PDB-2vi5: LUMAZINE SYNTHASE FROM MYCOBACTERIUM TUBERCULOSIS BOUND TO N-6-(r...

ID or keywords:

Entry

Database: PDB / ID: 2vi5

Title

LUMAZINE SYNTHASE FROM MYCOBACTERIUM TUBERCULOSIS BOUND TO N-6-(ribitylamino)pyrimidine-2,4(1H,3H)-dione-5-yl-propionamide

Components

6,7-DIMETHYL-8-RIBITYLLUMAZINE SYNTHASE

Lumazine synthase

Keywords

TRANSFERASE /

LUMAZINE SYNTHASE /

RIBOFLAVIN BIOSYNTHESIS /

MYCOBACTERIUM TUBERCULOSIS

Function / homology

Function and homology information

6,7-dimethyl-8-ribityllumazine synthase /

6,7-dimethyl-8-ribityllumazine synthase activity /

riboflavin synthase complex / riboflavin biosynthetic process /

cytosol
Similarity search - Function

Biological species

MYCOBACTERIUM TUBERCULOSIS (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.3 Å

Authors

Morgunova, E. / Zhang, Y. / Jin, G. / Illarionov, B. / Bacher, A. / Fischer, M. / Cushman, M. / Ladenstein, R.

Citation

Journal: J.Org.Chem. / Year: 2008
Title: A New Series of N-[2,4-Dioxo-6-D-Ribitylamino-1,2, 3,4-Tetrahydropyrimidin-5-Yl]Oxalamic Acid Derivatives as Inhibitors of Lumazine Syntase and Riboflavin Synthase: Design, Synthesis, ...
Authors: Zhang, Y. / Illarionov, B. / Morgunova, E. / Bacher, A. / Fischer, M. / Ladenstein, R. / Cushman, M.

History

Deposition	Nov 27, 2007	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Apr 8, 2008	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Version format compliance
Revision 1.2	Apr 10, 2019	Group: Data collection / Other / Source and taxonomy Category: entity_src_gen / pdbx_database_proc / pdbx_database_status Item: _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_variant / _pdbx_database_status.recvd_author_approval
Revision 1.3	Dec 13, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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.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_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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	2vi5.cif.gz	292.3 KB	Display	PDBx/mmCIF format
PDB format	pdb2vi5.ent.gz	237.7 KB	Display	PDB format
PDBx/mmJSON format	2vi5.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/vi/2vi5 ftp://data.pdbj.org/pub/pdb/validation_reports/vi/2vi5	HTTPS FTP

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Related structure data

Related structure data	1w19S 1w29 2c92 2c94 2c97 2c9b 2c9d S: Starting model for refinement
Similar structure data	2c9b-1 1w29-d 1w19-d 2c9d-1 2c92-d 2c94-d 2c9d-2 4j07-d 2c97-d 2c9b-2 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: 6,7-DIMETHYL-8-RIBITYLLUMAZINE SYNTHASE

B: 6,7-DIMETHYL-8-RIBITYLLUMAZINE SYNTHASE

C: 6,7-DIMETHYL-8-RIBITYLLUMAZINE SYNTHASE

D: 6,7-DIMETHYL-8-RIBITYLLUMAZINE SYNTHASE

E: 6,7-DIMETHYL-8-RIBITYLLUMAZINE SYNTHASE

F: 6,7-DIMETHYL-8-RIBITYLLUMAZINE SYNTHASE

G: 6,7-DIMETHYL-8-RIBITYLLUMAZINE SYNTHASE

H: 6,7-DIMETHYL-8-RIBITYLLUMAZINE SYNTHASE

I: 6,7-DIMETHYL-8-RIBITYLLUMAZINE SYNTHASE

J: 6,7-DIMETHYL-8-RIBITYLLUMAZINE SYNTHASE

hetero molecules

169 kDa, 10 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: 6,7-DIMETHYL-8-RIBITYLLUMAZINE SYNTHASE

B: 6,7-DIMETHYL-8-RIBITYLLUMAZINE SYNTHASE

C: 6,7-DIMETHYL-8-RIBITYLLUMAZINE SYNTHASE

D: 6,7-DIMETHYL-8-RIBITYLLUMAZINE SYNTHASE

E: 6,7-DIMETHYL-8-RIBITYLLUMAZINE SYNTHASE

hetero molecules

defined by author&software
84.5 kDa, 5 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

F: 6,7-DIMETHYL-8-RIBITYLLUMAZINE SYNTHASE

G: 6,7-DIMETHYL-8-RIBITYLLUMAZINE SYNTHASE

H: 6,7-DIMETHYL-8-RIBITYLLUMAZINE SYNTHASE

I: 6,7-DIMETHYL-8-RIBITYLLUMAZINE SYNTHASE

J: 6,7-DIMETHYL-8-RIBITYLLUMAZINE SYNTHASE

hetero molecules

defined by author&software
84.3 kDa, 5 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	77.033, 76.692, 86.254
Angle α, β, γ (deg.)	64.32, 64.41, 63.60
Int Tables number	1
Space group name H-M	P1

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B
3	1	C
4	1	D
5	1	E
6	1	F
7	1	G
8	1	H
9	1	I
10	1	J

NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Refine code	Auth asym-ID	Auth seq-ID
1	1	1	2	A	15 - 164
2	1	1	2	B	15 - 164
3	1	1	2	C	15 - 164
4	1	1	2	D	15 - 164
5	1	1	2	E	15 - 164
6	1	1	2	F	15 - 164
7	1	1	2	G	15 - 164
8	1	1	2	H	15 - 164
9	1	1	2	I	15 - 164
10	1	1	2	J	15 - 164

#1: Protein	6,7-DIMETHYL-8-RIBITYLLUMAZINE SYNTHASE / Lumazine synthase / DMRL SYNTHASE / LUMAZINE SYNTHASE / RIBOFLAVIN SYNTHASE BETA CHAIN Mass: 16387.559 Da / Num. of mol.: 10 Source method: isolated from a genetically manipulated source Source: (gene. exp.) MYCOBACTERIUM TUBERCULOSIS (bacteria) / Plasmid: PNCO-MT-LS / Production host: ESCHERICHIA COLI (E. coli) / Variant (production host): XL1-BLUE References: UniProt: P66034, UniProt: P9WHE9*PLUS, riboflavin synthase
#2: Chemical	ChemComp-Y19 / 1-deoxy-1-{[(5S)-2,6-dioxo-5-(propanoylamino)-1,2,5,6-tetrahydropyrimidin-4-yl]amino}-D-ribitol Mass: 332.310 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C₁₂H₂₀N₄O₇
#3: Chemical	ChemComp-K / POTASSIUM ION Mass: 39.098 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: K
#4: Chemical	ChemComp-PO4 / PHOSPHATE ION / Phosphate Mass: 94.971 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: PO₄
#5: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 770 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.5 Å³/Da / Density % sol: 50 % / Description: NONE
Crystal grow	pH: 7 / Details: pH 7

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.97873
Detector	Type: MARRESEARCH / Detector: CCD / Date: May 7, 2007
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97873 Å / Relative weight: 1
Reflection	Resolution: 2.3→30 Å / Num. obs: 62709 / % possible obs: 97.7 % / Observed criterion σ(I): 2 / Redundancy: 2.7 % / R_merge(I) obs: 0.08 / Net I/σ(I): 6.9
Reflection shell	Resolution: 2.3→2.36 Å / Redundancy: 2.5 % / R_merge(I) obs: 0.44 / Mean I/σ(I) obs: 1.3 / % possible all: 96.4

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Processing

Software

Name	Version	Classification
REFMAC	5.2.0019	refinement
HKL-2000		data reduction
SCALEPACK		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1W19

1w19

Resolution: 2.3→30 Å / Cor.coef. F_o:F_c: 0.904 / Cor.coef. F_o:F_c free: 0.881 / SU B: 19.706 / SU ML: 0.27 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.534 / ESU R Free: 0.305 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.299	3352	5.1 %	RANDOM
R_work	0.26	-	-	-
obs	0.262	62709	97.7 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 39.41 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-1.02 Å²	-0.9 Å²	1.63 Å²
2-	-	0.33 Å²	0.9 Å²
3-	-	-	-0.71 Å²

Refinement step

Cycle: LAST / Resolution: 2.3→30 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	10701	0	295	770	11766

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.006	0.021	11094
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.041	1.991	15162
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.02	5	1470
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	33.041	23.873	408
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.961	15	1673
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	14.417	15	90
X-RAY DIFFRACTION	r_chiral_restr	0.071	0.2	1916
X-RAY DIFFRACTION	r_gen_planes_refined	0.003	0.02	8206
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined	0.187	0.2	6395
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined	0.29	0.2	7562
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.135	0.2	929
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.235	0.2	66
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.104	0.2	13
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	0.157	1.5	7333
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	0.29	2	11737
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	0.341	3	3781
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it	0.583	4.5	3425
X-RAY DIFFRACTION	r_scangle_other
X-RAY DIFFRACTION	r_long_range_B_refined
X-RAY DIFFRACTION	r_long_range_B_other
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-ID	Auth asym-ID	Number	Type	Rms dev position (Å)	Weight position
1	A	584	tight positional	0.02	0.05
2	B	584	tight positional	0.02	0.05
3	C	584	tight positional	0.02	0.05
4	D	584	tight positional	0.02	0.05
5	E	584	tight positional	0.04	0.05
6	F	584	tight positional	0.02	0.05
7	G	584	tight positional	0.02	0.05
8	H	584	tight positional	0.02	0.05
9	I	584	tight positional	0.04	0.05
10	J	584	tight positional	0.04	0.05
1	A	471	medium positional	0.53	0.5
2	B	471	medium positional	0.43	0.5
3	C	471	medium positional	0.42	0.5
4	D	471	medium positional	0.43	0.5
5	E	471	medium positional	0.53	0.5
6	F	471	medium positional	0.42	0.5
7	G	471	medium positional	0.46	0.5
8	H	471	medium positional	0.45	0.5
9	I	471	medium positional	0.46	0.5
10	J	471	medium positional	0.5	0.5
1	A	584	tight thermal	0.02	0.5
2	B	584	tight thermal	0.02	0.5
3	C	584	tight thermal	0.02	0.5
4	D	584	tight thermal	0.02	0.5
5	E	584	tight thermal	0.02	0.5
6	F	584	tight thermal	0.02	0.5
7	G	584	tight thermal	0.01	0.5
8	H	584	tight thermal	0.02	0.5
9	I	584	tight thermal	0.02	0.5
10	J	584	tight thermal	0.02	0.5
1	A	471	medium thermal	0.13	2
2	B	471	medium thermal	0.13	2
3	C	471	medium thermal	0.12	2
4	D	471	medium thermal	0.12	2
5	E	471	medium thermal	0.15	2
6	F	471	medium thermal	0.12	2
7	G	471	medium thermal	0.11	2
8	H	471	medium thermal	0.14	2
9	I	471	medium thermal	0.13	2
10	J	471	medium thermal	0.15	2

LS refinement shell

Resolution: 2.3→2.36 Å / Total num. of bins used: 20 /

	R_factor	Num. reflection
R_free	0.351	228
R_work	0.3	4576

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°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)
1	2.621	0.0942	0.6243	1.9058	0.6047	2.501	-0.0385	0.3914	0.221	-0.2547	0.0973	0.1288	-0.1843	-0.0018	-0.0587	-0.1129	-0.028	0.0063	-0.0991	0.0838	-0.1601	5.0011	18.1037	-8.2397
2	2.0588	-0.2376	0.0804	1.5091	0.1163	3.3499	-0.0694	0.4148	-0.1002	-0.1573	0.1283	-0.0988	0.2338	0.0471	-0.0589	-0.1122	0.0255	0.0506	-0.0119	-0.0756	-0.1561	18.6845	-1.511	-9.1238
3	3.6284	0.3503	0.3055	2.0362	0.0232	3.6015	-0.0951	0.3512	-0.56	-0.2896	0.0134	-0.0973	0.6204	-0.0325	0.0817	0.1543	-0.0265	0.113	-0.1831	-0.0362	0.0157	7.311	-18.6862	2.8167
4	2.3709	0.2992	-0.1408	2.7536	0.0032	2.854	-0.0326	0.1526	-0.2128	-0.1224	0.02	0.2456	0.4338	-0.2478	0.0126	-0.074	-0.0602	0.0144	-0.1902	0.0068	-0.0756	-13.0683	-9.9491	11.1914
5	2.449	0.4094	-0.073	2.6611	0.1191	3.7443	-0.051	0.2218	0.103	-0.1313	0.0776	0.3018	0.066	-0.4638	-0.0267	-0.2358	-0.0139	-0.059	-0.094	0.0402	-0.1281	-14.9023	12.7941	4.4798
6	1.6252	0.2301	-0.0834	1.4122	0.455	3.8636	0.0248	-0.2256	-0.1744	0.2894	-0.0343	-0.063	0.296	0.2487	0.0094	0.0177	0.016	-0.0219	-0.1528	0.1291	-0.0791	11.0444	-6.1491	40.0607
7	2.3638	0.4555	0.4934	2.4867	0.321	3.652	-0.0036	-0.4491	-0.2562	0.1822	-0.0261	-0.3501	0.3524	0.5279	0.0297	-0.1268	0.1007	0.0025	0.0821	0.0745	-0.0126	31.5429	-3.818	28.0197
8	2.9171	-0.0159	-0.3704	2.0363	-0.4126	2.2075	0.0721	-0.2025	0.1939	0.1672	0.0364	-0.2067	-0.1073	0.4468	-0.1086	-0.2176	-0.0196	-0.0088	-0.037	-0.0345	-0.0884	32.7563	18.3538	19.8346
9	3.3726	-0.1347	0.0453	2.1782	-0.1114	2.2527	0.0952	-0.1691	0.3998	0.2497	-0.015	-0.0002	-0.3544	0.2203	-0.0802	-0.0772	-0.0572	0.0196	-0.1878	-0.0259	-0.0784	13.0285	30.0376	26.5908
10	2.5959	0.1451	0.5984	2.0762	0.8648	2.2473	0.0528	-0.3398	0.1588	0.2921	-0.0812	0.0172	0.0454	-0.0952	0.0284	-0.1215	-0.0107	0.0373	-0.0772	-0.0226	-0.194	-0.287	14.3772	39.4021

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	11 - 160
2	X-RAY DIFFRACTION	1	A	201
3	X-RAY DIFFRACTION	1	A	702
4	X-RAY DIFFRACTION	2	B	14 - 160
5	X-RAY DIFFRACTION	2	B	201
6	X-RAY DIFFRACTION	2	B	702
7	X-RAY DIFFRACTION	3	C	15 - 160
8	X-RAY DIFFRACTION	3	C	201
9	X-RAY DIFFRACTION	3	C	702
10	X-RAY DIFFRACTION	4	D	13 - 160
11	X-RAY DIFFRACTION	4	D	201
12	X-RAY DIFFRACTION	4	D	702
13	X-RAY DIFFRACTION	5	E	10 - 160
14	X-RAY DIFFRACTION	5	E	201
15	X-RAY DIFFRACTION	5	E	702
16	X-RAY DIFFRACTION	6	F	14 - 160
17	X-RAY DIFFRACTION	6	F	201
18	X-RAY DIFFRACTION	6	F	702
19	X-RAY DIFFRACTION	7	G	14 - 160
20	X-RAY DIFFRACTION	7	G	201
21	X-RAY DIFFRACTION	7	G	702
22	X-RAY DIFFRACTION	8	H	13 - 160
23	X-RAY DIFFRACTION	8	H	201
24	X-RAY DIFFRACTION	8	H	702
25	X-RAY DIFFRACTION	9	I	11 - 160
26	X-RAY DIFFRACTION	9	I	201
27	X-RAY DIFFRACTION	9	I	702
28	X-RAY DIFFRACTION	10	J	15 - 160
29	X-RAY DIFFRACTION	10	J	201
30	X-RAY DIFFRACTION	10	J	702

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