PDB-3i54: Crystal structure of MtbCRP in complex with cAMP

ID or keywords:

Entry

Database: PDB / ID: 3i54

Title

Crystal structure of MtbCRP in complex with cAMP

Components

Transcriptional regulator, Crp/Fnr family

Keywords

DNA BINDING PROTEIN / Mycobacterium tuberculosis / cAMP Receptor Protein / allosteric mechanism / DNA binding / inhibition / 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 /

SAD / Resolution: 2.2 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: Advisory / Version format compliance
Revision 1.2	Nov 1, 2017	Group: Refinement description / Category: software Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3	Feb 21, 2024	Group: Data collection / Database references / Derived calculations Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3i54.cif.gz	181.5 KB	Display	PDBx/mmCIF format
PDB format	pdb3i54.ent.gz	142.8 KB	Display	PDB format
PDBx/mmJSON format	3i54.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	3i54_validation.pdf.gz	1.5 MB	Display	wwPDB validaton report
Full document	3i54_full_validation.pdf.gz	1.6 MB	Display
Data in XML	3i54_validation.xml.gz	35.6 KB	Display
Data in CIF	3i54_validation.cif.gz	47.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/i5/3i54 ftp://data.pdbj.org/pub/pdb/validation_reports/i5/3i54	HTTPS FTP

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Related structure data

Related structure data	3i59C C: citing same article (ref.)
Similar structure data	4jvs-d 4bqz-d 2jlu-2 4mpc-d 3i59-d 3tcg-5 1b3l-2 4iz5-1 4iz5-3 4gl8-1 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
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 (10) #152 - Aug 2012 cAMP-dependent Protein Kinase similarity (6) #251 - Nov 2020 Adenylyl Cyclase similarity (6)

Deposited unit

A: Transcriptional regulator, Crp/Fnr family

B: Transcriptional regulator, Crp/Fnr family

C: Transcriptional regulator, Crp/Fnr family

D: Transcriptional regulator, Crp/Fnr family

hetero molecules

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

1

A: Transcriptional regulator, Crp/Fnr family

B: Transcriptional regulator, Crp/Fnr family

hetero molecules

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

2

C: Transcriptional regulator, Crp/Fnr family

D: Transcriptional regulator, Crp/Fnr family

hetero molecules

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

Unit cell

Length a, b, c (Å)	68.252, 96.335, 79.255
Angle α, β, γ (deg.)	90.000, 113.460, 90.000
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Transcriptional regulator, Crp/Fnr family Mass: 27597.293 Da / Num. of mol.: 4 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: Chemical	ChemComp-CMP / ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE / CYCLIC AMP / CAMP Mass: 329.206 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₁₀H₁₂N₅O₆P
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 102 / 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: 2.17 Å³/Da / Density % sol: 43.19 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 9.5 Details: 2 microliters of protein + 2 microliters of well solution. Well solution was 1M Sodium citrate, 100mM CHES pH 9.5, 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-B / Wavelength: 0.97932 Å
Detector	Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 9, 2006 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: 0.97932 Å / Relative weight: 1
Reflection	Resolution: 2.2→50 Å / Num. all: 91208 / Num. obs: 91208 / % possible obs: 96.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.8 % / B_iso Wilson estimate: 27.229 Å² / R_merge(I) obs: 0.046 / R_sym value: 0.046 / Χ²: 1.618 / Net I/σ(I): 16.1
Reflection shell	Resolution: 2.2→2.28 Å / Redundancy: 3.3 % / R_merge(I) obs: 0.369 / Mean I/σ(I) obs: 3.01 / Num. unique all: 7448 / R_sym value: 0.369 / Χ²: 1.008 / % possible all: 79.1

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Processing

Software

Name	Version	Classification
DENZO		data reduction
SCALEPACK		data scaling
REFMAC	5.2.0019	refinement
PDB_EXTRACT	3.005	data extraction
HKL-2000		data collection
HKL-2000		data reduction
SHARP		phasing

Refinement

Method to determine structure:

SAD / Resolution: 2.2→48.17 Å / Cor.coef. F_o:F_c: 0.952 / Cor.coef. F_o:F_c free: 0.934 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 13.651 / SU ML: 0.18 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.298 / ESU R Free: 0.235 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: 1. The Friedel pairs were used in phasing. 2. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.266	2366	5.1 %	RANDOM
R_work	0.211	-	-	-
all	0.213	46612	-	-
obs	0.213	46612	97.59 %	-

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 max: 80.93 Å² / B_iso mean: 33.45 Å² / B_iso min: 10.77 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.21 Å²	0 Å²	0.26 Å²
2-	-	-0.37 Å²	0 Å²
3-	-	-	0.37 Å²

Refinement step

Cycle: LAST / Resolution: 2.2→48.17 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6543	0	88	102	6733

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.016	0.022	6767
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.02	4577
X-RAY DIFFRACTION	r_angle_refined_deg	1.822	1.983	9196
X-RAY DIFFRACTION	r_angle_other_deg	1.2	3	11071
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	10.292	5	873
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	33.58	22.491	281
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	16.137	15	1077
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	16.824	15	75
X-RAY DIFFRACTION	r_chiral_restr	0.226	0.2	1071
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	7593
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	1420
X-RAY DIFFRACTION	r_nbd_refined	0.22	0.2	1413
X-RAY DIFFRACTION	r_nbd_other	0.211	0.2	4738
X-RAY DIFFRACTION	r_nbtor_refined	0.178	0.2	3271
X-RAY DIFFRACTION	r_nbtor_other	0.092	0.2	3701
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.164	0.2	207
X-RAY DIFFRACTION	r_xyhbond_nbd_other	0.077	0.2	1
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.168	0.2	10
X-RAY DIFFRACTION	r_symmetry_vdw_other	0.273	0.2	53
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.094	0.2	7
X-RAY DIFFRACTION	r_mcbond_it	0.75	1.5	4460
X-RAY DIFFRACTION	r_mcbond_other	0.178	1.5	1782
X-RAY DIFFRACTION	r_mcangle_it	1.227	2	6916
X-RAY DIFFRACTION	r_scbond_it	1.979	3	2585
X-RAY DIFFRACTION	r_scangle_it	3.042	4.5	2278

LS refinement shell

Resolution: 2.2→2.257 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.3	145	-
R_work	0.223	2727	-
all	-	2872	-
obs	-	2727	82.7 %

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	32.7308	16.8056	12.2254	26.1328	11.1743	12.8664	-0.1171	1.6911	1.3988	1.9572	1.5131	-0.3876	-0.5692	-0.2142	-1.396	0.2969	0.0479	-0.0129	0.4985	-0.0475	0.2171	12.835	20.956	27.792
2	2.8097	-0.8348	0.053	6.6899	0.8768	6.4683	0.3677	0.1024	0.2826	-0.547	-0.2058	-0.0603	-0.1347	0.2382	-0.1619	0.2589	-0.0244	0.0303	0.266	0.0318	0.0461	-2.474	22.169	15.114
3	17.1087	-12.0001	-0.3337	37.825	1.5255	12.5664	0.3664	0.259	-0.0932	-1.4662	-0.765	-1.0834	1.2021	0.7731	0.3986	0.5509	0.0436	0.2284	0.7166	0.0519	0.1855	8.583	14.619	5.022
4	23.972	-3.1998	-3.571	4.5111	1.7089	3.4078	0.4173	-0.4161	-0.0968	0.2252	-0.1172	-0.2858	0.1483	0.3611	-0.3001	0.3314	0.0054	-0.0778	0.3288	0.0091	0.0093	-4.089	7.122	14.569
5	3.9067	1.9208	0.2054	2.9493	-0.8742	3.38	0.3153	-0.3173	-0.1613	-0.0046	-0.0659	0.0861	0.0394	-0.1448	-0.2493	0.0247	-0.0028	0.0108	0.2291	0.0557	0.0558	-17.531	17.739	32.986
6	12.628	4.6187	-0.7246	6.9534	4.3651	7.9667	-0.1601	-0.3176	-0.5862	0.2371	-0.5223	0.0938	1.0239	0.1146	0.6824	0.2401	0.1092	0.0772	0.4612	0.063	0.0425	-5.719	-3.495	-10.347
7	12.8213	1.9173	-8.1698	6.3279	-4.7375	13.8483	-0.6931	-0.5807	-1.5276	-0.4698	-0.7819	-0.8493	1.8137	1.2219	1.475	0.663	0.0775	-0.0619	0.5895	-0.0326	0.4214	-7.908	-11.003	-3.457
8	5.0794	0.3633	0.967	3.7888	-2.1633	7.5425	0.0012	-0.0577	-0.4878	0.2277	-0.1592	0.0523	0.4246	-0.4866	0.158	0.2886	-0.0676	0.0201	0.3558	0.0111	0.1313	-14.718	-4.602	7.346
9	14.0058	-9.0773	-1.9616	7.5151	1.0414	2.0601	0.5556	0.238	-0.3343	-0.496	-0.4511	0.2701	-0.2082	-0.0354	-0.1045	0.306	0.0255	-0.0921	0.336	0.013	0.0917	-5.969	5.533	5.863
10	5.1995	-4.3379	0.3529	8.8813	2.1862	4.4244	0.1774	0.0741	-0.1312	-0.9088	-0.1801	0.8914	-0.331	-0.4482	0.0027	0.2301	0.0098	-0.0133	0.6195	0.0711	0.2954	-31.033	9.699	-2.602
11	6.3715	-1.1618	-1.8796	1.5835	-0.5267	3.1919	0.0415	0.1976	-0.5481	0.1582	-0.1761	0.2848	-0.0677	-0.331	0.1346	0.1887	-0.1126	0.019	0.2145	-0.1679	0.1969	-1.042	24.924	44.558
12	2.3085	-1.1127	-0.2754	4.2251	0.4585	2.6846	0.1909	0.0239	-0.0512	-0.0807	-0.2468	0.0105	-0.1351	-0.1103	0.0559	0.16	-0.0688	-0.0187	0.2052	-0.0457	0.0981	8.341	29.433	43.471
13	2.3767	0.4381	0.4533	4.1586	-0.6314	0.6854	-0.0244	0.22	0.2142	0.1832	-0.1052	0.2682	-0.2038	-0.1128	0.1296	0.2548	-0.0309	-0.0043	0.274	-0.0803	0.0924	3.99	40.975	42.22
14	5.8084	1.344	0.117	6.8105	3.8356	5.8863	0.484	-0.6178	-0.1702	0.8728	-0.2473	-0.5254	0.2007	0.0703	-0.2366	0.2659	-0.1648	-0.1203	0.2544	0.0311	0.0282	18.961	32.614	61.968
15	15.6944	6.0893	-4.8441	13.991	1.6812	11.4752	0.1235	-0.8753	0.9051	0.145	0	0.2402	0.0273	-0.6464	-0.1236	0.2062	-0.1875	0.0285	0.4217	-0.2006	0.0201	20.727	41.957	67.865
16	6.8824	4.8952	-1.0247	16.0025	4.7562	2.5555	-0.2165	-0.5843	0.4587	0.4867	-0.2984	0.1016	-0.1616	-0.73	0.5149	0.1696	0.0863	-0.0993	0.5224	-0.0422	0.0669	5.807	53.612	18.593
17	4.9991	-0.9289	0.7596	4.2021	-0.3969	6.9195	0.0884	-0.0817	0.2292	-0.0032	-0.2124	0.1984	-0.0219	-0.6191	0.124	0.1513	0.0749	-0.0197	0.1407	-0.0721	0.1464	14.125	58.519	31.097
18	82.0279	5.4969	26.4794	11.8022	3.7266	82.6938	0.1124	-4.8171	2.6971	1.537	0.2018	-0.8994	-2.4044	0.9718	-0.3142	0.3263	0.1117	-0.1733	0.5403	-0.2004	0.3791	30.545	51.086	41.349
19	2.2299	0.0545	0.6647	2.5402	-0.3713	1.1019	0.2626	0.2434	-0.3174	-0.1434	-0.2571	-0.2968	0.3444	0.0487	-0.0055	0.2325	0.107	-0.0734	0.2139	-0.0414	0.1959	20.778	46.75	30.609
20	15.0887	-13.6537	-0.4174	20.5986	-5.4751	4.1669	1.1591	0.9292	-0.7432	-0.1374	-1.5656	-1.771	0.5893	1.4343	0.4065	0.7565	0.1662	-0.0786	0.6599	-0.2788	0.4633	32.584	38.951	20.458

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	-3 - 3
2	X-RAY DIFFRACTION	2	A	4 - 104
3	X-RAY DIFFRACTION	3	A	105 - 114
4	X-RAY DIFFRACTION	4	A	115 - 139
5	X-RAY DIFFRACTION	5	A	140 - 223
6	X-RAY DIFFRACTION	6	B	-6 - 11
7	X-RAY DIFFRACTION	7	B	12 - 35
8	X-RAY DIFFRACTION	8	B	36 - 104
9	X-RAY DIFFRACTION	9	B	105 - 143
10	X-RAY DIFFRACTION	10	B	144 - 223
11	X-RAY DIFFRACTION	11	C	22 - 40
12	X-RAY DIFFRACTION	12	C	41 - 98
13	X-RAY DIFFRACTION	13	C	99 - 143
14	X-RAY DIFFRACTION	14	C	144 - 211
15	X-RAY DIFFRACTION	15	C	212 - 223
16	X-RAY DIFFRACTION	16	D	-4 - 11
17	X-RAY DIFFRACTION	17	D	12 - 62
18	X-RAY DIFFRACTION	18	D	63 - 68
19	X-RAY DIFFRACTION	19	D	69 - 205
20	X-RAY DIFFRACTION	20	D	206 - 223

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