PDB-4ben: R39-imipenem Acyl-enzyme crystal structure

ID or keywords:

Entry

Database: PDB / ID: 4ben

Title

R39-imipenem Acyl-enzyme crystal structure

Components

D-ALANYL-D-ALANINE CARBOXYPEPTIDASE

Keywords

HYDROLASE / PENICILLIN-BINDING / ACYL-ENZYME

Function / homology

Function and homology information

serine-type D-Ala-D-Ala carboxypeptidase / serine-type D-Ala-D-Ala carboxypeptidase activity / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / response to antibiotic / proteolysis / extracellular region
Similarity search - Function

Biological species

ACTINOMADURA SP. R39 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.15 Å

Authors

Van Elder, D. / Sauvage, E. / Herman, R. / Kerff, F. / Rocaboy, M. / Charlier, P.

Citation

Journal: To be Published
Title: Crystal Structures of R39-Imipenem Acyl-Enzyme.
Authors: Sauvage, E. / Van Elder, D. / Herman, R. / Kerff, F. / Pratt, R.F. / Charlier, P.

History

Deposition	Mar 11, 2013	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Mar 20, 2013	Provider: repository / Type: Initial release
Revision 1.1	Dec 20, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description / Structure summary Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_database_status / pdbx_entity_nonpoly / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site Item: _chem_comp.name / _database_2.pdbx_DOI ..._chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.name / _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_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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2	Oct 16, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	4ben.cif.gz	705.4 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	4ben_validation.pdf.gz	1.4 MB	Display	wwPDB validaton report
Full document	4ben_full_validation.pdf.gz	1.5 MB	Display
Data in XML	4ben_validation.xml.gz	75.2 KB	Display
Data in CIF	4ben_validation.cif.gz	107.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/be/4ben ftp://data.pdbj.org/pub/pdb/validation_reports/be/4ben	HTTPS FTP

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Related structure data

Related structure data	1w8qS S: Starting model for refinement
Similar structure data	2xk1-2 1w8q-4 2xdm-1 1w8y-2 3zvw-1 1w79-1 2vgk-2 2y55-4 2wke-1 1w8q-1 2wke-2 1w8q-3 2xdm-2 2y4a-2 3zvt-2 2vgj-4 4b4x-2 4b4x-1 4b4z-4 2vgk-4 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) 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

Related structure data

1w8qS

S: Starting model for refinement

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#29 - May 2002 Penicillin-binding Proteins similarity (1)

Deposited unit

A: D-ALANYL-D-ALANINE CARBOXYPEPTIDASE

B: D-ALANYL-D-ALANINE CARBOXYPEPTIDASE

C: D-ALANYL-D-ALANINE CARBOXYPEPTIDASE

D: D-ALANYL-D-ALANINE CARBOXYPEPTIDASE

hetero molecules

195 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: D-ALANYL-D-ALANINE CARBOXYPEPTIDASE

hetero molecules

defined by author&software
49.1 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: D-ALANYL-D-ALANINE CARBOXYPEPTIDASE

hetero molecules

defined by author&software
48.7 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

C: D-ALANYL-D-ALANINE CARBOXYPEPTIDASE

hetero molecules

defined by author&software
48.6 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

4

D: D-ALANYL-D-ALANINE CARBOXYPEPTIDASE

hetero molecules

defined by author&software
49 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	103.623, 91.911, 106.924
Angle α, β, γ (deg.)	90.00, 94.50, 90.00
Int Tables number	4
Space group name H-M	P12₁1

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Protein , 1 types, 4 molecules ABCD

#1: Protein	D-ALANYL-D-ALANINE CARBOXYPEPTIDASE / DD-CARBOXYPEPTIDASE / DD-PEPTIDASE / PENICILLIN-BINDING PROTEIN / PBP Mass: 47647.004 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) ACTINOMADURA SP. R39 (bacteria) References: UniProt: P39045, serine-type D-Ala-D-Ala carboxypeptidase

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Non-polymers , 6 types, 1014 molecules

#2: Chemical	ChemComp-IM2 / (5R)-5-[(1S,2R)-1-formyl-2-hydroxypropyl]-3-[(2-{[(E)-iminomethyl]amino}ethyl)sulfanyl]-4,5-dihydro-1H-pyrrole-2-carbox ylic acid / IMIPENEM, open form / N-FORMIMIDOYL-THIENAMYCINE, open form Mass: 301.362 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₁₂H₁₉N₃O₄S / Comment: antibiotic*YM
#3: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#4: Chemical	... ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 33 / Source method: obtained synthetically / Formula: SO₄
#5: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₃H₈O₃
#6: Chemical	ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₆H₁₃NO₄S / Comment: pH buffer*YM
#7: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 970 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has protein modification	Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.48 Å³/Da / Density % sol: 50 % / Description: NONE

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.9797
Detector	Type: ADSC CCD / Detector: CCD / Date: Apr 16, 2011
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9797 Å / Relative weight: 1
Reflection	Resolution: 2.15→25.7 Å / Num. obs: 108662 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 3.5 % / R_merge(I) obs: 0.08 / Net I/σ(I): 10
Reflection shell	Resolution: 2.15→2.27 Å / Redundancy: 3.5 % / R_merge(I) obs: 0.49 / Mean I/σ(I) obs: 2.5 / % possible all: 99.4

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Processing

Software

Name	Version	Classification
REFMAC	5.5.0109	refinement
MOSFLM		data reduction
SCALA		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1W8Q

1w8q

Resolution: 2.15→35.72 Å / Cor.coef. F_o:F_c: 0.954 / Cor.coef. F_o:F_c free: 0.927 / SU B: 11.18 / SU ML: 0.142 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.234 / ESU R Free: 0.193 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.23441	5420	5 %	RANDOM
R_work	0.18719	-	-	-
obs	0.18951	103175	99.77 %	-

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: 43.552 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.03 Å²	0 Å²	0 Å²
2-	-	0.02 Å²	0 Å²
3-	-	-	0.01 Å²

Refinement step

Cycle: LAST / Resolution: 2.15→35.72 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	13394	0	273	970	14637

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.013	0.021	13848
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.366	1.98	18956
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.905	5	1858
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	35.535	25.47	574
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	12.958	15	1920
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	16.571	15	68
X-RAY DIFFRACTION	r_chiral_restr	0.088	0.2	2183
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.021	10676
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
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
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
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	0.862	1.5	9178
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	1.588	2	14556
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	2.274	3	4670
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it	3.765	4.5	4400
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

LS refinement shell

Resolution: 2.15→2.206 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.332	394	-
R_work	0.267	7550	-
obs	-	-	99.23 %

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	2.9198	-6.8149	-0.6615	16.6641	2.6117	2.1982	0.4655	-0.1357	-0.45	-0.3754	0.2084	0.6147	1.0884	-0.2746	-0.6739	0.8562	-0.2774	-0.4425	0.1777	0.0091	0.5896	-14.562	-30.978	38.17
2	0.9341	0.246	-0.0043	0.7015	0.0409	0.6609	0.0124	-0.0166	0.0017	0.0162	-0.0068	-0.0054	0.0499	-0.0343	-0.0055	0.1374	0.0331	0.0115	0.1438	0.0082	0.1039	12.442	0.095	39.673
3	1.1372	-0.7012	-0.0405	0.5458	0.15	0.2539	-0.0039	-0.0106	0.0599	-0.0041	-0.0051	0.0297	-0.0026	-0.0619	0.0091	0.1046	-0.0022	0.002	0.1032	-0.0003	0.1114	-0.045	17.97	41.657
4	0.9279	0.3304	0.0838	0.6354	0.1761	0.5339	-0.0039	-0.0452	0.1205	0.0447	0.0144	-0.0974	-0.0384	0.1342	-0.0104	0.1133	0.0043	-0.009	0.1222	0.0023	0.1006	19.872	7.581	43.984
5	0.968	0.4673	-0.1969	0.55	-0.1734	0.6801	-0.0077	0.0276	-0.1083	0.0009	0.015	0.0023	0.1	-0.0511	-0.0073	0.1106	0.0026	0.0025	0.0975	-0.0046	0.0944	3.79	-11.549	38.23
6	1.2665	0.8614	-1.3434	1.259	0.0815	3.6786	-0.0827	-0.0262	-0.1801	0.0567	0.0015	-0.0476	0.3578	-0.1938	0.0811	0.0953	-0.0471	0.0128	0.1657	0.0067	0.1533	-9.696	-18.402	42.231
7	0.7088	0.0789	0.0753	0.5022	-0.1358	1.6651	-0.0404	0.0808	0.2162	-0.0593	0.0338	0.0548	-0.4079	-0.1703	0.0065	0.1788	0.0336	-0.0117	0.0796	-0.0066	0.1464	54.327	34.429	27.849
8	0.5006	-0.0683	-0.0206	0.5839	-0.107	2.189	-0.0072	-0.1755	-0.0248	0.123	0.0125	-0.0615	0.0342	0.0372	-0.0054	0.1001	-0.0035	-0.0137	0.125	-0.0025	0.1153	62.236	11.785	57.403
9	1.2072	-0.1844	-0.9103	0.1419	0.3604	1.1489	-0.086	-0.1388	-0.0841	0.0234	0.0397	-0.0147	0.1266	0.1704	0.0462	0.1102	0.0234	0.0058	0.1321	0.0322	0.114	77.856	8.425	42.587
10	0.7537	0.2797	0.1681	2.057	-1.528	2.8148	0.0183	-0.3033	-0.0357	0.325	-0.0016	0.0151	-0.0248	-0.0097	-0.0167	0.1264	0.024	0.0004	0.2025	-0.0099	0.0175	62.274	12.921	65.083
11	0.4842	0.1907	-0.3157	0.6627	-0.6838	1.1958	0.0366	-0.0783	0.1003	0.0796	-0.0112	0.0096	-0.2574	-0.082	-0.0253	0.1295	0.0141	-0.0077	0.0806	-0.0239	0.1123	56.673	29.789	37.52
12	1.916	0.8422	-0.0123	3.9319	0.6349	1.5473	0.0528	-0.0674	0.3342	0.0054	-0.0212	-0.0033	-0.4156	-0.0271	-0.0316	0.203	0.0151	-0.0013	0.0533	0.0252	0.1254	62.128	39.512	24.296
13	2.5322	0.3308	-0.1848	4.1856	0.8854	2.5514	0.0001	0.2392	0.3622	-0.3325	-0.1182	0.0489	-0.5237	-0.1497	0.1181	0.188	-0.0181	-0.0042	0.1288	0.0529	0.1104	14.54	87.505	-32.296
14	0.7015	-0.0308	0.0085	0.8322	-0.4536	0.8896	-0.0102	-0.186	-0.037	0.1168	0.0193	-0.0082	-0.0058	-0.0842	-0.009	0.1114	-0.0288	-0.0053	0.1634	-0.0518	0.1033	12.733	63.355	1.754
15	1.1901	-0.2532	-0.5767	0.0606	0.1322	0.4773	-0.0488	-0.0644	-0.0819	-0.0001	0.0012	0.0039	0.0893	0.0213	0.0476	0.134	-0.0214	-0.0009	0.0944	0.0026	0.1162	27.28	52.17	-10.715
16	0.6222	0.0753	-0.0421	0.7385	-0.5652	0.9788	-0.0032	-0.2063	-0.0847	0.1114	-0.0034	-0.0457	0.0579	-0.0413	0.0067	0.1146	-0.0255	-0.0117	0.154	-0.0221	0.0788	12.673	59.731	4.245
17	0.8771	0.4185	-0.0617	0.7791	-0.3183	0.5428	0.0134	-0.0857	0.1198	0.0931	0.0029	0.0307	-0.0849	-0.1067	-0.0164	0.1139	0.0042	-0.0092	0.1066	-0.0237	0.109	13.092	78.142	-13.251
18	1.6341	0.4324	0.725	3.0829	0.8557	1.7295	-0.0663	-0.0908	0.2472	0.055	0.0687	-0.1087	-0.2326	-0.0229	-0.0024	0.1333	0.0093	-0.0129	0.104	-0.0009	0.1149	18.475	86.346	-21.827
19	1.697	-0.2825	0.2805	0.8617	-0.0641	0.852	0.0373	-0.0286	-0.3046	0.0475	-0.0359	-0.1479	0.2623	0.2209	-0.0014	0.1728	0.0321	0.0022	0.1011	0.0168	0.1343	51.033	71.027	21.749
20	1.2348	-0.2689	0.3193	0.6247	-0.1763	0.5517	-0.0027	0.1007	0.0746	-0.0727	0.0193	0.1341	-0.1112	-0.1448	-0.0165	0.1224	0.0074	0.0035	0.1171	0.0088	0.1153	21.786	99.391	8.002
21	1.1307	0.5654	-0.2983	0.6823	-0.3721	0.2366	-0.0041	0.0647	0.0651	-0.0035	0.0046	-0.0514	-0.0169	0.019	-0.0004	0.1312	0.0011	-0.0044	0.0895	0.0026	0.1047	47.827	105.175	9.025
22	0.7239	-0.1122	0.1282	0.7047	-0.1996	0.687	0.0099	0.1039	0.068	-0.0235	0.0141	0.1444	-0.0589	-0.1727	-0.024	0.1133	-0.0059	0.0043	0.1116	-0	0.0922	28.882	95.2	9.194
23	0.9382	-0.1964	-0.0793	0.4777	0.2244	0.7444	-0.0064	-0.0171	-0.1198	0.0179	0.0135	-0.0204	0.0732	0.0539	-0.0071	0.1145	-0.0026	0.0078	0.0648	0.003	0.1121	43.45	76.553	17.563
24	2.0307	-0.7134	-0.4583	1.7139	1.2397	2.3279	0.0248	0.095	-0.3121	-0.0455	0.0033	-0.1363	0.0906	0.1586	-0.028	0.0883	0.0399	0.0009	0.0931	0.0106	0.1525	57.239	71.19	15.325

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	1 - 7
2	X-RAY DIFFRACTION	2	A	8 - 138
3	X-RAY DIFFRACTION	3	A	139 - 249
4	X-RAY DIFFRACTION	4	A	250 - 313
5	X-RAY DIFFRACTION	5	A	314 - 423
6	X-RAY DIFFRACTION	6	A	424 - 466
7	X-RAY DIFFRACTION	7	B	1 - 72
8	X-RAY DIFFRACTION	8	B	73 - 155
9	X-RAY DIFFRACTION	9	B	156 - 250
10	X-RAY DIFFRACTION	10	B	251 - 288
11	X-RAY DIFFRACTION	11	B	289 - 423
12	X-RAY DIFFRACTION	12	B	424 - 465
13	X-RAY DIFFRACTION	13	C	1 - 23
14	X-RAY DIFFRACTION	14	C	24 - 132
15	X-RAY DIFFRACTION	15	C	133 - 250
16	X-RAY DIFFRACTION	16	C	251 - 326
17	X-RAY DIFFRACTION	17	C	327 - 423
18	X-RAY DIFFRACTION	18	C	424 - 465
19	X-RAY DIFFRACTION	19	D	1 - 70
20	X-RAY DIFFRACTION	20	D	71 - 138
21	X-RAY DIFFRACTION	21	D	139 - 231
22	X-RAY DIFFRACTION	22	D	232 - 313
23	X-RAY DIFFRACTION	23	D	314 - 414
24	X-RAY DIFFRACTION	24	D	415 - 466

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