730.60350.0721-0.02990.9048-0.21890.662921.45614.063-37.402
302.218-0.83940.3454.17150.1150.1897-0.20340.14460.161-0.2536-0.0928-1.3825-0.82520.33730.03641.548-0.0169-0.00621.3013-0.54751.46720.591-0.248-47.511
319.74497.54464.01115.83613.06422.1744-0.41371.36690.2786-0.7720.9568-2.1538-1.18150.8379-0.27771.5189-0.0481-0.15651.6928-0.09491.4089-5.18617.348-64.064
320.07240.0439-0.00570.07240.03910.0435-1.41362.07010.53750.1254-0.02390.2667-1.46211.62221.21821.5384-0.2083-0.50162.01710.06881.231-9.44723.854-58.104
332.6599-1.2674-0.2892.4702-1.83475.30880.00470.3711-0.4744-0.30980.25720.92150.6904-1.4035-0.32580.6825-0.2277-0.22340.9222-0.04160.8919-9.7212.277-38.143
341.8248-0.48330.4611.58490.04410.1995-0.76211.43470.0724-2.31950.80070.3137-0.72560.142-0.06051.3425-0.4596-0.17991.4807-0.27020.9246-19.80523.764-44.175
353.40790.40462.67762.4243-0.85246.52490.9248-0.9049-0.5927-0.42960.40181.20061.126-2.3583-1.10840.7488-0.36390.01581.2530.15620.9148-16.11317.751-24.028
362.7077-0.77761.66352.52350.75014.4780.046-0.1346-0.4789-0.1110.18890.23180.465-0.6611-0.28840.504-0.0927-0.04260.69070.08510.5869-1.04418.705-29.855
370.31061.2198-0.97975.3743-4.49443.99540.5491.33010.3065-0.55230.35090.63540.5508-1.76-0.750.72280.1709-0.24961.24280.31951.1757-14.48531.779-43.41
382.85650.4207-0.22833.36780.50323.15070.2618-0.2137-0.5414-0.1346-0.00090.770.5677-0.8562-0.28670.4688-0.1333-0.05410.72770.07560.6648-7.47317.088-26.797
396.9161.22130.17578.0784-1.96587.6906-0.0218-1.1179-0.93690.4826-0.2256-0.90410.36690.24770.19270.6944-0.0279-0.1120.68060.12880.63799.18314.091-18.003
405.26270.16070.60397.13241.11765.56030.49560.9624-0.661-0.8287-0.5188-0.60780.29330.7357-0.09340.7640.0341-0.1031.0042-0.19320.5779.28913.492-49.012
414.1737-0.5532-0.23342.27010.86715.90110.62351.0552-1.4926-0.2521-0.3534-0.24290.72050.2488-0.39741.27320.1637-0.23751.1557-0.39590.96159.12.751-54.279
427.33925.2569-0.8977.0972-0.30271.9935-0.03712.1817-0.5511-0.87280.29870.52171.2483-0.1425-0.2151.2570.0312-0.33011.3014-0.40250.88672.1773.62-64.335
432.22271.58420.54594.32091.74941.14580.39051.008-0.4663-0.3054-0.22290.58110.4738-0.0177-0.14850.9401-0.0874-0.21681.0792-0.27140.7622-3.16910.824-51.784
443.24850.2979-0.92173.69270.15410.45370.08340.6857-0.70360.5722-0.1644-0.1544-0.02110.0073-0.12531.1286-0.2148-0.30311.2622-0.32620.8865-6.1713.96-52.094
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 2:14 )A2 - 14
2X-RAY DIFFRACTION2( CHAIN A AND RESID 15:74 )A15 - 74
3X-RAY DIFFRACTION3( CHAIN A AND RESID 75:84 )A75 - 84
4X-RAY DIFFRACTION4( CHAIN A AND RESID 85:105 )A85 - 105
5X-RAY DIFFRACTION5( CHAIN A AND RESID 106:120 )A106 - 120
6X-RAY DIFFRACTION6( CHAIN A AND RESID 121:145 )A121 - 145
7X-RAY DIFFRACTION7( CHAIN A AND RESID 146:150 )A146 - 150
8X-RAY DIFFRACTION8( CHAIN A AND RESID 151:174 )A151 - 174
9X-RAY DIFFRACTION9( CHAIN A AND RESID 175:183 )A175 - 183
10X-RAY DIFFRACTION10( CHAIN B AND RESID 6:28 )B6 - 28
11X-RAY DIFFRACTION11( CHAIN B AND RESID 29:49 )B29 - 49
12X-RAY DIFFRACTION12( CHAIN B AND RESID 50:105 )B50 - 105
13X-RAY DIFFRACTION13( CHAIN B AND RESID 106:174 )B106 - 174
14X-RAY DIFFRACTION14( CHAIN B AND RESID 175:183 )B175 - 183
15X-RAY DIFFRACTION15( CHAIN C AND RESID 1:20 )C1 - 20
16X-RAY DIFFRACTION16( CHAIN C AND RESID 21:28 )C21 - 28
17X-RAY DIFFRACTION17( CHAIN C AND RESID 29:49 )C29 - 49
18X-RAY DIFFRACTION18( CHAIN C AND RESID 50:74 )C50 - 74
19X-RAY DIFFRACTION19( CHAIN C AND RESID 75:84 )C75 - 84
20X-RAY DIFFRACTION20( CHAIN C AND RESID 85:105 )C85 - 105
21X-RAY DIFFRACTION21( CHAIN C AND RESID 106:120 )C106 - 120
22X-RAY DIFFRACTION22( CHAIN C AND RESID 121:174 )C121 - 174
23X-RAY DIFFRACTION23( CHAIN C AND RESID 175:186 )C175 - 186
24X-RAY DIFFRACTION24( CHAIN D AND RESID 3:28 )D3 - 28
25X-RAY DIFFRACTION25( CHAIN D AND RESID 29:74 )D29 - 74
26X-RAY DIFFRACTION26( CHAIN D AND RESID 75:105 )D75 - 105
27X-RAY DIFFRACTION27( CHAIN D AND RESID 106:120 )D106 - 120
28X-RAY DIFFRACTION28( CHAIN D AND RESID 121:150 )D121 - 150
29X-RAY DIFFRACTION29( CHAIN D AND RESID 151:174 )D151 - 174
30X-RAY DIFFRACTION30( CHAIN D AND RESID 175:182 )D175 - 182
31X-RAY DIFFRACTION31( CHAIN E AND RESID 10:14 )E10 - 14
32X-RAY DIFFRACTION32( CHAIN E AND RESID 15:28 )E15 - 28
33X-RAY DIFFRACTION33( CHAIN E AND RESID 29:74 )E29 - 74
34X-RAY DIFFRACTION34( CHAIN E AND RESID 75:90 )E75 - 90
35X-RAY DIFFRACTION35( CHAIN E AND RESID 91:105 )E91 - 105
36X-RAY DIFFRACTION36( CHAIN E AND RESID 106:145 )E106 - 145
37X-RAY DIFFRACTION37( CHAIN E AND RESID 146:150 )E146 - 150
38X-RAY DIFFRACTION38( CHAIN E AND RESID 151:174 )E151 - 174
39X-RAY DIFFRACTION39( CHAIN E AND RESID 175:185 )E175 - 185
40X-RAY DIFFRACTION40( CHAIN F AND RESID 28:49 )F28 - 49
41X-RAY DIFFRACTION41( CHAIN F AND RESID 50:74 )F50 - 74
42X-RAY DIFFRACTION42( CHAIN F AND RESID 75:105 )F75 - 105
43X-RAY DIFFRACTION43( CHAIN F AND RESID 106:150 )F106 - 150
44X-RAY DIFFRACTION44( CHAIN F AND RESID 151:183 )F151 - 183

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