PDB-3dn7: Cyclic nucleotide binding regulatory protein from Cytophaga hutch...

ID or keywords:

Entry

Database: PDB / ID: 3dn7

Title

Cyclic nucleotide binding regulatory protein from Cytophaga hutchinsonii.

Components

Cyclic nucleotide binding regulatory protein

Keywords

structural genomics / unknown function / APC88869 / Cyclic nucleotide binding regulatory protein / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG

Function / homology

Jelly Rolls / Jelly Rolls / Sandwich / Mainly Beta / Cyclic nucleotide binding regulatory protein

Function and homology information

Biological species

Cytophaga hutchinsonii (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 1.8 Å

Authors

Osipiuk, J. / Maltseva, N. / Abdullah, J. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)

Citation

Journal: To be Published
Title: X-ray crystal structure of cyclic nucleotide binding regulatory protein from Cytophaga hutchinsonii.
Authors: Osipiuk, J. / Maltseva, N. / Abdullah, J. / Joachimiak, A.

History

Deposition	Jul 1, 2008	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Aug 26, 2008	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.2	Oct 25, 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	Nov 6, 2024	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / 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_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

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3dn7.cif.gz	83.9 KB	Display	PDBx/mmCIF format
PDB format	pdb3dn7.ent.gz	64 KB	Display	PDB format
PDBx/mmJSON format	3dn7.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/dn/3dn7 ftp://data.pdbj.org/pub/pdb/validation_reports/dn/3dn7	HTTPS FTP

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Related structure data

Similar structure data	3ob1-d 3t9w-d 5mu8-1 2ckh-d 1pnf-d 5an4-d 4xgv-3 2yvp-1 6rlw-5 6nnq-d Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search
Other databases	TargetDB: APC88869

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Cyclic nucleotide binding regulatory protein

B: Cyclic nucleotide binding regulatory protein

hetero molecules

47 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)	43.728, 83.519, 89.633
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

Details

putative biological unit is the same as asymetric unit

#1: Protein	Cyclic nucleotide binding regulatory protein Mass: 23390.320 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Cytophaga hutchinsonii (bacteria) / Strain: ATCC 33406 / Gene: CHU_1942 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q11TQ6
#2: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂H₆O₂
#3: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃H₈O₃
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 199 / Source method: isolated from a natural source / Formula: H₂O
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 grow	Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 0.1 mM HEPES buffer, 10% PEG 6000, 5 mM cAMP, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9792 Å
Detector	Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 14, 2008
Radiation	Monochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9792 Å / Relative weight: 1
Reflection	Resolution: 1.8→44.9 Å / Num. all: 30873 / Num. obs: 30873 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.8 % / B_iso Wilson estimate: 37.4 Å² / R_merge(I) obs: 0.081 / Χ²: 1.559 / Net I/σ(I): 10.3
Reflection shell	Resolution: 1.8→1.83 Å / Redundancy: 4.4 % / R_merge(I) obs: 0.686 / Mean I/σ(I) obs: 2.02 / Num. unique all: 1361 / Χ²: 0.941 / % possible all: 87.6

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Processing

Software

Name	Version	Classification
DENZO		data reduction
SCALEPACK		data scaling
REFMAC	5.2.0019	refinement
PDB_EXTRACT	3.006	data extraction
SBC-Collect		data collection
HKL-3000		data reduction
SHELXD		phasing
MLPHARE		phasing
DM		phasing
SOLVE		phasing
RESOLVE		phasing
HKL-3000		phasing

Refinement

Method to determine structure:

SAD / Resolution: 1.8→44.8 Å / Cor.coef. F_o:F_c: 0.967 / Cor.coef. F_o:F_c free: 0.963 / Occupancy max: 1 / Occupancy min: 0.35 / SU B: 4.918 / SU ML: 0.077 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.123 / ESU R Free: 0.107 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.19	1549	5 %	RANDOM
R_work	0.172	-	-	-
all	0.173	30799	-	-
obs	0.173	30799	98.61 %	-

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: 58.77 Å² / B_iso mean: 31.352 Å² / B_iso min: 20.56 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.03 Å²	0 Å²	0 Å²
2-	-	1.21 Å²	0 Å²
3-	-	-	-1.23 Å²

Refinement step

Cycle: LAST / Resolution: 1.8→44.8 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2475	0	14	199	2688

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.017	0.022	2612
X-RAY DIFFRACTION	r_angle_refined_deg	1.607	1.942	3522
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.331	5	312
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	33.653	24.014	142
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.695	15	491
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	19.587	15	17
X-RAY DIFFRACTION	r_chiral_restr	0.119	0.2	376
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.02	1981
X-RAY DIFFRACTION	r_nbd_refined	0.204	0.2	1189
X-RAY DIFFRACTION	r_nbtor_refined	0.31	0.2	1797
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.142	0.2	163
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.347	0.2	23
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.174	0.2	12
X-RAY DIFFRACTION	r_mcbond_it	0.967	1.5	1553
X-RAY DIFFRACTION	r_mcangle_it	1.492	2	2423
X-RAY DIFFRACTION	r_scbond_it	2.559	3	1216
X-RAY DIFFRACTION	r_scangle_it	3.805	4.5	1089

LS refinement shell

Resolution: 1.799→1.846 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.292	84	-
R_work	0.24	1873	-
all	-	1957	-
obs	-	1957	86.33 %

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	4.8006	4.3605	-3.3426	4.727	-5.9425	13.3505	-0.0432	0.1365	0.2961	-0.0129	0.1258	0.5176	-0.2882	-0.4722	-0.0826	-0.1098	-0.0382	-0.0191	0.044	0.0153	-0.043	2.8614	76.8081	11.1426
2	0.8751	-0.5371	-0.9314	3.5897	0.5944	3.9711	-0.0099	-0.0921	0.1467	0.0868	0.1248	0.4373	-0.3937	-0.0761	-0.115	-0.1253	0.0746	0.0117	0.0049	0.0335	-0.0401	3.2532	86.8325	12.4337
3	6.6846	2.1298	4.1673	1.787	0.1452	3.8596	-0.159	0.3223	0.4338	-0.1006	0.0646	-0.074	-0.2434	-0.0392	0.0943	-0.0313	0.0204	-0.0222	-0.0103	0.0589	-0.1026	17.7419	91.6713	-4.0639
4	0.9728	0.2143	0.2473	0.0557	0.1478	1.0867	-0.0159	0.16	0.113	-0.0538	0.0093	0.0093	-0.0156	-0.0639	0.0066	-0.0628	0.0039	-0.0077	-0.0626	0.0097	-0.0573	20.1143	86.9775	3.2447
5	1.7978	-0.5222	-2.376	2.0211	-0.4946	4.4166	0.1788	-0.291	-0.0052	-0.158	-0.1969	-0.1889	-0.0569	0.3215	0.0182	-0.0354	0.0115	0.0101	-0.0585	0.0252	-0.0803	25.2637	81.7073	-0.5398
6	1.4228	-0.6056	-1.4734	1.3914	1.1214	3.8856	-0.0636	-0.1068	0.0343	0.0518	0.0213	-0.1452	0.0098	0.181	0.0423	-0.0641	-0.0087	-0.0231	-0.078	0.0058	-0.0546	25.85	87.8668	10.2585
7	1.415	0.0928	-0.2142	0.445	-1.3621	4.1731	0.0949	0.146	0.1101	0.0204	0.0784	-0.0011	-0.1444	-0.2199	-0.1733	-0.0669	0.0205	-0.0147	-0.0662	0.0116	-0.0894	14.1995	87.4619	3.0118
8	1.7458	1.1357	-0.7504	7.0926	-1.6716	1.9145	0.0395	-0.1365	0.0754	0.2181	0.0264	0.1595	-0.2402	-0.3041	-0.066	-0.062	0.0467	0.006	-0.0006	-0.0136	-0.092	9.9262	82.9384	20.465
9	0.0343	-0.0721	0.1188	0.1513	-0.2496	0.4116	-0.11	0.0843	0.1071	-0.0348	0.0992	-0.0128	0.1315	-0.0522	0.0109	-0.0374	-0.0002	-0.0035	-0.0351	-0.006	-0.0802	21.1425	71.9279	10.5482
10	74.2221	32.7587	0.2181	14.8934	-4.7155	53.2299	1.3748	1.7978	-2.7946	-1.2225	-0.4926	-0.7762	0.7518	-1.2085	-0.8822	0.3997	0.1081	-0.0883	0.5033	-0.0315	0.2128	33.0578	66.9872	-1.6532
11	8.1551	-2.0425	-2.4137	8.6366	1.5417	4.2339	-0.1247	-0.3791	-0.336	0.7001	0.1053	-0.4267	0.3404	0.1537	0.0194	0.0066	-0.0393	-0.019	-0.0072	-0.0109	-0.0846	25.2214	71.967	33.6561
12	2.0279	-2.7877	0.5819	15.563	0.3052	0.2711	0.0419	-0.1645	0.0201	0.0617	0.1009	-0.2147	0.1541	-0.4297	-0.1428	0.0342	0.0016	0.0486	-0.0272	-0.0011	-0.1452	16.6671	68.8482	36.5344
13	9.5376	-3.1258	-2.0074	2.7576	-0.4657	2.8384	-0.2526	-0.2891	-0.1736	0.0688	-0.0422	-0.2319	0.2194	0.1278	0.2947	-0.0556	0.0073	0.0044	-0.0901	0.0458	-0.0386	31.0964	59.4992	29.0825
14	11.4831	3.1212	8.8953	3.2756	3.0814	8.9614	0.1781	-0.2114	-0.5459	-0.1035	-0.1049	-0.3049	0.3986	0.2095	-0.0733	-0.0886	0.05	0.0431	-0.0876	0.0261	-0.006	36.4817	56.9765	16.3553
15	1.046	0.1962	-0.8771	0.4032	-0.0079	2.0915	0.0253	-0.051	-0.1236	-0.0434	-0.0734	-0.1329	0.0773	0.1617	0.0481	-0.073	0.0194	0.0275	-0.059	0.0106	-0.049	35.2954	64.3184	14.1116
16	2.1482	0.8305	-0.3605	1.8662	1.099	2.5802	-0.0095	0.1113	-0.0119	-0.2272	-0.1654	0.0133	-0.0732	-0.0967	0.175	-0.0534	0.0018	0.0059	-0.0793	-0.0001	-0.0795	28.3326	63.8154	15.1914
17	8.2149	0.5879	0.2007	0.043	-0.0234	1.6185	-0.069	-0.0287	-0.055	0.0282	-0.0326	-0.0649	0.1313	-0.0502	0.1016	-0.0724	-0.016	-0.0036	-0.0914	0.032	-0.0572	26.44	62.0915	24.6371
18	6.3032	-3.9587	-1.4404	10.7256	7.312	5.3119	-0.1173	-0.1014	-0.4646	0.7676	-0.1468	0.4876	0.4796	-0.2221	0.2641	-0.0608	-0.0756	0.0461	0.0428	0.032	-0.0709	12.2165	64.9059	27.427
19	0.913	0.4483	-0.2725	0.5348	-0.5744	0.9968	-0.0701	-0.0837	-0.0005	-0.008	-0.0495	-0.0571	0.0212	-0.0161	0.1196	-0.0571	0.0137	-0.0081	-0.0675	0.0131	-0.0627	22.2492	76.0932	18.5457
20	28.4149	-0.1243	-7.5577	13.3913	-9.9557	27.8729	-0.2987	0.6194	0.4052	-0.7578	0.18	-1.5409	-0.4388	1.9046	0.1187	0.053	-0.0409	0.0214	0.1889	0.0747	0.1622	35.8071	79.8591	3.9307

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	1 - 16	4 - 19
2	X-RAY DIFFRACTION	2	A	A	17 - 30	20 - 33
3	X-RAY DIFFRACTION	3	A	A	31 - 40	34 - 43
4	X-RAY DIFFRACTION	4	A	A	41 - 60	44 - 63
5	X-RAY DIFFRACTION	5	A	A	61 - 79	64 - 82
6	X-RAY DIFFRACTION	6	A	A	80 - 95	83 - 98
7	X-RAY DIFFRACTION	7	A	A	96 - 109	99 - 112
8	X-RAY DIFFRACTION	8	A	A	110 - 123	113 - 126
9	X-RAY DIFFRACTION	9	A	A	124 - 141	127 - 144
10	X-RAY DIFFRACTION	10	A	A	142 - 146	145 - 149
11	X-RAY DIFFRACTION	11	B	B	-2 - 13	1 - 16
12	X-RAY DIFFRACTION	12	B	B	14 - 25	17 - 28
13	X-RAY DIFFRACTION	13	B	B	26 - 33	29 - 36
14	X-RAY DIFFRACTION	14	B	B	34 - 43	37 - 46
15	X-RAY DIFFRACTION	15	B	B	44 - 74	47 - 77
16	X-RAY DIFFRACTION	16	B	B	75 - 98	78 - 101
17	X-RAY DIFFRACTION	17	B	B	99 - 112	102 - 115
18	X-RAY DIFFRACTION	18	B	B	113 - 118	116 - 121
19	X-RAY DIFFRACTION	19	B	B	119 - 139	122 - 142
20	X-RAY DIFFRACTION	20	B	B	140 - 145	143 - 148

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