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- PDB-6cl6: Structure of P. aeruginosa R2 pyocin fiber PA0620 comprising C-te... -

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Basic information

Entry
Database: PDB / ID: 6cl6
TitleStructure of P. aeruginosa R2 pyocin fiber PA0620 comprising C-terminal residues 323-691
ComponentsTail fiber protein
KeywordsVIRAL PROTEIN / R-type pyocin / Pseudomonas aeruginosa / contractile injection system / receptor-binding protein
Function / homology
Function and homology information


Immunoglobulin-like - #3940 / Phage tail fibre protein / : / Phage tail-collar fibre protein, N-terminal / Putative tail fiber protein gp53-like, C-terminal / : / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
: / Probable bacteriophage protein
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.898 Å
AuthorsButh, S.A. / Shneider, M.M. / Leiman, P.G.
Funding support Switzerland, 2items
OrganizationGrant numberCountry
SNSF31003A_127092 Switzerland
EPFL running cost grant577-1 Switzerland
CitationJournal: Viruses / Year: 2018
Title: Structure and Analysis of R1 and R2 Pyocin Receptor-Binding Fibers.
Authors: Buth, S.A. / Shneider, M.M. / Scholl, D. / Leiman, P.G.
History
DepositionMar 1, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 27, 2018Provider: repository / Type: Initial release
Revision 1.1Jul 17, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_struct_conn_angle / struct_conn
Item: _citation.country / _database_2.pdbx_DOI ..._citation.country / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Revision 1.3Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tail fiber protein
B: Tail fiber protein
C: Tail fiber protein
D: Tail fiber protein
E: Tail fiber protein
F: Tail fiber protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)240,02538
Polymers238,2596
Non-polymers1,76632
Water72,5104025
1
A: Tail fiber protein
B: Tail fiber protein
C: Tail fiber protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,95118
Polymers119,1303
Non-polymers82115
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area34340 Å2
ΔGint-251 kcal/mol
Surface area39510 Å2
MethodPISA
2
D: Tail fiber protein
E: Tail fiber protein
F: Tail fiber protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,07520
Polymers119,1303
Non-polymers94517
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area33980 Å2
ΔGint-254 kcal/mol
Surface area39440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.320, 126.946, 432.938
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 6 molecules ABCDEF

#1: Protein
Tail fiber protein


Mass: 39709.871 Da / Num. of mol.: 6 / Fragment: C-terminal domain (UNP residues 323-691)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria)
Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1
Gene: PA0620 / Plasmid: pTSL (pET23 derivative)
Details (production host): pET23 with cloned SlyD gene, N-terminal His-tag and a TEV recognition site
Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: G3XD71

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Non-polymers , 5 types, 4057 molecules

#2: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca
#5: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 22 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4025 / 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: 3.25 Å3/Da / Density % sol: 62.13 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 3-5% PEG6000, 100 mM Tris-HCl, pH 8.5, 160-210 mM potassium chloride

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: vaporized nitrogen stream
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jul 17, 2011 / Details: Dynamically bendable mirror and KB mirror pair
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.898→50 Å / Num. obs: 472358 / % possible obs: 99.6 % / Redundancy: 3.8 % / Biso Wilson estimate: 25.1 Å2 / CC1/2: 0.994 / Rrim(I) all: 0.13 / Net I/σ(I): 8.77
Reflection shellResolution: 1.9→2.01 Å / Redundancy: 3.4 % / Mean I/σ(I) obs: 2.5 / Num. unique obs: 75624 / CC1/2: 0.797 / Rrim(I) all: 0.537 / % possible all: 98.3

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Processing

Software
NameVersionClassification
PHENIX(dev_3042: ???)refinement
XDSSeptember 26, 2012data reduction
XDSSeptember 26, 2012data scaling
PHASER2.1.4phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: A SeMet derivative, not deposited

Resolution: 1.898→49.961 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.21 / Phase error: 19.46 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2082 7071 1.5 %
Rwork0.1597 --
obs0.1604 472266 99.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.898→49.961 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16560 0 98 4025 20683
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00917328
X-RAY DIFFRACTIONf_angle_d0.89123701
X-RAY DIFFRACTIONf_dihedral_angle_d9.3979855
X-RAY DIFFRACTIONf_chiral_restr0.0572477
X-RAY DIFFRACTIONf_plane_restr0.0073136
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8975-1.91910.25722190.229814615X-RAY DIFFRACTION94
1.9191-1.94170.27462410.225715682X-RAY DIFFRACTION100
1.9417-1.96540.25392370.219315320X-RAY DIFFRACTION100
1.9654-1.99020.27692420.21515605X-RAY DIFFRACTION100
1.9902-2.01640.25252370.205415663X-RAY DIFFRACTION100
2.0164-2.04410.2372300.203115398X-RAY DIFFRACTION100
2.0441-2.07330.27492380.201615650X-RAY DIFFRACTION100
2.0733-2.10420.25312320.195315478X-RAY DIFFRACTION100
2.1042-2.13710.20292380.185115503X-RAY DIFFRACTION100
2.1371-2.17210.2172400.175515643X-RAY DIFFRACTION100
2.1721-2.20960.20692330.179315404X-RAY DIFFRACTION100
2.2096-2.24980.2392350.177815612X-RAY DIFFRACTION99
2.2498-2.2930.25862340.174515480X-RAY DIFFRACTION100
2.293-2.33980.22792420.174715536X-RAY DIFFRACTION100
2.3398-2.39070.24742340.165815589X-RAY DIFFRACTION100
2.3907-2.44630.19792360.159315570X-RAY DIFFRACTION100
2.4463-2.50750.2182360.16215406X-RAY DIFFRACTION100
2.5075-2.57530.22212410.158315691X-RAY DIFFRACTION100
2.5753-2.65110.22232310.158215481X-RAY DIFFRACTION100
2.6511-2.73660.18362390.157815525X-RAY DIFFRACTION100
2.7366-2.83440.23312330.161815645X-RAY DIFFRACTION100
2.8344-2.94790.19952350.158515494X-RAY DIFFRACTION100
2.9479-3.08210.21322360.151815519X-RAY DIFFRACTION100
3.0821-3.24450.20452350.1515521X-RAY DIFFRACTION100
3.2445-3.44780.19862310.145915518X-RAY DIFFRACTION100
3.4478-3.71390.1942380.142115571X-RAY DIFFRACTION100
3.7139-4.08750.19082360.130515538X-RAY DIFFRACTION100
4.0875-4.67860.172360.111915519X-RAY DIFFRACTION100
4.6786-5.8930.13532440.117615508X-RAY DIFFRACTION100
5.893-49.97820.18462320.175115511X-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)
10.0026-0.0020.00260.0016-0.00030.002600.02430.0119-0.02120.0290.02330.0133-0.010900.54870.0686-0.0680.4172-0.10440.264-4.9936107.6623-48.0197
20.1227-0.087-0.010.0790.02660.05850.02090.0824-0.09740.0218-0.02350.06910.0582-0.0508-0.01780.1218-0.01070.01280.0019-0.04220.1688-5.6071101.7917-13.4014
30.00760.0121-0.00740.0102-0.00110.0118-0.0023-0.02350.0177-0.05690.01730.1038-0.0498-0.06750.00010.13010.0231-0.0230.08920.00370.1487-7.2471112.217916.597
40.3324-0.0153-0.04280.1606-0.04330.374-0.0075-0.25960.0244-0.0366-0.00870.10520.0164-0.0394-0.02080.02110.03030.03160.1759-0.04420.0704-2.9131110.284946.3934
50.0556-0.0176-0.02320.00660.00280.0187-0.04930.1657-0.0154-0.04410.0464-0.0119-0.0047-0.0141-0.01940.21660.0288-0.040.6114-0.02330.039610.8382116.3805125.647
60.0025-0.0025-0.0010.00540.00620.00550.0263-0.00020.0139-0.00890.0392-0.01130.02530.0411-00.2189-0.0171-0.01660.48020.04290.173215.864117.6654144.6305
70.102-0.002-0.03570.10870.02870.0230.02270.17330.02970.0176-0.02730.0118-0.02350.3023-0.00870.1519-0.0404-0.01560.30960.04610.143719.7305118.5127161.2991
80.0210.0116-0.0110.0132-0.02050.03590.01790.0119-0.0022-0.03490.0210.0005-0.00420.00770.00680.50090.07760.0310.41740.06990.1135-1.7958115.4926-49.1839
90.0346-0.05380.01030.1121-0.05020.04010.0012-0.02070.0493-0.03020.01850.0141-0.04460.01210.02480.108-0.00810.00720.0771-0.01870.1545-2.375118.128-12.4678
100.05030.0079-0.0180.0288-0.01270.02210.0402-0.04680.0484-0.0950.0324-0.0259-0.05180.05040.00020.12810.0055-0.0060.1288-0.03480.157712.5963114.590424.3742
110.22980.006-0.04770.08180.08560.08980.0449-0.35730.04540.0530.088-0.033-0.04180.0450.25030.10030.0641-0.0010.342-0.08150.03034.0856112.17357.503
120.0166-0.01480.00820.015-0.0050.0236-0.0250.00380.0036-0.03190.01310.0010.05630.0391-0.0020.37590.0288-0.02690.7917-0.04140.14879.0581108.4062114.611
130.07870.0447-0.05110.0429-0.03220.03470.05480.0932-0.0098-0.01990.0280.01020.0498-0.04760.01790.22330.0076-0.01390.5212-0.0630.14534.719110.0523141.5395
140.026-0.0016-0.00150.0174-0.02260.0214-0.00930.0781-0.0173-0.0140.01790.02410.1511-0.00130.0090.1417-0.0069-0.00020.1737-0.01980.11194.7179109.7569162.9419
150.03-0.00110.01230.0032-0.00110.0070.0660.0782-0.0741-0.13450.0204-0.03170.0209-0.00540.00940.23780.01850.00350.1225-0.02110.095-0.8234108.6602-38.2778
160.1405-0.10050.10780.1376-0.02720.1280.04590.1021-0.05770.09050.0896-0.20040.05970.18440.12280.1310.013-0.01640.0588-0.07050.231112.7821107.4891-10.7151
170.1889-0.0046-0.03740.02230.01770.0379-0.0298-0.0874-0.0943-0.02450.0241-0.03960.07120.05910.02190.10790.02050.00720.0852-0.01920.13826.020396.566925.0075
180.0173-0.03140.01950.0884-0.02260.17090.0165-0.27370.00650.0478-0.0745-0.00720.0137-0.018-0.06050.10280.0118-0.00850.3264-0.04620.0815-0.3631109.35759.2682
190.01160.00850.0050.02730.00280.05640.00370.15820.013-0.044-0.0259-0.0018-0.0024-0.0721-0.0270.23630.008-0.01640.710.01640.02893.6745115.5067117.7614
200.00390.0027-0.00010.003-0.00330.00350.05170.0720.02640.0039-0.00170.0125-0.0174-0.028500.21430.0132-0.02570.45890.04370.19452.9766121.2896144.115
210.0409-0.0194-0.01540.024-0.02770.10930.10010.15230.18150.0359-0.0136-0.0466-0.2892-0.09850.0110.20330.0075-0.00520.22030.03280.17974.713126.9019161.539
220.0190.00120.01010.00010.00120.00630.02110.0042-0.0049-0.06990.023-0.0011-0.00260.00670.00610.4836-0.0904-0.04650.3929-0.0610.137211.9597167.0997-46.9669
230.162-0.0394-0.00720.03830.01830.03160.02630.099-0.06050.00310.01570.090.093-0.06480.05250.1715-0.0299-0.01040.0505-0.0140.16218.6439164.3506-12.4941
240.0137-0.0069-0.00760.05250.01330.0223-0.0245-0.04770.0114-0.04660.01990.07820.0265-0.087600.14750.0011-0.00810.1301-0.01430.15845.8826176.192724.4758
250.03730.01290.00880.00480.00290.00530.0268-0.25750.00590.0578-0.0475-0.02890.07880.0015-0.01460.12640.0141-0.01270.37760.0030.039918.8295175.582663.1952
260.00580.00280.00060.0013-0.00060.0012-0.00550.0106-0.007-0.00570.0033-0.0072-0.00280.0131-0.00180.29-0.0037-0.05060.68450.00580.155520.9645177.4868106.8363
270.05930.0094-0.01490.00820.0180.04210.03640.061-0.0108-0.0163-0.0321-0.03510.04820.05070.03340.17260.0126-0.04030.64960.11760.069130.7515178.96141.9049
280.03080.0125-0.03550.07-0.00170.0522-0.0060.15220.025-0.01050.0098-0.0092-0.02030.1390.03050.0849-0.05310.02710.44720.14810.120733.4291180.6288159.76
290.0021-0.0005-0.00010.00080.00050.00140.00590.00940.0034-0.00710.0098-0.0122-0.0019-0.000900.6156-0.04160.00210.43920.06990.262413.8488175.1469-51.362
300.09920.00270.01770.1127-0.02930.048-0.03410.09940.1117-0.10320.04870.0577-0.0982-0.0190.02860.1808-0.022-0.00270.1062-0.00330.182911.9376180.8724-14.81
310.0804-0.05310.0010.08710.0270.0417-0.0376-0.05390.0001-0.03620.0387-0.0151-0.02920.0125-0.00620.10410.00420.00110.0853-0.01250.132225.3601180.108825.9688
320.0317-0.00040.01050.01040.00890.02140.0383-0.2203-0.02530.0583-0.01410.01290.0366-0.01540.02760.2864-0.02430.00920.4720.0460.047516.6651171.665675.6441
330.0509-0.01680.02170.0153-0.01850.05470.02210.0824-0.0014-0.0713-0.03670.01490.09370.0514-0.03090.26360.0111-0.03460.75520.03040.031221.2585171.8424126.8717
340.0023-0.0007-0.00010.0001-0.00070.00150.00970.01580.0145-0.02250.00730.00620.0059-0.008900.1596-0.0148-0.02250.32570.02920.131318.3276172.2208150.3144
350.01560.0235-0.01470.0273-0.02630.03120.030.13030.0383-0.0234-0.0201-0.00040.11690.0043-0.0010.1573-0.01860.00020.26140.02710.126419.3809171.4359162.5966
360.0011-0.0020.00290.0013-0.00360.0056-0.0080.0379-0.0005-0.10750.02960.0217-0.03620.023300.4587-0.0756-0.04010.36280.02440.1413.3403170.6725-42.9877
370.08890.0045-0.04280.02960.00450.04680.01840.0677-0.02060.00840.0918-0.14420.04310.11640.06520.1556-0.0112-0.00770.1001-0.03920.178626.2783169.9315-12.5254
380.0012-0.0015-0.00180.00220.00170.00140.01470.03960.0308-0.03430.02430.00430.02360.0172-00.1609-0.0269-0.00070.1142-0.01380.18216.2393168.24979.1676
390.56810.0191-0.01760.2663-0.06890.237-0.0463-0.2549-0.179-0.0579-0.0364-0.04150.09340.0278-0.34660.0483-0.0023-0.02030.08780.00960.055419.0714165.431840.6341
400.0243-0.0031-0.01680.02730.00760.04760.01430.18140.0117-0.0109-0.03890.0010.0018-0.0712-0.02660.2295-0.0015-0.02540.67020.12320.064317.2898179.3653124.0687
410.02480.00450.01450.00090.00240.00880.00650.03430.0033-0.0068-0.00570.0075-0.0165-0.0211-0.00390.187-0.0298-0.01680.45350.11370.140316.0655181.281141.174
420.0987-0.07050.120.0786-0.05170.28560.10840.16920.11760.0407-0.03710.0399-0.2522-0.06310.05680.1669-0.0210.00340.27240.09180.170919.2052188.704160.4638
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 328:338)
2X-RAY DIFFRACTION2(chain A and resid 339:437)
3X-RAY DIFFRACTION3(chain A and resid 438:469)
4X-RAY DIFFRACTION4(chain A and resid 470:569)
5X-RAY DIFFRACTION5(chain A and resid 570:609)
6X-RAY DIFFRACTION6(chain A and resid 610:622)
7X-RAY DIFFRACTION7(chain A and resid 623:691)
8X-RAY DIFFRACTION8(chain B and resid 328:337)
9X-RAY DIFFRACTION9(chain B and resid 338:440)
10X-RAY DIFFRACTION10(chain B and resid 441:514)
11X-RAY DIFFRACTION11(chain B and resid 515:567)
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19X-RAY DIFFRACTION19(chain C and resid 557:609)
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