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- PDB-6s0t: The crystal structure of kanamycin B dioxygenase (KanJ) from Stre... -

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Basic information

Entry
Database: PDB / ID: 6s0t
TitleThe crystal structure of kanamycin B dioxygenase (KanJ) from Streptomyces kanamyceticus in complex with nickel, sulfate, soaked with iodide
ComponentsKanamycin B dioxygenase
KeywordsMETAL BINDING PROTEIN / non-heme iron dioxygenase / alpha-ketoglutarate dioxygenase / Kanamycin biosynthesis / KanJ / OXIDOREDUCTASE
Function / homologykanamycin B dioxygenase / : / kanamycin biosynthetic process / Phytanoyl-CoA dioxygenase / Phytanoyl-CoA dioxygenase (PhyH) / 2-oxoglutarate-dependent dioxygenase activity / IODIDE ION / NICKEL (II) ION / Kanamycin B dioxygenase
Function and homology information
Biological speciesStreptomyces kanamyceticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsMrugala, B. / Porebski, P.J. / Niedzialkowska, E. / Cymborowski, M.T. / Minor, W. / Borowski, T.
Funding support Poland, United States, 2items
OrganizationGrant numberCountry
Polish National Science Centre2014/15/B/NZ1/03331 Poland
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)R01-GM117325-01 United States
CitationJournal: Febs J. / Year: 2021
Title: A study on the structure, mechanism, and biochemistry of kanamycin B dioxygenase (KanJ)-an enzyme with a broad range of substrates.
Authors: Mrugala, B. / Milaczewska, A. / Porebski, P.J. / Niedzialkowska, E. / Guzik, M. / Minor, W. / Borowski, T.
History
DepositionJun 18, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 8, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 25, 2020Group: Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / pdbx_struct_conn_angle / struct_conn
Item: _citation.title / _citation_author.identifier_ORCID ..._citation.title / _citation_author.identifier_ORCID / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_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
Revision 1.2Feb 24, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID
Revision 1.3Mar 30, 2022Group: Author supporting evidence / Database references / Category: database_2 / pdbx_audit_support
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization
Revision 1.4Jan 24, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._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

Downloads & links

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Assembly

Deposited unit
A: Kanamycin B dioxygenase
B: Kanamycin B dioxygenase
C: Kanamycin B dioxygenase
D: Kanamycin B dioxygenase
E: Kanamycin B dioxygenase
F: Kanamycin B dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)193,86237
Polymers191,0476
Non-polymers2,81531
Water29,3101627
1
A: Kanamycin B dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,1885
Polymers31,8411
Non-polymers3474
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Kanamycin B dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,3156
Polymers31,8411
Non-polymers4745
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Kanamycin B dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,2846
Polymers31,8411
Non-polymers4435
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Kanamycin B dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,2846
Polymers31,8411
Non-polymers4435
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Kanamycin B dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,2846
Polymers31,8411
Non-polymers4435
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Kanamycin B dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,5078
Polymers31,8411
Non-polymers6667
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.614, 186.468, 110.828
Angle α, β, γ (deg.)90.00, 95.74, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14A
24E
15A
25F
16B
26C
17B
27D
18B
28E
19B
29F
110C
210D
111C
211E
112C
212F
113D
213E
114D
214F
115E
215F

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ALAALALEULEUAA2 - 2765 - 279
21ALAALALEULEUBB2 - 2765 - 279
12ALAALAHISHISAA2 - 2755 - 278
22ALAALAHISHISCC2 - 2755 - 278
13ALAALAHISHISAA2 - 2755 - 278
23ALAALAHISHISDD2 - 2755 - 278
14ALAALAASPASPAA2 - 2725 - 275
24ALAALAASPASPEE2 - 2725 - 275
15ALAALAASPASPAA2 - 2745 - 277
25ALAALAASPASPFF2 - 2745 - 277
16ALAALAHISHISBB2 - 2755 - 278
26ALAALAHISHISCC2 - 2755 - 278
17ALAALAHISHISBB2 - 2755 - 278
27ALAALAHISHISDD2 - 2755 - 278
18ALAALAASPASPBB2 - 2725 - 275
28ALAALAASPASPEE2 - 2725 - 275
19ALAALAASPASPBB2 - 2745 - 277
29ALAALAASPASPFF2 - 2745 - 277
110ALAALAHISHISCC0 - 2753 - 278
210ALAALAHISHISDD0 - 2753 - 278
111ALAALAASPASPCC0 - 2723 - 275
211ALAALAASPASPEE0 - 2723 - 275
112METMETASPASPCC1 - 2744 - 277
212METMETASPASPFF1 - 2744 - 277
113ALAALAASPASPDD0 - 2723 - 275
213ALAALAASPASPEE0 - 2723 - 275
114METMETASPASPDD1 - 2744 - 277
214METMETASPASPFF1 - 2744 - 277
115METMETASPASPEE1 - 2724 - 275
215METMETASPASPFF1 - 2724 - 275

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15

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Components

#1: Protein
Kanamycin B dioxygenase / Kanamycin biosynthesis protein J


Mass: 31841.100 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces kanamyceticus (bacteria) / Gene: kanJ, kacB / Plasmid: pMCSG7 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): MAGIC / References: UniProt: Q6L732, kanamycin B dioxygenase
#2: Chemical
ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ni / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical...
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 23 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: I / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1627 / Source method: isolated from a natural source / Formula: H2O
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: 2.72 Å3/Da / Density % sol: 54.84 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 1:1 of 28% PEG4000 (w/v), 0.5 M lithium sulfate, 0.1 M HEPES, 0.1 M sodium acetate and 15mg/ml protein in 0.05 M bis-tris methane, 0.15 M NaCl; soaked with 0.1 M potassium iodide

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 9, 2017 / Details: beryllium lens
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 118025 / % possible obs: 96.42 % / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Biso Wilson estimate: 29.7 Å2 / CC1/2: 0.754 / Rmerge(I) obs: 0.063 / Χ2: 0.994 / Net I/σ(I): 9.6
Reflection shellResolution: 2.1→2.14 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.666 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 5861 / CC1/2: 0.829 / Χ2: 0.815 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6S0R
Resolution: 2.1→50 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.941 / SU B: 9.033 / SU ML: 0.127 / Cross valid method: THROUGHOUT / ESU R: 0.203 / ESU R Free: 0.164 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20424 5621 4.9 %RANDOM
Rwork0.1692 ---
obs0.17091 108651 96.42 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 35.984 Å2
Baniso -1Baniso -2Baniso -3
1--0.34 Å20 Å20.48 Å2
2--0.09 Å2-0 Å2
3---0.15 Å2
Refinement stepCycle: 1 / Resolution: 2.1→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12937 0 123 1627 14687
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.01913735
X-RAY DIFFRACTIONr_bond_other_d0.0060.0212469
X-RAY DIFFRACTIONr_angle_refined_deg1.5151.98118969
X-RAY DIFFRACTIONr_angle_other_deg0.97329010
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.26851745
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.77723.498626
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.268152019
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.01615110
X-RAY DIFFRACTIONr_chiral_restr0.0910.22154
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02115339
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022635
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.3521.2886747
X-RAY DIFFRACTIONr_mcbond_other1.3521.2886746
X-RAY DIFFRACTIONr_mcangle_it2.2171.9238449
X-RAY DIFFRACTIONr_mcangle_other2.2171.9248450
X-RAY DIFFRACTIONr_scbond_it1.911.56988
X-RAY DIFFRACTIONr_scbond_other1.6531.4316893
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.5472.08910336
X-RAY DIFFRACTIONr_long_range_B_refined7.07220.05215214
X-RAY DIFFRACTIONr_long_range_B_other6.92118.97214755
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded15.53258
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A179380.07
12B179380.07
21A180100.06
22C180100.06
31A178760.07
32D178760.07
41A177640.06
42E177640.06
51A179520.05
52F179520.05
61B177420.06
62C177420.06
71B175620.06
72D175620.06
81B175860.05
82E175860.05
91B176760.06
92F176760.06
101C176720.07
102D176720.07
111C177120.06
112E177120.06
121C177420.06
122F177420.06
131D175060.06
132E175060.06
141D177220.06
142F177220.06
151E175560.05
152F175560.05
LS refinement shellResolution: 2.101→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.281 278 -
Rwork0.238 5655 -
obs--68.75 %
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)
13.466-0.1487-1.85831.79091.84343.61240.10130.01650.5028-0.5089-0.16470.2938-0.6907-0.42310.06340.28040.1095-0.11690.1716-0.01550.214736.92450.41963.58
21.15040.394-0.33731.82060.6692.27040.0039-0.1370.173-0.3339-0.2060.1004-0.285-0.23540.20220.10760.0632-0.03010.1287-0.04550.06839.66443.88369.068
37.8373-0.45721.91624.72530.69685.12120.1899-0.3614-0.71790.1904-0.33720.43880.7902-0.43210.14740.1536-0.09710.03590.3055-0.0680.13429.20130.01378.01
41.37340.2657-0.28662.0770.59552.74970.0018-0.16510.2366-0.3188-0.18920.0355-0.3023-0.20940.18750.10080.0736-0.02160.0816-0.04340.090241.7246.15270.105
539.99979.865220.732410.987210.98314.7846-0.30610.3351-0.4022-0.41960.7127-0.3692-0.37760.6783-0.40660.46020.03690.10280.58870.0280.434459.1843.97863.659
61.47720.4242-0.55071.13540.09292.10240.20310.05760.2665-0.0227-0.0225-0.0177-0.3290.0008-0.18050.0869-0.02330.0570.056-0.00980.080938.41530.523136.872
71.04630.20360.22931.7389-0.1761.47920.0839-0.0279-0.09770.26350.04920.2405-0.1303-0.1295-0.1330.0825-0.01370.06130.0421-0.00230.084433.04421.546143.341
815.0229-10.0934-3.477215.73681.797812.9054-0.1917-0.531-0.8190.83530.10170.18580.50490.28930.09010.225-0.0728-0.03840.06850.00570.201137.7294.635151.512
90.97440.0048-0.00252.0378-0.58011.36090.10920.0852-0.07520.19940.0550.1933-0.0798-0.0908-0.16410.0684-0.00990.04460.0387-0.01450.064133.34120.759141.391
1020.7473.99739.87171.86032.3945.87030.5374-0.76410.2690.3543-0.4523-0.06710.2552-0.1867-0.0850.3198-0.01130.04490.3823-0.01150.3111.15825.308144.459
112.54792.03740.25833.0490.19912.64630.0814-0.2732-0.09340.5091-0.1594-0.44530.39890.3140.07810.32330.0663-0.11860.1045-0.01070.140829.45460.726131.885
120.79550.20240.03032.59940.25312.17710.0438-0.09060.05870.6126-0.0549-0.02160.1344-0.04760.01110.22590.0064-0.060.0322-0.00910.05222.33968.124131.542
135.92860.2293-2.48768.39171.60819.5080.187-0.23980.83090.3269-0.130.4951-0.831-0.6163-0.05710.19680.0564-0.03390.1205-0.0380.246917.70483.169120.36
141.0721-0.04680.04212.80970.33672.09790.089-0.14580.08780.74-0.0829-0.06960.2187-0.0281-0.00620.2921-0.0294-0.07470.0388-0.01340.060922.82267.641134.227
150.07240.3604-0.97257.8526-5.544717.01130.07250.10050.03080.65440.73880.88660.6674-1.3649-0.81140.861-0.01350.07980.7469-0.04120.86917.23256.721143.436
164.66640.46460.813513.70774.111710.71260.0310.1457-0.3154-0.39670.187-0.38030.43910.1304-0.2180.1803-0.06890.03790.12710.03420.0886-4.68530.748116.551
175.81632.37760.63462.87930.04781.9258-0.03540.109-0.3379-0.02140.0218-0.21940.19160.14460.01360.11420.00990.04130.1571-0.02130.0395.27236.595108.882
181.1994-0.12330.54741.0093-0.33912.72760.00070.2349-0.02360.0592-0.0906-0.02920.05650.13420.08980.0455-0.03750.03350.1093-0.02030.03481.41440.965104.687
192.6221-0.27281.24331.4371-0.61853.3253-0.13270.08990.12810.25570.06320.1944-0.3959-0.38170.06940.12550.00180.05070.1184-0.01840.057-8.07145.997110.031
207.05-2.39590.98772.7083-1.55123.8225-0.03790.34140.1791-0.1176-0.1498-0.32210.22680.59420.18770.09440.03220.06360.2799-0.03910.08669.94137.19392.449
215.29061.66132.06642.44260.380417.2392-0.1028-0.22570.31380.11880.0387-0.1327-0.6877-0.00170.06420.2851-0.111300.1585-0.04630.235814.40122.09872.528
220.56171.05640.61722.78530.06714.35040.13170.0088-0.1350.44650.0646-0.5895-0.02070.7875-0.19620.5035-0.0692-0.170.4533-0.14130.349722.02713.39676.882
230.6934-0.0996-0.24341.5385-0.57912.79210.0512-0.0013-0.09560.1327-0.0201-0.18280.1480.4153-0.03120.2643-0.0506-0.11020.1329-0.00130.186415.1042.57463.617
240.76080.12910.06962.273-0.3273.34190.0589-0.01140.01570.20830.05370.2625-0.1153-0.1664-0.11250.2526-0.0639-0.05490.05280.00830.13525.6111.1367.077
259.04420.0032-2.99562.97850.60382.4262-0.13660.0066-0.39290.0859-0.0359-0.5170.32970.48650.17240.35120.0633-0.12250.25170.07290.287423.636-8.62269.06
265.14210.49752.56610.9148-0.64614.7040.59870.5339-0.7517-0.79850.13480.28812.29640.1974-0.73361.4650.0587-0.54470.2193-0.09490.61916.66471.67386.937
273.3597-1.14391.06731.593-2.16435.50460.50160.3455-0.0435-0.4058-0.3672-0.01060.48610.9106-0.13440.27890.1551-0.050.2021-0.02250.233417.62584.76393.619
281.9822-1.56792.26882.111-1.97243.83610.3149-0.1188-0.2536-0.2480.10620.30440.5153-0.0869-0.42110.0801-0.0031-0.06150.02290.01680.16957.53587.24898.918
293.0617-1.2392.09193.1105-2.21384.41370.3555-0.3008-0.4276-0.20360.37810.65720.6642-0.5808-0.73370.1817-0.0694-0.16610.08290.10120.31561.88881.50499.899
306.9512-2.4135-2.62194.9798-0.24572.24180.39110.15790.233-0.5882-0.3908-0.39710.11230.536-0.00040.2520.21710.00940.5436-0.00420.148617.42592.62983.771
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 72
2X-RAY DIFFRACTION2A73 - 170
3X-RAY DIFFRACTION3A171 - 194
4X-RAY DIFFRACTION4A195 - 270
5X-RAY DIFFRACTION5A271 - 277
6X-RAY DIFFRACTION6B2 - 65
7X-RAY DIFFRACTION7B66 - 176
8X-RAY DIFFRACTION8B177 - 183
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