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- PDB-3klz: Pentameric formate channel with formate bound -

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Basic information

Entry
Database: PDB / ID: 3klz
TitlePentameric formate channel with formate bound
ComponentsPutative formate transporter 1
KeywordsMEMBRANE PROTEIN / channel / formate / Structural Genomics / PSI-2 / Protein Structure Initiative / New York Consortium on Membrane Protein Structure / NYCOMPS
Function / homology
Function and homology information


formate transport / formate transmembrane transporter activity / identical protein binding / plasma membrane
Similarity search - Function
Formate transporter FocA, putative / Formate and nitrite transporters signature 1. / Formate and nitrite transporters signature 2. / Formate/nitrite transporter / Formate/nitrite transporter, conserved site / Formate/nitrite transporter / Glycerol uptake facilitator protein / Glycerol uptake facilitator protein. / Aquaporin-like / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
FORMIC ACID / Formate transporter 1, putative
Similarity search - Component
Biological speciesVibrio cholerae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.5 Å
AuthorsWaight, A.B. / Wang, D.N. / New York Consortium on Membrane Protein Structure (NYCOMPS)
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2010
Title: Structure and mechanism of a pentameric formate channel
Authors: Waight, A.B. / Love, J. / Wang, D.N.
History
DepositionNov 9, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 15, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 29, 2020Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Structure summary
Category: chem_comp / database_PDB_caveat ...chem_comp / database_PDB_caveat / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _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: Putative formate transporter 1
B: Putative formate transporter 1
C: Putative formate transporter 1
D: Putative formate transporter 1
E: Putative formate transporter 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)158,77458
Polymers152,8865
Non-polymers5,88853
Water4,089227
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area30840 Å2
ΔGint-163 kcal/mol
Surface area44750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.779, 100.456, 192.955
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Putative formate transporter 1


Mass: 30577.186 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae (bacteria) / Gene: VC_1695 / Plasmid: pBAD / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q9KRE7
#2: Sugar
ChemComp-BOG / octyl beta-D-glucopyranoside / Beta-Octylglucoside / octyl beta-D-glucoside / octyl D-glucoside / octyl glucoside / Octyl glucoside


Type: D-saccharide / Mass: 292.369 Da / Num. of mol.: 14
Source method: isolated from a genetically manipulated source
Formula: C14H28O6 / Comment: detergent*YM
IdentifierTypeProgram
b-octylglucosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#3: Chemical...
ChemComp-FMT / FORMIC ACID / Formic acid


Mass: 46.025 Da / Num. of mol.: 39 / Source method: obtained synthetically / Formula: CH2O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 227 / Source method: isolated from a natural source / Formula: H2O

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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: 3.16 Å3/Da / Density % sol: 61.11 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.02M MOPS, PH 6.8, 29% (W/V) PEG 550MME, 120MM SODIUM FORMATE, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.9795
DetectorType: ADSC / Detector: CCD / Date: Apr 24, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 62189 / Redundancy: 7.3 % / Rsym value: 0.17 / Net I/σ(I): 14.6

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.5_2)refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.5→48.24 Å / SU ML: 0.31 / σ(F): 0.15 / Phase error: 19.44 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.223 1921 3 %
Rwork0.173 --
obs0.175 62180 94.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 69.19 Å2 / ksol: 0.31 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.3689 Å20 Å2-0 Å2
2--4.1167 Å2-0 Å2
3----2.7478 Å2
Refinement stepCycle: LAST / Resolution: 2.5→48.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9822 0 397 227 10446
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00810416
X-RAY DIFFRACTIONf_angle_d1.02614043
X-RAY DIFFRACTIONf_dihedral_angle_d17.5933715
X-RAY DIFFRACTIONf_chiral_restr0.0731683
X-RAY DIFFRACTIONf_plane_restr0.0041643
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.56250.22621310.17274140X-RAY DIFFRACTION89
2.5625-2.63180.22311260.15524186X-RAY DIFFRACTION90
2.6318-2.70920.22481350.1464285X-RAY DIFFRACTION93
2.7092-2.79670.22131340.14414302X-RAY DIFFRACTION93
2.7967-2.89660.19521410.14564416X-RAY DIFFRACTION95
2.8966-3.01260.21531360.14014460X-RAY DIFFRACTION96
3.0126-3.14970.21461380.1514517X-RAY DIFFRACTION97
3.1497-3.31570.22461440.14784535X-RAY DIFFRACTION98
3.3157-3.52340.18531430.15994588X-RAY DIFFRACTION98
3.5234-3.79530.23541110.16953676X-RAY DIFFRACTION78
3.7953-4.1770.21191410.16194682X-RAY DIFFRACTION99
4.177-4.7810.18881450.15484708X-RAY DIFFRACTION99
4.781-6.02170.21861440.18264744X-RAY DIFFRACTION99
6.0217-48.24770.26951520.22724942X-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)
10.08640.0316-0.11890.1852-0.04730.17210.3140.09870.0037-0.46370.978-0.2384-0.1989-0.1107-0.00090.8166-0.01340.23321.00340.22530.416974.327493.310285.1424
20.0324-0.0680.12830.1233-0.24650.44890.03620.0337-0.03950.097-0.07910.1831-0.1478-0.1446-00.252-0.01470.00890.26330.04750.228656.776977.180498.3519
30.8699-0.24120.71470.67040.52791.44150.150.45870.2070.20060.01420.13610.0154-0.3567-0.00010.16750.0199-0.00090.2344-0.02830.246656.802574.8467107.1288
40.0277-0.0396-0.00080.11320.09520.16261.0033-0.41870.1954-0.97581.1684-1.115-0.43521.36330.01020.7099-0.4635-0.03950.8643-0.27191.109771.031793.5744105.3286
50.0237-0.04930.01890.1228-0.05830.03430.13810.13970.7862-0.67450.95860.44530.0160.51730.00811.4825-0.71220.59871.208-0.41761.792875.552100.7641102.5024
60.0450.0121-0.10190.1457-0.08480.456-0.0209-0.0688-0.0024-1.0108-0.26690.0621-1.32152.53260.01150.7237-0.41370.17551.00010.03850.880168.791797.949996.8131
71.3249-0.74910.25930.5298-0.17181.80880.01090.17120.0568-0.0472-0.11410.0751-0.1591-0.0687-00.1684-0.0117-0.02420.24920.07340.193650.535282.5766101.4371
83.9625-5.2478-3.29718.54744.72753.6711-0.1319-1.05351.1984-0.46961.188-1.7002-0.58341.37740.22340.2727-0.07620.0830.44130.02820.429975.527178.5129110.3209
91.7451-0.86510.0061.1145-0.41331.61530.09380.30660.1422-0.0047-0.01260.0583-0.161-0.1997-00.1699-0.01220.00080.2170.07070.187148.770982.3435102.2403
102.46180.14692.00290.8441-0.52753.13251.45271.0992-0.60710.3765-1.426-1.31360.07422.17570.0050.6367-0.2942-0.14710.71060.15480.646573.957794.1324115.7877
112.19090.47010.3693.7932-5.20037.6146-0.1659-0.4990.25880.37120.70150.0596-1.23090.21150.19080.4961-0.4421-0.34651.0028-0.02251.092281.638597.417128.5593
120.8167-0.991-0.01441.23510.23821.01290.0564-0.39270.1122-0.0593-0.2459-0.1632-0.0771-0.011900.183-0.0241-0.02460.13280.01320.189361.127382.1531124.3157
131.1758-1.1765-0.61263.2651-0.41732.41430.0877-0.06940.42270.1476-0.0070.4789-0.04740.01070.00410.13740.002-0.00640.10930.00840.085759.749672.4266124.3377
140.0881-0.15480.00930.3204-0.20580.73880.4678-1.3184-0.44691.0391-0.15720.27271.32990.7133-0.03230.68420.1951-0.17290.75930.1991.036874.271280.5489134.2738
150.4190.08210.03430.17250.08370.03940.65750.1507-0.6239-1.76750.5787-1.4655-0.5942-0.6801-0.02051.2594-0.1498-0.41431.5007-0.4911.510985.567386.6378139.8587
160.30840.22290.06910.21990.11270.0837-1.0951-0.4290.37250.5476-0.9424-0.3931-0.52910.46830.01410.9901-0.0905-0.19941.26-0.06460.45676.680288.7368138.5214
171.2006-0.7144-0.72030.6419-0.10511.5441-0.0892-0.11490.12930.19240.1030.0557-0.2919-0.04820.00040.21250.0011-0.04690.0788-0.05430.201956.602581.4912131.8091
180.2937-0.1929-0.4560.9807-0.05841.2963-0.115-0.253-0.7817-0.0083-0.2784-1.4838-0.10961.5911-0.09010.1937-0.0581-0.05220.48510.04960.50579.79569.0824124.8353
190.7847-0.2527-0.46780.40220.36581.4065-0.0428-0.08370.11170.1433-0.06190.1445-0.137-0.1087-0.02050.1679-0.0302-0.01560.0919-0.0540.173455.090480.5827132.4257
200.9117-0.5591-0.27920.50.470.66970.5125-0.12481.5715-0.3265-0.5294-1.2653-1.69380.37340.03460.46010.0069-0.09590.85880.18860.569383.667969.3706141.14
211.27510.123-0.25440.0785-0.09230.11950.3546-0.4425-0.2569-0.1350.82210.23820.11760.58750.00341.02110.09550.21361.4289-0.26371.900494.508258.4225147.4215
220.692-0.2759-0.79180.62060.66282.3973-0.0003-0.3709-0.27940.1920.02710.04870.10650.08690.0210.10910.0350.01250.04670.08920.101366.524457.5133132.7958
235.4429-4.0636-0.37353.05720.49292.03320.33140.1339-1.3304-1.8856-0.31450.16361.03870.22770.07141.13420.20740.40121.4307-0.11860.406678.886148.0648134.3767
240.13580.18870.03250.5221-0.10360.1056-0.78680.1068-0.59090.023-0.55690.00990.70730.03170.01060.71320.176-0.38312.07470.3011.472490.043542.6067134.6276
250.06890.0219-0.0270.008-0.00860.00940.11810.3360.04760.5197-0.3720.5345-0.7518-0.77090.00821.03760.0445-1.03991.65060.44612.640291.304342.7859142.7624
260.2761-0.06940.06570.0185-0.0180.02060.0623-0.9173-0.8851-1.05660.2955-0.09130.39470.73840.00130.710.005-0.12250.75540.38220.980383.917746.0362143.1434
271.53891.1673-0.58010.8545-0.43352.038-0.0443-0.1545-0.1960.2341-0.0668-0.02990.16550.0896-0.00030.2670.0451-0.00310.17710.04820.17162.556352.092139.4345
280.0669-0.010.1210.34630.00080.2568-0.22160.2015-0.3516-0.3284-0.1074-1.03230.41890.6851-0.0030.23820.06420.02230.36120.02330.37977.851655.8934119.4446
291.9498-0.3914-0.36081.6188-1.31391.38050.1151-0.23140.00070.1108-0.0120.1173-0.0748-0.1130.00130.16350.00270.00290.11940.05950.160260.148349.8345141.1325
300.2371-0.068-0.01860.02230.01320.0594-0.0342-0.6752-0.9340.07770.7321-1.12940.13761.7608-0.00360.67330.119-0.08421.17570.05930.995387.234736.0638122.5936
310.3652-0.37070.03271.029-0.41011.2962-0.08250.2672-1.0755-0.3451-0.16370.32150.62940.1128-0.00080.36490.12640.15370.15240.01160.387669.659637.6604117.3813
321.3657-0.91071.7950.9959-1.03932.41790.0368-1.3319-0.20960.70610.14961.03680.0404-1.11390.06730.2646-0.04540.07550.3655-0.01420.407450.080849.7144112.9883
330.30530.4169-0.38780.5552-0.52840.494-0.6912-0.0993-1.0282-0.2620.376-0.06690.78350.26150.00120.36780.07930.12610.3406-0.04320.500471.901842.7926112.3282
340.0407-0.0183-0.01570.0533-0.01020.012-0.4397-0.14240.3322-0.8490.6772-0.39490.16930.9418-0.00421.46390.40150.38251.218-0.13280.872678.282936.9036103.3524
350.0141-0.0094-0.02180.0090.03170.1135-0.0797-0.3969-0.18280.15820.29790.5972-0.0244-0.4898-0.00431.79750.52250.77881.7275-0.77592.04986.422530.744497.4558
360.09910.0575-0.09930.22560.03360.1418-1.196-0.1373-0.4821-0.6047-0.1045-0.099-0.02430.7744-0.01321.5374-0.42330.53011.3355-1.08871.36380.449126.9856103.9181
371.61020.5243-0.50960.7688-0.42582.6629-0.03360.1806-0.4342-0.0162-0.04350.16260.7455-0.37980.04820.42980.01910.06120.0164-0.04430.368159.882634.8279113.7792
380.144-0.01790.06180.0272-0.04840.0990.3641.23110.1871-1.3574-0.5067-1.4050.04231.24990.00140.4730.13170.1560.51150.08270.516477.744652.0028102.692
391.5180.3349-0.08460.55390.05542.1056-0.07270.2078-0.4297-0.0519-0.00890.14290.756-0.28180.12660.39270.0360.10370.0588-0.0950.329158.9935.185112.3325
400.02690.0202-0.01220.0738-0.05520.0421-0.3680.0234-0.9296-0.9458-0.5843-0.72131.17430.60330.00210.86970.17940.11321.0514-0.13660.711379.558642.77587.0646
410.27420.2964-0.0090.40520.10490.15660.20490.50980.4696-0.0339-0.12190.19470.0981-0.3031-0.00641.6777-0.09131.86541.0818-0.31162.189981.51648.692774.9963
420.1399-0.487-0.04953.57130.0610.02460.78670.63120.2738-0.6303-0.4606-1.07120.4608-0.1202-0.01750.7050.00580.36830.8544-0.12740.350573.489648.924980.4802
430.17160.0783-0.17360.0334-0.08510.16730.08790.38160.3249-0.39330.1153-0.0734-0.1143-0.05120.00010.3044-0.01190.01350.3174-0.07210.239657.868951.08396.2023
440.4138-0.25440.42792.23110.2430.5428-0.0950.2989-0.2927-0.16720.0893-0.0280.40880.0224-0.00010.2298-0.02130.00170.3184-0.04380.259257.098357.928100.6345
450.05370.0373-0.01950.19720.14150.1625-0.97850.2458-1.0779-0.1385-0.5694-0.3404-1.82370.4339-0.00460.9795-0.28610.1751.37010.28051.424774.970163.314778.9968
460.8213-0.4015-0.1290.5096-0.18190.5973-0.52440.56511.2513-1.3973-1.1195-2.7887-0.87140.7844-0.02510.8181-0.11940.11891.20180.15950.822170.259559.985673.4564
471.18380.09390.28561.6820.19061.8540.01360.4466-0.1429-0.2419-0.02250.09760.1683-0.07690.00490.174-0.01170.02280.2446-0.09490.075255.956156.351292.468
480.0280.00820.04170.0812-0.03940.0918-0.740.1846-1.481-0.36060.804-1.0790.5810.3822-0.00230.6101-0.0533-0.04440.8785-0.10740.659741.688537.995889.9048
491.8656-0.4484-0.56471.4563-0.6061.55910.16620.8813-0.7128-0.10990.03690.64060.409-0.63920.21830.2144-0.0364-0.08460.3953-0.0941-0.086646.941354.536286.1355
500.0732-0.0299-0.07960.08990.08150.2247-0.14850.8439-0.8122-1.47860.3297-0.3539-0.3372-0.0764-0.00290.86950.09020.05490.82640.25120.781172.993980.30183.818
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 22:31)A22 - 31
2X-RAY DIFFRACTION2(chain A and resid 32:58)A32 - 58
3X-RAY DIFFRACTION3(chain A and resid 59:90)A59 - 90
4X-RAY DIFFRACTION4(chain A and resid 91:99)A91 - 99
5X-RAY DIFFRACTION5(chain A and resid 100:106)A100 - 106
6X-RAY DIFFRACTION6(chain A and resid 107:113)A107 - 113
7X-RAY DIFFRACTION7(chain A and resid 114:178)A114 - 178
8X-RAY DIFFRACTION8(chain A and resid 179:185)A179 - 185
9X-RAY DIFFRACTION9(chain A and resid 186:263)A186 - 263
10X-RAY DIFFRACTION10(chain A and resid 264:278)A264 - 278
11X-RAY DIFFRACTION11(chain B and resid 24:31)B24 - 31
12X-RAY DIFFRACTION12(chain B and resid 32:58)B32 - 58
13X-RAY DIFFRACTION13(chain B and resid 59:88)B59 - 88
14X-RAY DIFFRACTION14(chain B and resid 89:94)B89 - 94
15X-RAY DIFFRACTION15(chain B and resid 95:108)B95 - 108
16X-RAY DIFFRACTION16(chain B and resid 109:113)B109 - 113
17X-RAY DIFFRACTION17(chain B and resid 114:178)B114 - 178
18X-RAY DIFFRACTION18(chain B and resid 179:185)B179 - 185
19X-RAY DIFFRACTION19(chain B and resid 186:266)B186 - 266
20X-RAY DIFFRACTION20(chain B and resid 267:278)B267 - 278
21X-RAY DIFFRACTION21(chain C and resid 20:27)C20 - 27
22X-RAY DIFFRACTION22(chain C and resid 28:88)C28 - 88
23X-RAY DIFFRACTION23(chain C and resid 89:94)C89 - 94
24X-RAY DIFFRACTION24(chain C and resid 95:100)C95 - 100
25X-RAY DIFFRACTION25(chain C and resid 101:108)C101 - 108
26X-RAY DIFFRACTION26(chain C and resid 109:113)C109 - 113
27X-RAY DIFFRACTION27(chain C and resid 114:178)C114 - 178
28X-RAY DIFFRACTION28(chain C and resid 179:194)C179 - 194
29X-RAY DIFFRACTION29(chain C and resid 195:270)C195 - 270
30X-RAY DIFFRACTION30(chain C and resid 271:279)C271 - 279
31X-RAY DIFFRACTION31(chain D and resid 27:58)D27 - 58
32X-RAY DIFFRACTION32(chain D and resid 59:72)D59 - 72
33X-RAY DIFFRACTION33(chain D and resid 73:90)D73 - 90
34X-RAY DIFFRACTION34(chain D and resid 91:96)D91 - 96
35X-RAY DIFFRACTION35(chain D and resid 97:106)D97 - 106
36X-RAY DIFFRACTION36(chain D and resid 107:113)D107 - 113
37X-RAY DIFFRACTION37(chain D and resid 114:178)D114 - 178
38X-RAY DIFFRACTION38(chain D and resid 179:185)D179 - 185
39X-RAY DIFFRACTION39(chain D and resid 186:271)D186 - 271
40X-RAY DIFFRACTION40(chain D and resid 272:278)D272 - 278
41X-RAY DIFFRACTION41(chain E and resid 23:28)E23 - 28
42X-RAY DIFFRACTION42(chain E and resid 29:34)E29 - 34
43X-RAY DIFFRACTION43(chain E and resid 35:58)E35 - 58
44X-RAY DIFFRACTION44(chain E and resid 59:88)E59 - 88
45X-RAY DIFFRACTION45(chain E and resid 89:105)E89 - 105
46X-RAY DIFFRACTION46(chain E and resid 106:113)E106 - 113
47X-RAY DIFFRACTION47(chain E and resid 114:222)E114 - 222
48X-RAY DIFFRACTION48(chain E and resid 223:228)E223 - 228
49X-RAY DIFFRACTION49(chain E and resid 229:270)E229 - 270
50X-RAY DIFFRACTION50(chain E and resid 271:279)E271 - 279

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