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- PDB-5unm: LarE, a sulfur transferase involved in synthesis of the cofactor ... -

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Basic information

Entry
Database: PDB / ID: 5unm
TitleLarE, a sulfur transferase involved in synthesis of the cofactor for lactate racemase, substrate free form with flexible loop
ComponentsATP-utilizing enzyme of the PP-loopsuperfamily
KeywordsTRANSFERASE / Lar / sulfur transferase / LarE / AMPylation / hexamer / trimer / PP-loop / ATP pyrophophatase domain / lactate / lactate racemization / lactate racemase
Function / homology
Function and homology information


pyridinium-3,5-bisthiocarboxylic acid mononucleotide synthase / NAD+ synthase (glutamine-hydrolyzing) activity / sulfurtransferase activity / lyase activity / ATP binding
Similarity search - Function
Pyridinium-3,5-bisthiocarboxylic acid mononucleotide synthase LarE / NAD/GMP synthase / NAD synthase / Rossmann-like alpha/beta/alpha sandwich fold
Similarity search - Domain/homology
PHOSPHATE ION / Lactate racemization operon protein LarE / Pyridinium-3,5-bisthiocarboxylic acid mononucleotide synthase
Similarity search - Component
Biological speciesLactobacillus plantarum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.58 Å
AuthorsFellner, M. / Desguin, B. / Hausinger, R.P. / Hu, J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)CHE-1516126 United States
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017
Title: Structural insights into the catalytic mechanism of a sacrificial sulfur insertase of the N-type ATP pyrophosphatase family, LarE.
Authors: Fellner, M. / Desguin, B. / Hausinger, R.P. / Hu, J.
History
DepositionJan 31, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 23, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 30, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Mar 6, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ATP-utilizing enzyme of the PP-loopsuperfamily
B: ATP-utilizing enzyme of the PP-loopsuperfamily
C: ATP-utilizing enzyme of the PP-loopsuperfamily
D: ATP-utilizing enzyme of the PP-loopsuperfamily
E: ATP-utilizing enzyme of the PP-loopsuperfamily
F: ATP-utilizing enzyme of the PP-loopsuperfamily
hetero molecules


Theoretical massNumber of molelcules
Total (without water)190,88212
Polymers190,3136
Non-polymers5706
Water6,359353
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15300 Å2
ΔGint-105 kcal/mol
Surface area62260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.339, 107.339, 318.902
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number91
Space group name H-MP4122
Components on special symmetry positions
IDModelComponents
11B-55-

GLU

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 2 through 6 or (resid 7...
21(chain B and ((resid 2 through 3 and (name N...
31(chain C and ((resid 2 through 3 and (name N...
41(chain D and ((resid 2 through 3 and (name N...
51(chain E and ((resid 2 through 3 and (name N...
61(chain F and ((resid 2 through 3 and (name N...

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
11ALAALATHRTHR(chain A and (resid 2 through 6 or (resid 7...AA2 - 62 - 6
12LYSLYSLYSLYS(chain A and (resid 2 through 6 or (resid 7...AA77
13ALAALATRPTRP(chain A and (resid 2 through 6 or (resid 7...AA2 - 2792 - 279
14ALAALATRPTRP(chain A and (resid 2 through 6 or (resid 7...AA2 - 2792 - 279
15ALAALATRPTRP(chain A and (resid 2 through 6 or (resid 7...AA2 - 2792 - 279
16ALAALATRPTRP(chain A and (resid 2 through 6 or (resid 7...AA2 - 2792 - 279
21ALAALATHRTHR(chain B and ((resid 2 through 3 and (name N...BB2 - 32 - 3
22ALAALAARGARG(chain B and ((resid 2 through 3 and (name N...BB2 - 2592 - 259
23ALAALAARGARG(chain B and ((resid 2 through 3 and (name N...BB2 - 2592 - 259
24ALAALAARGARG(chain B and ((resid 2 through 3 and (name N...BB2 - 2592 - 259
25ALAALAARGARG(chain B and ((resid 2 through 3 and (name N...BB2 - 2592 - 259
31ALAALATHRTHR(chain C and ((resid 2 through 3 and (name N...CC2 - 32 - 3
32ALAALAPHEPHE(chain C and ((resid 2 through 3 and (name N...CC2 - 2582 - 258
33ALAALAPHEPHE(chain C and ((resid 2 through 3 and (name N...CC2 - 2582 - 258
34ALAALAPHEPHE(chain C and ((resid 2 through 3 and (name N...CC2 - 2582 - 258
35ALAALAPHEPHE(chain C and ((resid 2 through 3 and (name N...CC2 - 2582 - 258
41ALAALATHRTHR(chain D and ((resid 2 through 3 and (name N...DD2 - 32 - 3
42ALAALAPHEPHE(chain D and ((resid 2 through 3 and (name N...DD2 - 2582 - 258
43ALAALAPHEPHE(chain D and ((resid 2 through 3 and (name N...DD2 - 2582 - 258
44ALAALAPHEPHE(chain D and ((resid 2 through 3 and (name N...DD2 - 2582 - 258
45ALAALAPHEPHE(chain D and ((resid 2 through 3 and (name N...DD2 - 2582 - 258
51ALAALATHRTHR(chain E and ((resid 2 through 3 and (name N...EE2 - 32 - 3
52ALAALATRPTRP(chain E and ((resid 2 through 3 and (name N...EE2 - 2792 - 279
53ALAALATRPTRP(chain E and ((resid 2 through 3 and (name N...EE2 - 2792 - 279
54ALAALATRPTRP(chain E and ((resid 2 through 3 and (name N...EE2 - 2792 - 279
55ALAALATRPTRP(chain E and ((resid 2 through 3 and (name N...EE2 - 2792 - 279
61ALAALATHRTHR(chain F and ((resid 2 through 3 and (name N...FF2 - 32 - 3
62ALAALAPHEPHE(chain F and ((resid 2 through 3 and (name N...FF2 - 2582 - 258
63ALAALAPHEPHE(chain F and ((resid 2 through 3 and (name N...FF2 - 2582 - 258
64ALAALAPHEPHE(chain F and ((resid 2 through 3 and (name N...FF2 - 2582 - 258
65ALAALAPHEPHE(chain F and ((resid 2 through 3 and (name N...FF2 - 2582 - 258

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Components

#1: Protein
ATP-utilizing enzyme of the PP-loopsuperfamily / PP-loop superfamily ATP-binding protein / TIGR00268 family protein


Mass: 31718.766 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactobacillus plantarum (bacteria)
Gene: A8P51_04975, IV39_GL000116, LPJSA22_00116, Nizo1839_0768, Nizo2891_3302, SRCM101060_01452
Plasmid: pGIR076 / Production host: Escherichia coli (E. coli) / Strain (production host): Arctic express DE3 / References: UniProt: A0A0G9FES3, UniProt: F9UST4*PLUS
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 353 / 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: 2.41 Å3/Da / Density % sol: 49.03 % / Mosaicity: 0.09 °
Crystal growTemperature: 294.15 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 5 ul ~25 mg/ml LarE (100 mM Tris-HCl pH 7.5, 300 mM NaCl) mixed with 5 ul reservoir solution. Hanging drop reservoir contained 100 ul of 21% Tacsimate pH 6.1.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.9774 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 21, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9774 Å / Relative weight: 1
ReflectionResolution: 2.58→48.83 Å / Num. obs: 59917 / % possible obs: 99.8 % / Redundancy: 10.7 % / Biso Wilson estimate: 40.26 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.138 / Rpim(I) all: 0.043 / Rrim(I) all: 0.144 / Net I/σ(I): 15.4 / Num. measured all: 644043 / Scaling rejects: 0
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Rpim(I) allRrim(I) all% possible all
2.58-2.659.30.9880.670.3341.04698.5
11.23-48.839.20.0390.9990.0130.04198.6

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation8.26 Å48.83 Å
Translation8.26 Å48.83 Å

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Processing

Software
NameVersionClassification
Aimless0.5.25data scaling
PHASER2.6.0phasing
PHENIX1.11.1-2575refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.58→48.829 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.91 / Phase error: 23.22
RfactorNum. reflection% reflection
Rfree0.2426 5553 4.94 %
Rwork0.1891 --
obs0.1917 112296 99.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 122.04 Å2 / Biso mean: 49.0689 Å2 / Biso min: 15.4 Å2
Refinement stepCycle: final / Resolution: 2.58→48.829 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11630 0 30 353 12013
Biso mean--59 40.82 -
Num. residues----1525
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00511849
X-RAY DIFFRACTIONf_angle_d0.80316074
X-RAY DIFFRACTIONf_chiral_restr0.0571876
X-RAY DIFFRACTIONf_plane_restr0.0052081
X-RAY DIFFRACTIONf_dihedral_angle_d14.7884177
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A6243X-RAY DIFFRACTION9.909TORSIONAL
12B6243X-RAY DIFFRACTION9.909TORSIONAL
13C6243X-RAY DIFFRACTION9.909TORSIONAL
14D6243X-RAY DIFFRACTION9.909TORSIONAL
15E6243X-RAY DIFFRACTION9.909TORSIONAL
16F6243X-RAY DIFFRACTION9.909TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5758-2.60510.38521710.3163402357395
2.6051-2.63580.38461710.302835583729100
2.6358-2.66790.37461930.284135823775100
2.6679-2.70170.341910.278535303721100
2.7017-2.73720.32851930.271935733766100
2.7372-2.77470.32181820.252135273709100
2.7747-2.81440.27542150.243635723787100
2.8144-2.85640.31791830.238735703753100
2.8564-2.9010.27171730.234536013774100
2.901-2.94850.29781820.235435553737100
2.9485-2.99940.31341640.257735813745100
2.9994-3.05390.33062280.255735213749100
3.0539-3.11260.32621990.238435403739100
3.1126-3.17620.26511770.232935833760100
3.1762-3.24520.28591730.212636053778100
3.2452-3.32070.31941890.213435253714100
3.3207-3.40370.28822060.203935373743100
3.4037-3.49570.33051870.191635893776100
3.4957-3.59850.24931680.186735793747100
3.5985-3.71470.26471750.177235933768100
3.7147-3.84740.18791870.164135613748100
3.8474-4.00130.18071760.150935913767100
4.0013-4.18340.20481910.14235173708100
4.1834-4.40380.19361560.138336093765100
4.4038-4.67950.16821980.134835603758100
4.6795-5.04050.18981790.138735693748100
5.0405-5.54710.2071940.153735473741100
5.5471-6.34820.16692000.172135663766100
6.3482-7.99240.20661940.16923531372599
7.9924-48.8380.15911580.16463569372799
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)
10.9127-0.1084-0.2136.36461.65951.1093-0.2088-0.0439-0.19420.91080.46060.12530.32260.0403-0.22430.60630.16490.0640.47260.07860.311634.7934-48.8842-18.4392
20.45360.01110.14574.3181.5260.4675-0.1843-0.1455-0.23190.78140.23550.79920.3415-0.0673-0.06120.61550.09960.15980.49170.18260.468527.3044-45.9294-15.7721
34.9316-1.0257-0.25753.06110.51213.42870.06340.2148-0.0751-0.0204-0.0487-0.0583-0.06510.2922-0.00030.29820.03890.02490.19760.01910.162236.3587-23.5596-2.0884
46.29571.92531.63251.19990.65281.2382-0.09830.82530.1917-0.2040.0780.39990.1787-0.16240.00960.41280.05550.01550.40670.0090.353821.7993-20.1816-6.0496
52.0473-0.2782-0.4472.64062.16223.46490.0003-0.1661-0.48110.2223-0.10.29080.3481-0.01020.07430.2626-0.01760.05450.23670.02230.489746.2225-55.195723.3318
60.6397-0.0191-0.25574.74812.38555.38160.18050.098-0.031-0.3948-0.13770.0192-0.79110.2203-0.05750.3867-0.01330.06780.3218-0.03820.662746.7123-50.96814.3602
73.9625-0.04761.51212.453-0.97061.8139-0.096-0.03670.001-0.12980.0329-0.1113-0.22780.01460.06570.2744-0.01790.05920.233-0.02550.201938.1926-28.835729.0709
83.7132-1.9756-0.42534.13020.54511.35480.1189-0.00420.1685-0.38380.0299-0.20930.15680.0507-0.13480.3617-0.0346-0.00970.1742-0.01620.18959.1764-57.96499.6801
94.6126-3.7858-1.4966.6810.49590.6719-0.1539-0.5712-0.16020.38580.29920.32340.32530.013-0.09280.4065-0.0828-0.00160.27550.02660.2872.0546-59.861416.5253
101.0047-2.691-0.58077.66931.42990.415-0.0987-0.3020.34250.26780.3639-0.69660.0990.2041-0.2660.31-0.0289-0.04360.3621-0.07110.366814.2613-51.900717.3757
112.57790.62690.23212.07611.78462.51520.02870.0282-0.1318-0.1880.13070.10430.165-0.0101-0.14710.32080.01910.02490.16890.00730.22559.2175-27.477512.7519
125.72715.66916.12135.92485.72766.9965-1.1545-1.28990.5447-0.52520.09320.535-0.0004-0.80331.03660.96110.14670.07360.6068-0.07160.610824.163526.046537.2293
132.4124-2.61160.83746.9697-2.69113.2119-0.0687-0.27270.2253-0.01220.2678-0.1429-0.5367-0.0762-0.19150.569-0.1202-0.04560.32130.00420.312343.264615.029934.7544
144.8683-5.45840.35816.4732-1.10210.710.13810.067-0.15440.1473-0.00870.255-0.215-0.1315-0.11040.6157-0.0912-0.03390.3936-0.0280.410333.56288.564131.7954
154.02980.66431.25093.30390.30572.4952-0.0741-0.0160.1752-0.2548-0.0066-0.0951-0.37750.17990.07530.3799-0.03150.03220.20470.01680.190342.2784-11.313922.9484
160.65581.1415-0.97882.9258-2.54522.2320.1996-0.12560.33860.7696-0.17090.1425-1.3361-0.0654-0.06570.96880.0132-0.04430.3299-0.01750.47632.184213.163726.5514
179.09017.3214.14236.08914.03167.5205-0.49220.72121.0138-1.42110.50991.4483-1.578-0.6794-0.02050.81060.25280.10010.64880.14650.5585-9.01949.570128.0346
184.9827-0.72-2.33024.9143-0.57915.2563-0.00080.5699-0.26610.5669-0.12950.1638-0.5653-0.55030.07110.78590.00710.00540.29460.06880.41552.534716.620415.4237
191.4299-0.61151.10341.89170.47741.4041-0.3416-0.24250.5592-0.2224-0.04220.1961-0.422-0.23810.25530.42110.0253-0.0290.2635-0.06430.31626.2656-4.649227.7296
203.4159-0.30830.05342.26641.57243.7239-0.0191-0.0851-0.0192-0.0550.04440.1117-0.16410.1162-0.01190.3001-0.01410.05380.2009-0.01240.177611.8475-15.341422.3225
211.23190.8862-0.0645.1018-0.03927.6785-0.2688-0.09520.0877-0.8288-0.16970.54150.0381-0.64910.44210.61860.1082-0.13790.5391-0.05190.41271.715-13.51564.3027
222.4606-0.06221.77452.32481.17672.8374-0.0545-0.02950.0741-0.2083-0.237-0.0016-0.1271-0.08450.26450.49620.01870.05580.19170.0390.32126.409425.50180.9951
232.1726-0.76550.09828.45942.97751.3814-0.1235-0.0293-0.2163-0.75770.1604-0.4732-0.45340.0922-0.04410.6556-0.03220.11960.36160.06750.355631.731715.1063-15.2352
245.5854-1.2112.53825.0868-1.53984.75180.07710.47710.004-0.182-0.2945-0.4991-0.12720.84830.23520.51470.0140.07730.1770.03280.370137.149424.96172.3255
250.18181.01170.73683.392.63162.54710.07920.03-0.0779-0.0347-0.2812-0.1050.211-0.37670.19210.5359-0.04380.11810.3010.05660.377129.14867.7638-2.3414
263.2152-1.45870.765.0024-0.26080.9626-0.00950.15980.2269-0.06080.06460.0689-0.31220.0771-0.04350.35650.02740.07540.18890.0080.231424.1645-8.0589-1.9233
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 115 )A2 - 115
2X-RAY DIFFRACTION2chain 'A' and (resid 116 through 189 )A116 - 189
3X-RAY DIFFRACTION3chain 'A' and (resid 190 through 245 )A190 - 245
4X-RAY DIFFRACTION4chain 'A' and (resid 246 through 279 )A246 - 279
5X-RAY DIFFRACTION5chain 'B' and (resid 2 through 114 )B2 - 114
6X-RAY DIFFRACTION6chain 'B' and (resid 115 through 177 )B115 - 177
7X-RAY DIFFRACTION7chain 'B' and (resid 178 through 259 )B178 - 259
8X-RAY DIFFRACTION8chain 'C' and (resid 2 through 95 )C2 - 95
9X-RAY DIFFRACTION9chain 'C' and (resid 96 through 146 )C96 - 146
10X-RAY DIFFRACTION10chain 'C' and (resid 147 through 189 )C147 - 189
11X-RAY DIFFRACTION11chain 'C' and (resid 190 through 258 )C190 - 258
12X-RAY DIFFRACTION12chain 'D' and (resid 2 through 18 )D2 - 18
13X-RAY DIFFRACTION13chain 'D' and (resid 19 through 146 )D19 - 146
14X-RAY DIFFRACTION14chain 'D' and (resid 147 through 189 )D147 - 189
15X-RAY DIFFRACTION15chain 'D' and (resid 190 through 258 )D190 - 258
16X-RAY DIFFRACTION16chain 'E' and (resid 2 through 95 )E2 - 95
17X-RAY DIFFRACTION17chain 'E' and (resid 96 through 115 )E96 - 115
18X-RAY DIFFRACTION18chain 'E' and (resid 116 through 164 )E116 - 164
19X-RAY DIFFRACTION19chain 'E' and (resid 165 through 206 )E165 - 206
20X-RAY DIFFRACTION20chain 'E' and (resid 207 through 265 )E207 - 265
21X-RAY DIFFRACTION21chain 'E' and (resid 266 through 279 )E266 - 279
22X-RAY DIFFRACTION22chain 'F' and (resid 2 through 80 )F2 - 80
23X-RAY DIFFRACTION23chain 'F' and (resid 81 through 114 )F81 - 114
24X-RAY DIFFRACTION24chain 'F' and (resid 115 through 164 )F115 - 164
25X-RAY DIFFRACTION25chain 'F' and (resid 165 through 189 )F165 - 189
26X-RAY DIFFRACTION26chain 'F' and (resid 190 through 258 )F190 - 258

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