PDB-3i59: Crystal structure of MtbCRP in complex with N6-cAMP

ID or keywords:

Entry

Database: PDB / ID: 3i59

Title

Crystal structure of MtbCRP in complex with N6-cAMP

Components

(Transcriptional regulator, Crp/Fnr ...

Transcriptional regulation) x 2

Keywords

DNA BINDING PROTEIN /

Mycobacterium Tuberculosis /

cAMP Receptor Protein / CRP / allosteric mechanism /

DNA binding /

inhibition / N6-cAMP /

Structural Genomics / TB Structural Genomics Consortium / TBSGC / DNA-binding /

Transcription /

Transcription regulation

Function / homology

Function and homology information

cell wall /

cAMP binding / peptidoglycan-based cell wall / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / regulation of DNA-templated transcription / positive regulation of DNA-templated transcription /

DNA binding /

plasma membrane /

cytosol
Similarity search - Function

Biological species

Mycobacterium tuberculosis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 2.29 Å

Authors

Reddy, M.C. / Palaninathan, S.K. / Bruning, J.B. / Thurman, C. / Smith, D. / Sacchettini, J.C. / TB Structural Genomics Consortium (TBSGC)

Citation

Journal: J.Biol.Chem. / Year: 2009
Title: Structural Insights into the Mechanism of the Allosteric Transitions of Mycobacterium tuberculosis cAMP Receptor Protein.
Authors: Reddy, M.C. / Palaninathan, S.K. / Bruning, J.B. / Thurman, C. / Smith, D. / Sacchettini, J.C.

History

Deposition	Jul 3, 2009	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Sep 8, 2009	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Version format compliance
Revision 1.2	Nov 1, 2017	Group: Refinement description / Category: software
Revision 1.3	Sep 6, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif / struct_site Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _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	Nov 22, 2023	Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3i59.cif.gz	181.5 KB	Display	PDBx/mmCIF format
PDB format	pdb3i59.ent.gz	141.7 KB	Display	PDB format
PDBx/mmJSON format	3i59.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/i5/3i59 ftp://data.pdbj.org/pub/pdb/validation_reports/i5/3i59	HTTPS FTP

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Related structure data

Related structure data	3i54SC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	4gl8-1 3i54-1 5qlw-d 4irl-2 4iz5-1 3q1p-d 6pd7-d 5qmt-d 6k0v-4 4iz5-4 Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search
Other databases	TargetDB: Rv3676

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#48 - Dec 2003 Catabolite Activator Protein similarity (9) #152 - Aug 2012 cAMP-dependent Protein Kinase similarity (5) #251 - Nov 2020 Adenylyl Cyclase similarity (5)

Deposited unit

A: Transcriptional regulator, Crp/Fnr family

B: Transcriptional regulator, Crp/Fnr family

hetero molecules

56.2 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	113.732, 75.716, 63.639
Angle α, β, γ (deg.)	90.000, 110.910, 90.000
Int Tables number	5
Space group name H-M	C121

Components on special symmetry positions

ID	Model	Components
1	1	A-270- HOH

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Transcriptional regulator, Crp/Fnr ... , 2 types, 2 molecules AB

#1: Protein	Transcriptional regulator, Crp/Fnr family / Transcriptional regulation Mass: 27644.188 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: MT3777, Rv3676 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O69644, UniProt: P9WMH3*PLUS
#2: Protein	Transcriptional regulator, Crp/Fnr family / Transcriptional regulation Mass: 27597.293 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: MT3777, Rv3676 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O69644, UniProt: P9WMH3*PLUS

#1: Protein

Transcriptional regulator, Crp/Fnr family /

Transcriptional regulation

Mass: 27644.188 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Mycobacterium tuberculosis (bacteria) / Gene: MT3777, Rv3676 / Plasmid: pET28 / Production host:

Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O69644, UniProt: P9WMH3*PLUS

#2: Protein

Transcriptional regulator, Crp/Fnr family /

Transcriptional regulation

Mass: 27597.293 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Mycobacterium tuberculosis (bacteria) / Gene: MT3777, Rv3676 / Plasmid: pET28 / Production host:

Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O69644, UniProt: P9WMH3*PLUS

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Non-polymers , 4 types, 95 molecules

#3: Chemical	ChemComp-N6R / (2R)-N6-(1-Methyl-2-phenylethyl)adenosine-3',5'-cyclic monophosphate / (2R,4aS,6R,7R,7aR)-6-(6-{[(1R)-1-methyl-2-phenylethyl]amino}-9H-purin-9-yl)tetrahydro-4H-furo[3,2-d][1,3,2]dioxaphosphinine-2,7-diol 2-oxide Mass: 447.382 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₉H₂₂N₅O₆P
#4: Chemical	ChemComp-CL / CHLORIDE ION / Chloride Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical	ChemComp-N6S / (2S)-N6-(1-Methyl-2-phenylethyl)adenosine-3',5'-cyclic monophosphate / (2S,4aS,6R,7R,7aR)-6-(6-{[(1S)-1-methyl-2-phenylethyl]amino}-9H-purin-9-yl)tetrahydro-4H-furo[3,2-d][1,3,2]dioxaphosphi nine-2,7-diol 2-oxide Mass: 447.382 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₉H₂₂N₅O₆P
#6: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 92 / 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: 2.32 Å³/Da / Density % sol: 46.91 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 2 microliters of protein + 2 microliters of well solution. Well solution was 0.4M NaH2PO4/1.6M K2HPO4, 0.1M Imidazole pH 8.0, 0.2M NaCl, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.9791 Å
Detector	Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 10, 2008 Details: Mirrors: Adjustable focus K-B pair Si plus Pt, Rh coatings
Radiation	Monochromator: Si(111) Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9791 Å / Relative weight: 1
Reflection	Resolution: 2.29→20 Å / Num. all: 22400 / Num. obs: 22400 / % possible obs: 97.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / B_iso Wilson estimate: 55.032 Å² / R_merge(I) obs: 0.058 / R_sym value: 0.058 / Χ²: 1.275 / Net I/σ(I): 15.1
Reflection shell	Resolution: 2.29→2.38 Å / Redundancy: 3.1 % / R_merge(I) obs: 0.419 / Mean I/σ(I) obs: 2.6 / Num. unique all: 2028 / R_sym value: 0.419 / Χ²: 1.038 / % possible all: 89

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Phasing

Phasing	Method: molecular replacement

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Processing

Software

Name	Version	Classification
DENZO		data reduction
SCALEPACK		data scaling
PHASER		phasing
PHENIX		refinement
PDB_EXTRACT	3.005	data extraction
HKL-2000		data collection

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB entry 3I54

3i54

Resolution: 2.29→19.477 Å / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.741 / Isotropic thermal model: TLS / σ(F): 0 / σ(I): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.284	1149	5.13 %	Random
R_work	0.234	-	-	-
all	0.234	22393	-	-
obs	0.234	22393	98.35 %	-

Solvent computation

B_sol: 56.737 Å² / k_sol: 0.285 e/Å³

Displacement parameters

B_iso max: 174.44 Å² / B_iso mean: 72.976 Å² / B_iso min: 29.75 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-1.701 Å²	0 Å²	0.338 Å²
2-	-	1.511 Å²	0 Å²
3-	-	-	0.19 Å²

Refinement step

Cycle: LAST / Resolution: 2.29→19.477 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3095	0	63	92	3250

Refine LS restraints

Refine-ID	Type	Dev ideal	Weight
X-RAY DIFFRACTION	f_angle_d	0.802	1
X-RAY DIFFRACTION	f_bond_d	0.006	1
X-RAY DIFFRACTION	f_chiral_restr	0.056	1
X-RAY DIFFRACTION	f_dihedral_angle_d	11.848	1
X-RAY DIFFRACTION	f_plane_restr	0.003	1
X-RAY DIFFRACTION	f_nbd_refined	4.067	1

LS refinement shell

Resolution (Å)	R_factor R_work	Num. reflection R_work	Refine-ID	Num. reflection obs	Total num. of bins used	% reflection obs (%)
2.29-2.309	0.338	430	X-RAY DIFFRACTION	430	42	79
2.309-2.328	0.315	462	X-RAY DIFFRACTION		42	89
2.328-2.348	0.32	495	X-RAY DIFFRACTION		42	90
2.348-2.368	0.301	515	X-RAY DIFFRACTION		42	92
2.368-2.389	0.326	453	X-RAY DIFFRACTION		42	92
2.389-2.411	0.293	526	X-RAY DIFFRACTION		42	94
2.411-2.434	0.33	516	X-RAY DIFFRACTION		42	96
2.434-2.457	0.301	526	X-RAY DIFFRACTION		42	95
2.457-2.482	0.274	473	X-RAY DIFFRACTION		42	92
2.482-2.507	0.277	497	X-RAY DIFFRACTION		42	93
2.507-2.534	0.276	567	X-RAY DIFFRACTION		42	97
2.534-2.562	0.283	479	X-RAY DIFFRACTION		42	96
2.562-2.591	0.29	516	X-RAY DIFFRACTION		42	95
2.591-2.621	0.287	509	X-RAY DIFFRACTION		42	96
2.621-2.653	0.264	536	X-RAY DIFFRACTION		42	96
2.653-2.687	0.264	487	X-RAY DIFFRACTION		42	94
2.687-2.722	0.318	515	X-RAY DIFFRACTION		42	94
2.722-2.759	0.285	506	X-RAY DIFFRACTION		42	94
2.759-2.798	0.277	534	X-RAY DIFFRACTION		42	96
2.798-2.84	0.272	493	X-RAY DIFFRACTION		42	96
2.84-2.884	0.273	536	X-RAY DIFFRACTION		42	96
2.884-2.931	0.292	489	X-RAY DIFFRACTION		42	95
2.931-2.982	0.287	531	X-RAY DIFFRACTION		42	95
2.982-3.036	0.266	516	X-RAY DIFFRACTION		42	96
3.036-3.094	0.271	514	X-RAY DIFFRACTION		42	95
3.094-3.157	0.242	523	X-RAY DIFFRACTION		42	96
3.157-3.225	0.248	505	X-RAY DIFFRACTION		42	95
3.225-3.3	0.276	508	X-RAY DIFFRACTION		42	94
3.3-3.382	0.245	513	X-RAY DIFFRACTION		42	95
3.382-3.473	0.24	505	X-RAY DIFFRACTION		42	96
3.473-3.574	0.223	544	X-RAY DIFFRACTION		42	96
3.574-3.689	0.222	506	X-RAY DIFFRACTION		42	95
3.689-3.82	0.216	518	X-RAY DIFFRACTION		42	95
3.82-3.971	0.218	523	X-RAY DIFFRACTION		42	94
3.971-4.15	0.18	498	X-RAY DIFFRACTION		42	94
4.15-4.366	0.179	513	X-RAY DIFFRACTION		42	95
4.366-4.636	0.161	512	X-RAY DIFFRACTION		42	93
4.636-4.988	0.201	508	X-RAY DIFFRACTION		42	93
4.988-5.479	0.215	518	X-RAY DIFFRACTION		42	94
5.479-6.247	0.245	529	X-RAY DIFFRACTION		42	96
6.247-7.779	0.224	517	X-RAY DIFFRACTION		42	93
7.779-18.961	0.209	383	X-RAY DIFFRACTION		42	67

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	5.5126	1.5505	-6.4702	5.6058	-5.3128	2.0784	0.0541	-0.5753	0.5108	-0.2676	-0.796	-1.0721	-0.3873	1.8339	0.7575	0.6504	0.1195	0.1642	0.6943	0.2821	0.5926	3.0241	11.9152	-50.7918
2	-0.2656	-0.5975	-4.3254	0.1503	2.4249	2.8738	0.4869	0.8846	0.5875	0.9458	0.1728	0.7244	0.57	0.7579	-0.7156	0.9812	0.436	0.1624	1.5236	-0.0752	1.0914	-0.2329	4.6379	-52.185
3	2.6062	-1.2959	0.3113	2.3603	-0.2291	2.5207	0.011	0.1492	0.4429	-0.0456	-0.1659	-0.1685	0.0239	-0.5206	0.1052	0.5286	0.0629	0.0154	0.4156	0.0621	0.499	-10.8584	21.1113	-45.2351
4	3.727	1.6416	0.1515	4.2639	3.0911	3.0965	-0.2456	0.2708	0.033	-0.5173	0.6133	-0.2071	-0.2729	0.7216	-0.1919	0.3921	-0.0771	0.0524	0.3728	0.036	0.3545	-0.8531	12.0441	-36.2982
5	7.1976	0.818	-0.9479	9.379	0.9035	4.0528	1.5635	-0.9653	0.7272	-0.6337	-0.7775	-0.4798	-1.3051	0.3206	-0.2842	0.6455	-0.1946	-0.0491	0.6301	0.0247	1.9258	2.9979	40.7917	-34.221
6	1.6985	3.6707	1.6732	-0.8105	-3.276	3.0368	-0.1161	0.4746	0.8144	0.2043	-0.0961	0.4062	-0.4124	0.37	0.2883	0.5043	0.0479	-0.0041	0.4945	0.2979	1.1553	3.572	38.4108	-45.9601
7	0.5923	2.8591	0.4208	3.9365	5.6612	2.1303	0.184	0.393	-0.0788	1.1255	-0.392	0.2976	3.1838	-0.5839	-0.0359	1.2697	-0.0369	0.0225	0.658	0.1084	0.8451	-12.3805	-0.2951	-18.9136
8	5.2991	-0.2081	-0.6378	0.8232	0.3883	5.2796	-1.0854	-0.5463	-0.5826	0.1184	0.4639	0.4344	0.2705	1.2607	0.4993	0.6667	0.0591	0.0436	0.5333	0.1007	0.6943	-1.0818	-1.927	-12.3173
9	0.657	0.0243	-1.1356	1.1781	-0.101	1.4569	-0.0337	0.3133	-0.0872	0.0933	-0.076	-0.1692	0.0036	0.33	0.0732	0.3634	-0.049	-0.027	0.5287	0.0081	0.3583	1.0733	13.9807	-17.094
10	2.1723	1.1664	0.9752	2.9253	1.3164	4.6937	0.373	0.2441	-0.428	0.1441	0.1932	-0.608	-0.3854	0.5969	-0.6014	0.3777	0.1542	-0.0418	0.563	-0.0831	0.4564	0.0997	-0.3123	-22.5469
11	1.2559	-0.1501	0.9639	2.9388	0.1449	1.0006	0.0746	-0.0917	0.1294	0.8194	0.2336	0.2383	0.1258	-0.6223	-0.2263	0.4722	0.0043	0.0232	0.5516	-0.0168	0.3931	-9.1327	12.9565	-29.617
12	3.093	-1.1317	-0.4602	3.7766	-0.823	1.8107	-0.1672	0.1553	0.2275	0.2299	0.3522	0.3663	-0.3561	-0.1134	-0.1483	0.5276	0.0188	0.0104	0.4847	0.1045	0.4916	-16.5584	27.1116	-11.0905

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	(chain A and resid 0:12)	A	0 - 12
2	X-RAY DIFFRACTION	2	(chain A and resid 13:27)	A	13 - 27
3	X-RAY DIFFRACTION	3	(chain A and resid 28:109)	A	28 - 109
4	X-RAY DIFFRACTION	4	(chain A and resid 110:140)	A	110 - 140
5	X-RAY DIFFRACTION	5	(chain A and resid 141:150)	A	141 - 150
6	X-RAY DIFFRACTION	6	(chain A and resid 151:9999)	A - B	151 - 9999
7	X-RAY DIFFRACTION	7	(chain B and resid 0:15)	B	0 - 15
8	X-RAY DIFFRACTION	8	(chain B and resid 16:31)	B	16 - 31
9	X-RAY DIFFRACTION	9	(chain B and resid 32:97)	B	32 - 97
10	X-RAY DIFFRACTION	10	(chain B and resid 98:116)	B	98 - 116
11	X-RAY DIFFRACTION	11	(chain B and resid 117:138)	B	117 - 138
12	X-RAY DIFFRACTION	12	(chain B and resid 139:223)	B	139 - 223

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Transcriptional regulator, Crp/Fnr ... , 2 types, 2 molecules AB

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Non-polymers , 4 types, 95 molecules

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-Transcriptional regulator, Crp/Fnr ... , 2 types, 2 molecules AB

-Non-polymers , 4 types, 95 molecules

-Experimental details

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-Data collection

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+About Yorodumi

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-Feb 9, 2022. New format data for meta-information of EMDB entries

-Aug 12, 2020. Covid-19 info

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Transcriptional regulator, Crp/Fnr ... , 2 types, 2 molecules AB

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Non-polymers , 4 types, 95 molecules

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Experimental details

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Experiment

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Sample preparation

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Yorodumi