PDB-2o20: Crystal structure of transcription regulator CcpA of Lactococcus ...

ID or keywords:

Entry

Database: PDB / ID: 2o20

Title

Crystal structure of transcription regulator CcpA of Lactococcus lactis

Components

Catabolite control protein A

Keywords

TRANSCRIPTION / ccpa /

transcriptional regulator /

helix-turn-helix

Function / homology

Function and homology information

negative regulation of DNA-templated transcription /

Biological species

Lactococcus lactis (lactic acid bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.9 Å

Authors

Loll, B. / Kowalczyk, M. / Alings, C. / Chieduch, A. / Bardowski, J. / Saenger, W. / Biesiadka, J.

Citation

Journal: Acta Crystallogr.,Sect.D / Year: 2007
Title: Structure of the transcription regulator CcpA from Lactococcus lactis
Authors: Loll, B. / Kowalczyk, M. / Alings, C. / Chieduch, A. / Bardowski, J. / Saenger, W. / Biesiadka, J.

History

Deposition	Nov 29, 2006	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Mar 27, 2007	Provider: repository / Type: Initial release
Revision 1.1	May 1, 2008	Group: Version format compliance
Revision 1.2	Jul 13, 2011	Group: Advisory / Version format compliance
Revision 1.3	Oct 20, 2021	Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4	Aug 30, 2023	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	2o20.cif.gz	452.5 KB	Display	PDBx/mmCIF format
PDB format	pdb2o20.ent.gz	369.7 KB	Display	PDB format
PDBx/mmJSON format	2o20.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/o2/2o20 ftp://data.pdbj.org/pub/pdb/validation_reports/o2/2o20	HTTPS FTP

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Related structure data

Related structure data	1zvvS 1rzr 1shi 1sxg 1sxh 2fep 2hsg S: Starting model for refinement
Similar structure data	3bbl-1 3vs1-2 2c0t-2 4qzt-d 4qzu-d 3kke-2 1sxh-d 3vs3-1 3vs4-2 4zgu-d 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

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	#39 - Mar 2003 lac Repressor similarity (6) #112 - Apr 2009 Oct and Sox Transcription Factors similarity (1) #241 - Jan 2020 Twenty Years of Molecules similarity (1)

Deposited unit

A: Catabolite control protein A

C: Catabolite control protein A

D: Catabolite control protein A

B: Catabolite control protein A

E: Catabolite control protein A

F: Catabolite control protein A

G: Catabolite control protein A

H: Catabolite control protein A

hetero molecules

294 kDa, 8 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Catabolite control protein A

B: Catabolite control protein A

hetero molecules

defined by author&software
73.7 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: Catabolite control protein A

D: Catabolite control protein A

defined by author&software
73.3 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

E: Catabolite control protein A

F: Catabolite control protein A

hetero molecules

defined by author&software
73.6 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

4

G: Catabolite control protein A

H: Catabolite control protein A

hetero molecules

defined by author&software
73.4 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	117.756, 74.267, 160.302
Angle α, β, γ (deg.)	90.00, 102.36, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Catabolite control protein A / Mass: 36642.613 Da / Num. of mol.: 8 / Mutation: D89A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lactococcus lactis (lactic acid bacteria) Strain: ssp.lactis IL1403 / Gene: ccpa / Plasmid: pQE30 / Production host: Escherichia coli (E. coli) / Strain (production host): XL1blue / References: UniProt: Q9CF33
#2: Chemical	ChemComp-SO4 / SULFATE ION / Sulfate Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO₄
#3: Chemical	ChemComp-CL / CHLORIDE ION / Chloride Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 1335 / 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: 2.34 Å³/Da / Density % sol: 47.33 %
Crystal grow	Temperature: 296 K / pH: 8 Details: PEG 3350 (22.5% (w/v), 100 mM Li2SO4, 100 mM Tris/HCl, VAPOR DIFFUSION, HANGING DROP, temperature 296K, pH 8.00

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
Detector	Type: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 12, 2005
Radiation	Monochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.933 Å / Relative weight: 1
Reflection	Resolution: 1.9→19.9 Å / Num. obs: 211799 / % possible obs: 99.4 % / Redundancy: 5.5 % / Net I/σ(I): 11.74
Reflection shell	Resolution: 1.9→1.95 Å / Redundancy: 4.4 % / Mean I/σ(I) obs: 4.49 / % possible all: 99.1

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Processing

Software

Name	Version	Classification
REFMAC	5.2.0005	refinement
XDS		data reduction
XDS		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1ZVV

1zvv

Resolution: 1.9→19.9 Å / Cor.coef. F_o:F_c: 0.955 / Cor.coef. F_o:F_c free: 0.935 / SU B: 5.396 / SU ML: 0.085 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: isotopic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.13 / ESU R Free: 0.124 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.211	10565	5 %	RANDOM
R_work	0.176	-	-	-
obs	0.177	201126	99.4 %	-
all	-	211799	-	-

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: 29.7 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.83 Å²	0 Å²	0.41 Å²
2-	-	0.18 Å²	0 Å²
3-	-	-	-0.84 Å²

Refinement step

Cycle: LAST / Resolution: 1.9→19.9 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	16891	0	41	1335	18267

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.012	0.022	17367
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	16068
X-RAY DIFFRACTION	r_angle_refined_deg	1.289	1.984	23521
X-RAY DIFFRACTION	r_angle_other_deg	0.808	3	37547
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.84	5	2164
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	42.66	25.466	761
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.91	15	3265
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	19.107	15	84
X-RAY DIFFRACTION	r_chiral_restr	0.076	0.2	2820
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.02	18975
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	3153
X-RAY DIFFRACTION	r_nbd_refined	0.197	0.2	3186
X-RAY DIFFRACTION	r_nbd_other	0.167	0.2	15257
X-RAY DIFFRACTION	r_nbtor_refined	0.162	0.2	8453
X-RAY DIFFRACTION	r_nbtor_other	0.079	0.2	9781
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.15	0.2	1027
X-RAY DIFFRACTION	r_xyhbond_nbd_other	0.114	0.2	2
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.207	0.2	14
X-RAY DIFFRACTION	r_symmetry_vdw_other	0.2	0.2	74
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.141	0.2	30
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	0.808	1.5	11180
X-RAY DIFFRACTION	r_mcbond_other	0.194	1.5	4432
X-RAY DIFFRACTION	r_mcangle_it	1.253	2	17658
X-RAY DIFFRACTION	r_scbond_it	1.984	3	6922
X-RAY DIFFRACTION	r_scangle_it	3.14	4.5	5863
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 1.9→1.95 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.276	727	-
R_work	0.225	14701	-
obs	-	-	99.03 %

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	1.1766	0.0886	0.4324	1.6346	-0.3011	1.0497	-0.0325	-0.1222	0.056	0.1691	-0.0393	-0.0441	-0.0836	0.0203	0.0719	-0.0163	-0.0388	0.0049	-0.0049	-0.0132	-0.0652	-2.9701	9.8169	76.7076
2	0.6563	-0.1371	-0.1995	0.9827	0.3543	0.8799	-0.004	-0.0105	-0.0376	-0.0364	-0.0199	0.028	-0.0794	-0.1198	0.0238	0.0033	-0.0035	0.0026	-0.0063	-0.02	-0.0762	-24.7775	13.9171	58.865
3	0.9042	0.0775	0.6434	1.1156	-0.0215	2.3102	0.0468	-0.0134	-0.0297	-0.1062	0.0246	-0.1519	0.1967	0.2771	-0.0713	-0.0254	0.0163	0.0332	0.001	0.0154	-0.0391	4.92	-14.1782	69.2438
4	0.4204	-0.2797	-0.0765	0.998	-0.3019	1.3252	0.0415	-0.0434	-0.009	-0.0932	-0.0235	-0.005	0.2362	-0.0083	-0.018	0.0919	-0.0282	-0.0018	-0.0776	0.0019	-0.069	-11.0933	-13.7956	45.5709
5	3.7808	0.6859	1.7003	2.7692	-0.5699	2.02	-0.1346	0.6585	-0.1405	-0.399	0.2317	-0.2381	0.3329	0.4463	-0.097	-0.0675	0.0219	0.0862	0.241	-0.04	-0.1579	57.2428	-7.172	59.6533
6	3.9799	-0.6556	0.3936	3.4217	0.4218	3.9956	0.1239	0.5611	-0.017	0.125	-0.1353	0.0626	0.2706	-0.1303	0.0114	-0.1871	-0.0412	0.1002	0.1159	-0.0439	-0.1868	32.1236	-7.7857	46.0972
7	3.496	-0.5543	1.0425	2.0659	-0.0868	2.7135	-0.3205	-0.0308	0.159	0.17	0.0367	-0.0525	0.1719	0.8989	0.2838	-0.2567	0.127	0.0584	0.3957	0.218	-0.1063	53.9544	16.8756	71.1771
8	2.4783	0.5137	-0.0153	1.4592	-0.2848	1.4398	-0.0592	0.0541	0.0584	-0.064	-0.0229	0.0444	0.1002	0.1001	0.0821	-0.1607	-0.0446	-0.0216	0.054	0.0836	-0.0379	26.9103	20.0265	64.8099
9	0.9302	0.0217	-0.4357	1.1923	-0.1396	0.8091	-0.0392	0.0371	-0.0656	-0.0258	-0.0239	-0.1082	-0.0048	0.0427	0.0631	-0.0513	0.0053	-0.0066	-0.041	0.0116	-0.0013	11.9814	-1.5982	6.8436
10	0.64	0.0624	0.1695	0.9014	0.188	0.5181	0.0009	0.0239	0.001	0.0515	-0.0346	0.0451	0.0252	-0.0377	0.0337	-0.0251	-0.0039	0.0151	-0.0346	-0.0192	-0.0268	-14.9606	-5.2251	14.2852
11	1.091	0.0933	-0.7562	1.1638	-0.3549	1.1606	0.0961	-0.0952	0.0364	0.1981	-0.1001	-0.1394	-0.1695	0.1626	0.004	0.0141	-0.0549	-0.0435	-0.033	0.0224	-0.0261	16.7471	22.0807	17.6457
12	0.4684	0.1672	-0.3633	0.937	-0.0232	1.1421	0.0739	-0.0388	0.0275	0.0567	-0.051	0.0091	-0.1367	0.0614	-0.023	0.0594	-0.0158	0.0198	-0.0703	-0.0072	-0.0529	-7.4206	22.1733	32.4302
13	2.0974	-0.1029	-0.2784	1.404	-0.0051	0.9828	0.0054	0.2122	0.0086	-0.1354	-0.0102	0.1398	0.0463	-0.0959	0.0048	-0.1137	0.0012	-0.0388	0.0147	-0.0273	0.0085	72.8589	4.6409	2.1546
14	2.4997	0.0595	0.0086	1.5771	0.5952	1.176	-0.002	-0.1696	0.2041	0.069	-0.0367	0.076	0.0703	-0.0907	0.0387	-0.1654	-0.041	0.0075	0.0351	-0.0345	0.011	50.4395	0.7117	19.1182
15	1.5248	0.3907	-0.1876	1.471	-0.5813	1.8577	0.0384	0.0055	0.1974	0.2013	-0.0888	-0.0084	-0.1327	-0.0114	0.0505	-0.1039	0.0173	-0.0206	-0.0726	-0.0219	0.055	80.5002	28.6222	10.2685
16	3.0964	0.7012	-1.0939	3.1154	0.279	3.4004	0.4593	-0.6025	0.4293	0.7927	-0.3479	0.4303	-0.162	-0.0867	-0.1114	0.109	-0.0956	0.1607	0.0464	-0.2407	-0.0485	63.0066	28.8036	32.8241

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	X-RAY DIFFRACTION	1	A	A	62 - 161	62 - 161
2	X-RAY DIFFRACTION	1	A	A	293 - 320	293 - 320
3	X-RAY DIFFRACTION	2	A	A	162 - 292	162 - 292
4	X-RAY DIFFRACTION	2	A	A	321 - 332	321 - 332
5	X-RAY DIFFRACTION	3	B	D	58 - 161	58 - 161
6	X-RAY DIFFRACTION	3	B	D	293 - 320	293 - 320
7	X-RAY DIFFRACTION	4	B	D	162 - 292	162 - 292
8	X-RAY DIFFRACTION	4	B	D	321 - 332	321 - 332
9	X-RAY DIFFRACTION	5	C	B	63 - 161	63 - 161
10	X-RAY DIFFRACTION	5	C	B	293 - 320	293 - 320
11	X-RAY DIFFRACTION	6	C	B	162 - 292	162 - 292
12	X-RAY DIFFRACTION	6	C	B	321 - 332	321 - 332
13	X-RAY DIFFRACTION	7	D	C	63 - 161	63 - 161
14	X-RAY DIFFRACTION	7	D	C	293 - 320	293 - 320
15	X-RAY DIFFRACTION	8	D	C	162 - 292	162 - 292
16	X-RAY DIFFRACTION	8	D	C	321 - 332	321 - 332
17	X-RAY DIFFRACTION	9	E	E	62 - 161	62 - 161
18	X-RAY DIFFRACTION	9	E	E	293 - 320	293 - 320
19	X-RAY DIFFRACTION	10	E	E	162 - 292	162 - 292
20	X-RAY DIFFRACTION	10	E	E	321 - 332	321 - 332
21	X-RAY DIFFRACTION	11	F	F	61 - 161	61 - 161
22	X-RAY DIFFRACTION	11	F	F	293 - 320	293 - 320
23	X-RAY DIFFRACTION	12	F	F	162 - 292	162 - 292
24	X-RAY DIFFRACTION	12	F	F	321 - 332	321 - 332
25	X-RAY DIFFRACTION	13	G	G	62 - 161	62 - 161
26	X-RAY DIFFRACTION	13	G	G	293 - 320	293 - 320
27	X-RAY DIFFRACTION	14	G	G	162 - 292	162 - 292
28	X-RAY DIFFRACTION	14	G	G	321 - 332	321 - 332
29	X-RAY DIFFRACTION	15	H	H	61 - 161	61 - 161
30	X-RAY DIFFRACTION	15	H	H	293 - 320	293 - 320
31	X-RAY DIFFRACTION	16	H	H	162 - 292	162 - 292
32	X-RAY DIFFRACTION	16	H	H	321 - 332	321 - 332

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