PDB-3u9f: Structure of CATI in complex with chloramphenicol

ID or keywords:

Entry

Database: PDB / ID: 3u9f

Title

Structure of CATI in complex with chloramphenicol

Components

Chloramphenicol acetyltransferase

Keywords

TRANSFERASE/ANTIBIOTIC /

bacterial resistance / acetylation of chloramphenicol / TRANSFERASE-ANTIBIOTIC complex

Function / homology

Function and homology information

chloramphenicol O-acetyltransferase /

chloramphenicol O-acetyltransferase activity / response to antibiotic
Similarity search - Function

Biological species

Escherichia coli (E. coli)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.9 Å

Authors

Biswas, T. / Garneau-Tsodikova, S. / Tsodikov, O.V.

Citation

Journal: Protein Sci. / Year: 2012
Title: The structural basis for substrate versatility of chloramphenicol acetyltransferase CAT(I).
Authors: Biswas, T. / Houghton, J.L. / Garneau-Tsodikova, S. / Tsodikov, O.V.

History

Deposition	Oct 18, 2011	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Feb 15, 2012	Provider: repository / Type: Initial release
Revision 1.1	Feb 29, 2012	Group: Structure summary
Revision 1.2	Apr 4, 2012	Group: Database references
Revision 1.3	Feb 28, 2024	Group: Data collection / Database references / Derived calculations Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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	3u9f.cif.gz	1.5 MB	Display	PDBx/mmCIF format
PDB format	pdb3u9f.ent.gz	1.3 MB	Display	PDB format
PDBx/mmJSON format	3u9f.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/u9/3u9f ftp://data.pdbj.org/pub/pdb/validation_reports/u9/3u9f	HTTPS FTP

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Related structure data

Related structure data	3u9bC C: citing same article (ref.)
Similar structure data	3u9b-1 1q23-3 3u9b-3 1q23-1 1pd5-1 3u9b-2 1q23-2 1noc-2 1pd5-2 1pd5-3 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) 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

3u9bC

C: citing same article (ref.)

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#153 - Sep 2012 Pyruvate Dehydrogenase Complex similarity (1) #154 - Oct 2012 Citric Acid Cycle similarity (1)

Deposited unit

A: Chloramphenicol acetyltransferase

B: Chloramphenicol acetyltransferase

C: Chloramphenicol acetyltransferase

D: Chloramphenicol acetyltransferase

E: Chloramphenicol acetyltransferase

F: Chloramphenicol acetyltransferase

G: Chloramphenicol acetyltransferase

H: Chloramphenicol acetyltransferase

I: Chloramphenicol acetyltransferase

J: Chloramphenicol acetyltransferase

K: Chloramphenicol acetyltransferase

L: Chloramphenicol acetyltransferase

M: Chloramphenicol acetyltransferase

N: Chloramphenicol acetyltransferase

O: Chloramphenicol acetyltransferase

P: Chloramphenicol acetyltransferase

R: Chloramphenicol acetyltransferase

S: Chloramphenicol acetyltransferase

hetero molecules

468 kDa, 18 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Chloramphenicol acetyltransferase

B: Chloramphenicol acetyltransferase

C: Chloramphenicol acetyltransferase

hetero molecules

defined by author&software
78 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

D: Chloramphenicol acetyltransferase

E: Chloramphenicol acetyltransferase

F: Chloramphenicol acetyltransferase

hetero molecules

defined by author&software
78 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

G: Chloramphenicol acetyltransferase

H: Chloramphenicol acetyltransferase

I: Chloramphenicol acetyltransferase

hetero molecules

defined by author&software
78 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

4

J: Chloramphenicol acetyltransferase

K: Chloramphenicol acetyltransferase

L: Chloramphenicol acetyltransferase

hetero molecules

defined by author&software
78 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

5

M: Chloramphenicol acetyltransferase

N: Chloramphenicol acetyltransferase

O: Chloramphenicol acetyltransferase

hetero molecules

defined by author&software
78 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

6

P: Chloramphenicol acetyltransferase

R: Chloramphenicol acetyltransferase

S: Chloramphenicol acetyltransferase

hetero molecules

defined by author&software
78 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	107.336, 114.429, 114.374
Angle α, β, γ (deg.)	119.97, 97.83, 98.64
Int Tables number	1
Space group name H-M	P1

#1: Protein	Chloramphenicol acetyltransferase / / CAT Mass: 25692.145 Da / Num. of mol.: 18 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: cat / Production host: Escherichia coli (E. coli) References: UniProt: P62577, chloramphenicol O-acetyltransferase
#2: Chemical	ChemComp-CLM / CHLORAMPHENICOL / Chloramphenicol Mass: 323.129 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: C₁₁H₁₂Cl₂N₂O₅ / Comment: antibiotic*YM
#3: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 364 / 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: 2.52 Å³/Da / Density % sol: 51.21 %
Crystal grow	Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 100 mM HEPES pH 7.5, 20% PEG 4000, isopropanol 10% v/v, reservoir solution contains 1 mM chloramphenicol, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å
Detector	Type: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 18, 2003
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.1 Å / Relative weight: 1
Reflection	Resolution: 2.9→50 Å / Num. all: 102933 / Num. obs: 89861 / % possible obs: 87.3 % / Observed criterion σ(I): 2.2

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Processing

Software

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

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.9→35 Å / Cor.coef. F_o:F_c: 0.923 / Cor.coef. F_o:F_c free: 0.869 / SU B: 63.183 / SU ML: 0.548 / Cross valid method: THROUGHOUT / ESU R Free: 0.601 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.30937	4368	5 %	RANDOM
R_work	0.23642	-	-	-
obs	0.2401	82522	86.84 %	-
all	-	94527	-	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 71.524 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	6.73 Å²	0.39 Å²	1.13 Å²
2-	-	-4.89 Å²	-3.07 Å²
3-	-	-	-4.49 Å²

Refinement step

Cycle: LAST / Resolution: 2.9→35 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	31825	0	360	364	32549

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.006	0.022	33261
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	0.909	1.91	45156
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	4.936	5	3821
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	36.964	24.144	1781
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	17.175	15	5132
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	16.258	15	90
X-RAY DIFFRACTION	r_chiral_restr	0.065	0.2	4641
X-RAY DIFFRACTION	r_gen_planes_refined	0.002	0.02	26196
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined	0.182	0.2	14664
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined	0.306	0.2	22425
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.107	0.2	910
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	0.167	0.2	109
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.135	0.2	8
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	0.213	1.5	19651
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	0.305	2	31004
X-RAY DIFFRACTION	r_scbond_it	0.462	3	15795
X-RAY DIFFRACTION	r_scangle_it	0.63	4.5	14152
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 2.9→2.975 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.427	295	-
R_work	0.344	5417	-
obs	-	-	77.77 %

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	1.4815	-0.5406	-0.1344	2.6116	0.4738	2.9241	0.0278	-0.1035	-0.0942	0.3175	-0.0785	0.0112	0.5358	-0.1694	0.0507	0.4127	-0.0311	0.1507	-0.3672	0.0336	-0.3782	-24.1882	-30.4308	20.3724
2	1.3885	0.6212	-0.5558	2.8185	0.1096	3.166	0.0768	0.0308	0.4374	0.1289	0.0362	0.097	-0.1673	-0.1039	-0.1131	0.2018	0.0949	0.1569	-0.4135	0.0143	-0.2547	-26.2438	-0.2647	12.0165
3	2.0073	-0.4066	-1.0236	3.3244	0.3553	1.9215	0.1	0.2877	0.0105	-0.2427	0.0097	-0.0143	-0.0389	-0.0756	-0.1096	0.2239	-0.0138	0.1183	-0.2848	-0.0098	-0.4362	-17.7582	-21.8097	-9.0277
4	1.2928	-0.3416	-0.3459	2.5405	0.7913	3.638	-0.0753	0.1654	0.2397	-0.5462	0.0258	-0.3118	-0.1706	0.4049	0.0495	0.2675	-0.0555	0.2207	-0.2929	0.0299	-0.3086	-2.0563	48.8763	-36.1151
5	2.1568	-1.0209	0.1145	2.7521	0.0816	2.8934	0.0105	-0.3742	0.12	0.2703	0.0757	-0.1135	-0.3334	0.2492	-0.0862	0.1308	-0.0633	0.136	-0.2976	-0.0985	-0.3186	-10.9157	54.4269	-7.4879
6	1.3758	0.4734	-0.3137	2.7414	0.122	2.9537	-0.1473	0.0265	-0.3156	0.1828	0.1696	-0.1812	0.5215	0.3602	-0.0223	0.257	0.1108	0.1126	-0.3296	-0.0351	-0.2784	-3.7014	25.8104	-15.7541
7	1.5965	0.8175	0.2752	2.6425	0.0416	3.2957	-0.0983	-0.0278	0.2582	-0.0205	-0.0599	0.1329	-0.2666	-0.2197	0.1582	0.3542	0.1144	0.0043	-0.4087	-0.0755	-0.2362	24.6101	-9.7289	19.3933
8	1.8072	-0.1272	-1.4577	1.6991	-0.1624	3.1963	-0.1776	0.2581	0.0635	-0.3468	0.0417	0.0594	0.0628	-0.1283	0.1359	0.4698	-0.089	0.0862	-0.4192	-0.0363	-0.34	33.3734	-26.4155	-5.1947
9	1.7987	-0.2678	-0.4603	2.5535	-0.0556	2.605	-0.1182	-0.1893	-0.1212	-0.023	-0.0962	0.0289	0.294	-0.1261	0.2144	0.3538	-0.0576	0.168	-0.4142	-0.0035	-0.2533	28.7832	-40.2898	22.153
10	1.7369	-0.4013	-0.1314	2.2595	0.2403	2.5841	0.0731	0.1054	-0.2205	0.0087	-0.041	0.0652	0.2778	-0.0616	-0.0321	0.1763	0.0353	0.0448	-0.4222	0.0001	-0.2565	18.0131	12.9119	40.0116
11	0.9681	-0.1217	0.3466	2.9884	0.0582	3.198	0.1807	-0.1988	0.0132	0.5704	-0.1902	0.2134	-0.1398	-0.1012	0.0095	0.334	0.0058	0.1952	-0.3669	-0.0175	-0.3785	9.1248	34.5017	61.0854
12	1.9947	0.3266	-0.9393	3.0694	0.3634	2.1744	0.1964	0.3286	0.3167	-0.0224	-0.0683	0.0989	-0.3613	-0.1188	-0.1281	0.2653	0.0974	0.1356	-0.3643	0.0814	-0.3457	15.5865	42.9919	31.5877
13	1.6977	-0.368	0.2736	2.1212	-0.92	2.7303	0.0137	-0.0136	0.2736	-0.1772	-0.0636	-0.3268	-0.5667	0.1471	0.05	0.2383	-0.0489	0.1214	-0.4044	0.0157	-0.1644	13.7792	105.455	77.0313
14	2.4935	-0.2247	-0.791	2.7308	-0.0926	2.7563	0.0425	-0.2208	-0.1778	0.3792	-0.155	-0.2298	0.1232	0.1528	0.1126	0.1604	-0.0117	0.0567	-0.3217	0.0515	-0.323	11.8469	82.333	97.3061
15	1.5484	0.4927	0.228	2.9187	0.1106	2.7775	-0.0653	0.3086	-0.1161	-0.3844	-0.0061	-0.3514	0.4947	0.4645	0.0714	0.2766	0.1489	0.241	-0.2567	0.02	-0.3294	20.4655	76.7128	68.2813
16	1.2051	0.3089	0.4495	2.4843	-0.3973	2.302	-0.1213	-0.2443	0.0171	0.2319	0.2547	0.1624	0.0914	-0.2716	-0.1334	0.2934	0.186	0.1512	-0.1917	-0.0211	-0.3999	61.3619	38.0454	56.8782
17	1.3417	0.2676	-0.0918	3.4472	-0.1434	2.5584	-0.0266	0.0445	0.1424	-0.2949	0.1355	0.0554	-0.1291	-0.096	-0.109	0.3037	0.051	0.0477	-0.3032	0.0057	-0.3749	66.1956	51.9692	29.5067
18	1.564	-0.4774	-1.0258	3.1146	-0.2338	1.5097	-0.1125	0.0937	-0.2462	-0.2111	0.0733	-0.104	0.2845	-0.0934	0.0393	0.3401	-0.007	0.1514	-0.3184	-0.059	-0.319	70.5974	21.4077	32.3269

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	2 - 216
2	X-RAY DIFFRACTION	1	A	221
3	X-RAY DIFFRACTION	2	B	2 - 216
4	X-RAY DIFFRACTION	2	B	221
5	X-RAY DIFFRACTION	3	C	2 - 217
6	X-RAY DIFFRACTION	3	C	221
7	X-RAY DIFFRACTION	4	D	7 - 217
8	X-RAY DIFFRACTION	4	D	221
9	X-RAY DIFFRACTION	5	E	7 - 217
10	X-RAY DIFFRACTION	5	E	221
11	X-RAY DIFFRACTION	6	F	7 - 217
12	X-RAY DIFFRACTION	6	F	221
13	X-RAY DIFFRACTION	7	G	4 - 217
14	X-RAY DIFFRACTION	7	G	221
15	X-RAY DIFFRACTION	8	H	5 - 217
16	X-RAY DIFFRACTION	8	H	221
17	X-RAY DIFFRACTION	9	I	5 - 217
18	X-RAY DIFFRACTION	9	I	221
19	X-RAY DIFFRACTION	10	J	2 - 217
20	X-RAY DIFFRACTION	10	J	221
21	X-RAY DIFFRACTION	11	K	2 - 217
22	X-RAY DIFFRACTION	11	K	221
23	X-RAY DIFFRACTION	12	L	2 - 217
24	X-RAY DIFFRACTION	12	L	221
25	X-RAY DIFFRACTION	13	M	7 - 217
26	X-RAY DIFFRACTION	13	M	221
27	X-RAY DIFFRACTION	14	N	6 - 217
28	X-RAY DIFFRACTION	14	N	221
29	X-RAY DIFFRACTION	15	O	7 - 217
30	X-RAY DIFFRACTION	15	O	221
31	X-RAY DIFFRACTION	16	P	3 - 217
32	X-RAY DIFFRACTION	16	P	221
33	X-RAY DIFFRACTION	17	R	4 - 217
34	X-RAY DIFFRACTION	17	R	221
35	X-RAY DIFFRACTION	18	S	4 - 217
36	X-RAY DIFFRACTION	18	S	221

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