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- PDB-7mj1: LarB, a carboxylase/hydrolase involved in synthesis of the cofact... -

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Basic information

Entry
Database: PDB / ID: 7mj1
TitleLarB, a carboxylase/hydrolase involved in synthesis of the cofactor for lactate racemase, in complex with NAD
ComponentsPyridinium-3,5-biscarboxylic acid mononucleotide synthase
KeywordsLYASE (CARBON-CARBON) / Carboxylase / Hydrolase
Function / homology
Function and homology information


pyridinium-3,5-biscarboxylic acid mononucleotide synthase / 'de novo' IMP biosynthetic process / transferase activity / hydrolase activity / plasma membrane
Similarity search - Function
Pyridinium-3,5-biscarboxylic acid mononucleotide synthase / PurE domain / AIR carboxylase / AIR carboxylase
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / Pyridinium-3,5-biscarboxylic acid mononucleotide synthase
Similarity search - Component
Biological speciesLactobacillus plantarum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.402 Å
AuthorsChatterjee, S. / Rankin, J.A. / Lagishetty, S. / Hu, J. / Hausinger, R.P.
Funding support United States, 2items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)CHE-1807073 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM128959 United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2021
Title: The LarB carboxylase/hydrolase forms a transient cysteinyl-pyridine intermediate during nickel-pincer nucleotide cofactor biosynthesis.
Authors: Rankin, J.A. / Chatterjee, S. / Tariq, Z. / Lagishetty, S. / Desguin, B. / Hu, J. / Hausinger, R.P.
History
DepositionApr 19, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 29, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Pyridinium-3,5-biscarboxylic acid mononucleotide synthase
C: Pyridinium-3,5-biscarboxylic acid mononucleotide synthase
D: Pyridinium-3,5-biscarboxylic acid mononucleotide synthase
E: Pyridinium-3,5-biscarboxylic acid mononucleotide synthase
F: Pyridinium-3,5-biscarboxylic acid mononucleotide synthase
B: Pyridinium-3,5-biscarboxylic acid mononucleotide synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)160,48712
Polymers159,0616
Non-polymers1,4266
Water00
1
A: Pyridinium-3,5-biscarboxylic acid mononucleotide synthase
B: Pyridinium-3,5-biscarboxylic acid mononucleotide synthase
hetero molecules

A: Pyridinium-3,5-biscarboxylic acid mononucleotide synthase
B: Pyridinium-3,5-biscarboxylic acid mononucleotide synthase
hetero molecules

A: Pyridinium-3,5-biscarboxylic acid mononucleotide synthase
B: Pyridinium-3,5-biscarboxylic acid mononucleotide synthase
hetero molecules

A: Pyridinium-3,5-biscarboxylic acid mononucleotide synthase
B: Pyridinium-3,5-biscarboxylic acid mononucleotide synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)212,17912
Polymers212,0828
Non-polymers974
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
crystal symmetry operation3_545-y+1/2,x-1/2,z1
crystal symmetry operation4_555y+1/2,-x+1/2,z1
Buried area19720 Å2
ΔGint-206 kcal/mol
Surface area56930 Å2
MethodPISA
2
C: Pyridinium-3,5-biscarboxylic acid mononucleotide synthase
D: Pyridinium-3,5-biscarboxylic acid mononucleotide synthase
hetero molecules

C: Pyridinium-3,5-biscarboxylic acid mononucleotide synthase
D: Pyridinium-3,5-biscarboxylic acid mononucleotide synthase
hetero molecules

C: Pyridinium-3,5-biscarboxylic acid mononucleotide synthase
D: Pyridinium-3,5-biscarboxylic acid mononucleotide synthase
hetero molecules

C: Pyridinium-3,5-biscarboxylic acid mononucleotide synthase
D: Pyridinium-3,5-biscarboxylic acid mononucleotide synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)214,93020
Polymers212,0828
Non-polymers2,84812
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-x,-y-1,z1
crystal symmetry operation3_445-y-1/2,x-1/2,z1
crystal symmetry operation4_545y+1/2,-x-1/2,z1
Buried area25530 Å2
ΔGint-282 kcal/mol
Surface area56280 Å2
MethodPISA
3
E: Pyridinium-3,5-biscarboxylic acid mononucleotide synthase
F: Pyridinium-3,5-biscarboxylic acid mononucleotide synthase
hetero molecules

E: Pyridinium-3,5-biscarboxylic acid mononucleotide synthase
F: Pyridinium-3,5-biscarboxylic acid mononucleotide synthase
hetero molecules

E: Pyridinium-3,5-biscarboxylic acid mononucleotide synthase
F: Pyridinium-3,5-biscarboxylic acid mononucleotide synthase
hetero molecules

E: Pyridinium-3,5-biscarboxylic acid mononucleotide synthase
F: Pyridinium-3,5-biscarboxylic acid mononucleotide synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)214,84116
Polymers212,0828
Non-polymers2,7598
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
crystal symmetry operation3_545-y+1/2,x-1/2,z1
crystal symmetry operation4_555y+1/2,-x+1/2,z1
Buried area26580 Å2
ΔGint-259 kcal/mol
Surface area55780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.445, 120.445, 213.589
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number90
Space group name H-MP4212

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Components

#1: Protein
Pyridinium-3,5-biscarboxylic acid mononucleotide synthase / P2CMN synthase / Lactate racemase accessory protein LarB / Lactate racemase activation protein LarB ...P2CMN synthase / Lactate racemase accessory protein LarB / Lactate racemase activation protein LarB / Lactate racemase maturation protein LarB / Lactate racemization operon protein LarB / Nickel-pincer cofactor biosynthesis protein LarB / Nicotinic acid adenine dinucleotide carboxylase/hydrolase / NaAD carboxylase/hydrolase


Mass: 26510.227 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactobacillus plantarum (bacteria) / Strain: ATCC BAA-793 / NCIMB 8826 / WCFS1 / Gene: larB, lp_0105 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: F9UST0, pyridinium-3,5-biscarboxylic acid mononucleotide synthase
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#4: Chemical ChemComp-NAI / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / NADH


Mass: 665.441 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H29N7O14P2 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

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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: 2.44 Å3/Da / Density % sol: 49.49 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 100 mM magnesium formate, 20% w/v PEG 3350, 2 mM nitrilotriacetic acid neutralized to a pH of ~7.5 with sodium hydroxide, and 0.7 mM zinc sulfate, 10 mM EDTA, 10 mM NAD+ (disodium salt)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.305 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Nov 6, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.305 Å / Relative weight: 1
ReflectionResolution: 3.4→41.762 Å / Num. obs: 20627 / % possible obs: 93.8 % / Redundancy: 4.5 % / CC1/2: 0.992 / Net I/σ(I): 7.6
Reflection shellResolution: 3.4→3.67 Å / Num. unique obs: 3997 / CC1/2: 0.674

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1D7A

1d7a


Resolution: 3.402→41.762 Å / SU ML: 0.47 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 29.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2689 983 4.78 %
Rwork0.2432 19568 -
obs0.2444 20551 92.02 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 306.51 Å2 / Biso mean: 110.678 Å2 / Biso min: 36.82 Å2
Refinement stepCycle: final / Resolution: 3.402→41.762 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8226 0 92 0 8318
Biso mean--116.7 --
Num. residues----1217
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0088479
X-RAY DIFFRACTIONf_angle_d0.87711666
X-RAY DIFFRACTIONf_dihedral_angle_d15.3562747
X-RAY DIFFRACTIONf_chiral_restr0.0511511
X-RAY DIFFRACTIONf_plane_restr0.0061491
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.4023-3.58160.34191410.3176251885
3.5816-3.80580.35211440.3134281495
3.8058-4.09950.30441370.2691273292
4.0995-4.51160.26371360.2324285495
4.5116-5.16340.23291680.2039284895
5.1634-6.50130.26931320.2715286093
6.5013-41.7620.23611250.2142294290
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)
13.12230.22783.34159.9775-0.99719.01590.714-1.67521.2239-0.6115-0.77551.0710.06772.5649-0.24721.27060.02040.7240.7665-0.41171.442445.8762-22.55422.9188
23.428-4.4698-1.14138.81154.47063.3346-1.74141.6189-1.5536-2.44330.9618-0.12272.26171.970.80552.0267-0.09030.54991.6224-0.40341.132244.3443-23.3193-2.2565
33.11051.0511-1.94362.0938-0.31091.2809-0.97611.2117-1.2152-1.795-0.1444-0.10930.9679-0.81570.36082.9957-0.76961.42491.5726-0.79771.389144.0691-18.7903-11.9789
44.683-0.5429-2.33731.6241-0.07951.6544-1.09970.989-1.5161-1.8045-0.8439-0.73030.9335-0.89610.34242.6177-0.6040.88131.54840.09540.279438.4711-14.7414-3.8248
53.0352-1.2193-4.61371.38451.89418.9927-0.7481.786-0.4622-1.504-0.44041.11840.6086-1.811.07710.8641-0.0291-0.16871.1593-0.23050.772732.2673-11.8197.1338
63.3542-0.3588-0.53472.43930.05877.5901-0.06530.00920.4639-0.995-0.00171.0287-0.7962-0.35610.1540.44970.0704-0.0960.637-0.06760.629529.606-3.24815.2863
78.49610.3549-0.82359.9931-0.53169.669-0.19520.48670.76870.5433-0.007-0.6187-0.0387-0.08090.19610.28620.1239-0.12160.5521-0.02050.545740.8697-7.762817.6491
86.9601-0.8586-0.30735.11552.44015.5421-0.65211.5396-0.40740.1574-0.27831.3790.0535-0.6304-0.96050.99240.5676-1.24091.4561-0.26171.7901-4.0532-31.433322.6098
94.8261-0.1001-1.82963.39782.08521.95970.90061.89010.6146-3.3611-0.383-0.46341.7625-0.6722-0.32651.92080.5796-0.47911.5972-0.22720.74323.5972-37.049916.8506
106.3565-0.24743.56356.81542.74378.1220.31830.53990.2095-1.2005-0.7522-0.6275-0.09010.40040.42550.55080.10630.14460.62440.1490.528219.4715-37.612133.9514
115.08192.9368-2.14162.7676-1.47986.9691-0.1481-0.5163-0.36140.3067-0.1550.09810.195-0.52430.2070.29770.06230.03510.73870.0840.51710.9017-42.42540.0297
123.1729-2.8659-1.75872.692.38418.32171.205-1.4103-0.911-0.80591.1366-0.20480.887-0.15881.13141.5349-0.3238-1.23151.90841.06970.581220.5345-40.371167.002
133.2079-0.06611.32683.424-0.88880.75880.4545-1.51620.56851.6172-0.5442-1.62580.2261-1.3653-0.08491.1588-0.680.06391.61760.01141.478320.7287-34.487367.8462
141.78390.4733-1.67181.995-0.29161.57590.0708-2.2337-0.22711.3698-0.2928-0.21390.20810.38690.0861.9015-0.95930.2373.2154-0.1456-0.147511.5818-35.980173.9399
156.19094.26053.8945.59490.96143.58861.78940.47220.30240.745-1.21250.3335-1.35670.7457-0.86490.9614-0.24120.32861.833-0.71851.09857.3339-24.645357.9035
169.16187.8833.87126.76743.35051.64010.28081.03761.0630.32560.25480.73680.14360.9849-0.290.6936-0.12570.06612.1735-0.22051.254.1872-34.336861.1106
171.5427-2.26162.76973.5727-3.46776.12980.5957-0.8596-0.72450.48370.09630.2699-1.0063-0.2335-0.06610.4372-0.2420.15631.1683-0.67291.2122-1.0375-29.046756.4327
182.6324-0.03051.45342.66382.08752.44140.1039-1.63791.2938-0.6658-0.64241.9351-0.3089-0.73760.5740.59470.1403-0.03630.6123-0.44321.3094-5.4038-30.352649.5757
197.42270.9303-1.07625.07350.59637.9853-0.1452-0.1105-0.21120.2921-0.3197-0.14760.44210.65810.39860.26420.0366-0.01180.5573-0.09890.69123.0499-39.03847.9627
208.9856-3.6639-0.55723.77383.12583.64340.02821.7384-0.09110.1060.2757-0.68920.8007-0.5753-0.19691.7448-0.0170.22331.21570.04230.999266.3311-28.55376.9213
213.64683.5481-5.7143.4105-5.51738.975-0.91040.495-1.059-3.37530.2258-0.19461.95030.02740.43251.56490.1760.52760.76250.01611.064361.4901-28.635370.9749
228.2852-4.0795-4.91444.11153.39888.55690.71050.9912-0.0042-1.2762-0.9520.00420.4293-0.55830.48271.26970.08390.05710.7868-0.04720.681449.9246-25.266871.1655
238.79451.5371.37792.6933-2.85067.78320.11250.1016-0.0306-0.7282-0.77241.18621.5212-2.11010.64511.1808-0.32770.2241.2004-0.30370.79538.4409-19.796782.6393
242.6539-0.2622-0.16849.4040.14948.538-0.897-0.59510.1282-0.89430.3287-1.37640.8768-0.22210.57240.739-0.17170.22430.7295-0.16210.88346.4442-16.197490.236
258.06765.106-0.68556.69982.85054.46961.0340.3601-1.57941.7857-0.0793-1.60491.5583-0.0082-0.95121.65280.314-0.22621.5285-0.76651.708940.019322.0466112.8802
265.75922.0328-0.37018.95660.64323.1968-0.1002-1.65340.2414.60180.2637-0.96430.11771.3836-0.13351.80310.3514-0.29811.8554-0.51271.119237.01217.9288121.4259
275.11221.78972.86832.81424.10038.0024-0.22140.3303-0.23781.7018-0.68850.98170.1002-1.88980.82810.89280.18570.22971.3716-0.19870.879129.61412.1603104.4962
288.0956-4.2813-0.85612.67460.95727.03580.2557-0.97240.4114-1.0745-0.2169-0.7615-1.1032-1.23860.09370.92350.1931-0.00010.84-0.17560.787639.4325.261598.7902
290.1485-0.44680.46042.1112-1.63561.41460.86540.11730.3845-0.72840.0173-0.4038-0.85880.4718-1.02531.32110.05850.30411.1711-0.67391.399631.5174-3.862343.6647
306.2953-0.4491-1.1864.8228-2.15237.8652-0.3417-1.93541.77772.0196-0.85410.7731-1.8894-0.8359-0.41670.73130.57150.35451.0722-0.95711.709832.4096-8.158547.8771
314.03653.73720.00869.29321.29863.54440.111-1.53031.13491.51290.04191.441-0.2872-0.40510.39931.32790.2665-0.12971.5219-0.03970.338736.3724-12.402151.6434
322.58960.4876-3.11038.06753.1285.8674-0.9092-0.10590.33570.72660.03321.6540.6440.04480.93970.7878-0.01310.27540.38020.09630.818333.1722-23.378135.8922
338.89520.5963-2.14367.41853.29415.4855-0.1471-1.3659-1.25511.3941-0.3148-0.19180.58780.54980.47330.6180.0850.05860.68450.25740.721842.3227-21.87436.83
342.73030.2364-3.38446.34024.51387.8326-0.9884-0.8807-2.88031.27060.6065-1.63650.85641.2310.38810.7559-0.13540.53150.70680.03022.072346.6942-33.483827.8662
359.11366.39017.44855.96846.8877.92480.0097-0.5521-1.86861.14510.4688-1.3476-0.65750.4175-0.0970.5890.04970.03670.32180.18310.740344.9505-21.886128.7628
366.1062-1.6566-2.31134.0479-2.75146.27361.0088-0.2680.0645-1.2081-0.9797-1.13670.50410.9552-0.14080.7910.11030.25650.39920.13060.703948.8058-19.898125.9657
372.9721-2.1581.02115.5085-6.94362.00290.2403-1.2149-0.45870.5427-0.24010.51940.7372-0.51050.11880.5352-0.02560.06230.6955-0.03650.518153.6185-11.548324.479
388.04931.17811.63076.93250.97796.37940.1374-0.3751-0.5867-0.2382-0.3030.08760.0779-0.75160.12760.523-0.06520.05090.3978-0.08940.488438.0045-14.714427.2061
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 46 through 60 )A46 - 60
2X-RAY DIFFRACTION2chain 'A' and (resid 61 through 84 )A61 - 84
3X-RAY DIFFRACTION3chain 'A' and (resid 85 through 94 )A85 - 94
4X-RAY DIFFRACTION4chain 'A' and (resid 95 through 107 )A95 - 107
5X-RAY DIFFRACTION5chain 'A' and (resid 108 through 141 )A108 - 141
6X-RAY DIFFRACTION6chain 'A' and (resid 142 through 190 )A142 - 190
7X-RAY DIFFRACTION7chain 'A' and (resid 191 through 246 )A191 - 246
8X-RAY DIFFRACTION8chain 'C' and (resid 46 through 75 )C46 - 75
9X-RAY DIFFRACTION9chain 'C' and (resid 76 through 107 )C76 - 107
10X-RAY DIFFRACTION10chain 'C' and (resid 108 through 190 )C108 - 190
11X-RAY DIFFRACTION11chain 'C' and (resid 191 through 246 )C191 - 246
12X-RAY DIFFRACTION12chain 'D' and (resid 46 through 66 )D46 - 66
13X-RAY DIFFRACTION13chain 'D' and (resid 67 through 82 )D67 - 82
14X-RAY DIFFRACTION14chain 'D' and (resid 83 through 107 )D83 - 107
15X-RAY DIFFRACTION15chain 'D' and (resid 108 through 125 )D108 - 125
16X-RAY DIFFRACTION16chain 'D' and (resid 126 through 141 )D126 - 141
17X-RAY DIFFRACTION17chain 'D' and (resid 142 through 156 )D142 - 156
18X-RAY DIFFRACTION18chain 'D' and (resid 157 through 188 )D157 - 188
19X-RAY DIFFRACTION19chain 'D' and (resid 189 through 246 )D189 - 246
20X-RAY DIFFRACTION20chain 'E' and (resid 36 through 58 )E36 - 58
21X-RAY DIFFRACTION21chain 'E' and (resid 59 through 82 )E59 - 82
22X-RAY DIFFRACTION22chain 'E' and (resid 83 through 125 )E83 - 125
23X-RAY DIFFRACTION23chain 'E' and (resid 126 through 177 )E126 - 177
24X-RAY DIFFRACTION24chain 'E' and (resid 178 through 246 )E178 - 246
25X-RAY DIFFRACTION25chain 'F' and (resid 44 through 60 )F44 - 60
26X-RAY DIFFRACTION26chain 'F' and (resid 61 through 106 )F61 - 106
27X-RAY DIFFRACTION27chain 'F' and (resid 107 through 190 )F107 - 190
28X-RAY DIFFRACTION28chain 'F' and (resid 191 through 246 )F191 - 246
29X-RAY DIFFRACTION29chain 'B' and (resid 44 through 66 )B44 - 66
30X-RAY DIFFRACTION30chain 'B' and (resid 67 through 87 )B67 - 87
31X-RAY DIFFRACTION31chain 'B' and (resid 88 through 107 )B88 - 107
32X-RAY DIFFRACTION32chain 'B' and (resid 108 through 125 )B108 - 125
33X-RAY DIFFRACTION33chain 'B' and (resid 126 through 156 )B126 - 156
34X-RAY DIFFRACTION34chain 'B' and (resid 157 through 168 )B157 - 168
35X-RAY DIFFRACTION35chain 'B' and (resid 169 through 180 )B169 - 180
36X-RAY DIFFRACTION36chain 'B' and (resid 181 through 207 )B181 - 207
37X-RAY DIFFRACTION37chain 'B' and (resid 208 through 220 )B208 - 220
38X-RAY DIFFRACTION38chain 'B' and (resid 221 through 246 )B221 - 246

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