PDB-3ctw: Crystal Structure of RcdA from Caulobacter crescentus CB15

ID or keywords:

Entry

Database: PDB / ID: 3ctw

Title

Crystal Structure of RcdA from Caulobacter crescentus CB15

Components

RcdA

Keywords

PROTEIN BINDING

Function / homology

Protein of unknown function DUF1465 / Protein of unknown function DUF1465 / AraC-like superfamily / Protein of unknown function (DUF1465) /

Helicase, Ruva Protein; domain 3 / Orthogonal Bundle / Mainly Alpha / Regulator of CtrA degradation

Function and homology information

Biological species

Caulobacter vibrioides (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MAD / Resolution: 2.9 Å

Authors

Wilbur, J.D. / Taylor, J.A. / Kathleen, R.R.

Citation

Journal: To be Published
Title: Crystal Structure of RcdA yields insights into efficient CtrA proteolysis
Authors: Wilbur, J.D. / Taylor, J.A. / Kathleen, R.R.

History

Deposition	Apr 14, 2008	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jul 14, 2009	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Version format compliance
Revision 1.2	Oct 25, 2017	Group: Refinement description / Category: software
Revision 1.3	Jun 6, 2018	Group: Data collection / Refinement description / Source and taxonomy Category: entity_src_gen / software Item: _entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id ..._entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _software.classification
Revision 1.4	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_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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PDBx/mmCIF format	3ctw.cif.gz	61 KB	Display	PDBx/mmCIF format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ct/3ctw ftp://data.pdbj.org/pub/pdb/validation_reports/ct/3ctw	HTTPS FTP

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Related structure data

Similar structure data	2ak3-2 5jkt-1 5g5x-d 6pdk-d 2o74-1 3u02-5 5eak-2 2o73-2 4e1b-d 3bbt-1 Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

B: RcdA

D: RcdA

hetero molecules

38.6 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)	75.458, 75.458, 81.419
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	78
Space group name H-M	P4₃

Details

biological unit is the same as asym.

#1: Protein	RcdA Mass: 19054.375 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Caulobacter vibrioides (bacteria) / Strain: CB15 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9A3A9
#2: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C₂H₆O₂
#3: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 6 / 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: 3.04 Å³/Da / Density % sol: 59.56 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 100mM HEPES, 1.75M Formate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

Diffraction

ID	Crystal-ID
1	1
2	1

Diffraction source

Source	Site	Beamline	ID	Wavelength (Å)
SYNCHROTRON	ALS	5.0.2	1	0.97957,1.01986,0.97972
SYNCHROTRON	ALS	8.3.1	2	1.1

Detector

Type: ADSC Q315 / Detector: CCD / Date: Aug 26, 2007

Radiation

ID	Protocol	Monochromatic (M) / Laue (L)	Scattering type	Wavelength-ID
1	MAD	M	x-ray	1
2	SINGLE WAVELENGTH	M	x-ray	1

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	0.97957	1
2	1.01986	1
3	0.97972	1
4	1.1	1

Reflection

Redundancy: 4.3 % / Av σ(I) over netI: 5.1 / Number: 32822 / R_merge(I) obs: 0.164 / Χ²: 1.47 / D res high: 3.2 Å / D res low: 50 Å / Num. obs: 7666 / % possible obs: 100

Diffraction reflection shell

Highest resolution (Å)	Lowest resolution (Å)	% possible obs (%)	ID	R_merge(I) obs	Chi squared	Redundancy
6.89	50	100	1	0.074	4.685	4.2
5.47	6.89	100	1	0.145	1.365	4.3
4.78	5.47	100	1	0.136	1.269	4.1
4.34	4.78	100	1	0.136	1.309	4.3
4.03	4.34	100	1	0.178	1.279	4.3
3.79	4.03	100	1	0.191	1.164	4.3
3.6	3.79	100	1	0.26	0.97	4.3
3.45	3.6	100	1	0.328	0.973	4.3
3.31	3.45	100	1	0.43	0.858	4.3
3.2	3.31	100	1	0.567	0.791	4.3

Reflection

Resolution: 2.8→50 Å / Num. obs: 10955 / % possible obs: 96.9 % / Redundancy: 4.8 % / R_merge(I) obs: 0.099 / Χ²: 1.033 / Net I/σ(I): 7.5

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique all	Χ²	Diffraction-ID	% possible all
2.8-2.9	3.9	0.458	834	0.733	1,2	75.4
2.9-3.02	4.3	0.488	1047	0.833	1,2	92.9
3.02-3.15	4.8	0.411	1111	0.893	1,2	99.9
3.15-3.32	5	0.284	1113	1.028	1,2	100
3.32-3.53	5	0.187	1140	1.154	1,2	100
3.53-3.8	5	0.131	1135	1.192	1,2	100
3.8-4.18	5	0.093	1136	1.072	1,2	100
4.18-4.79	5	0.075	1131	1.18	1,2	100
4.79-6.03	4.9	0.077	1133	1.152	1,2	100
6.03-50	4.8	0.039	1175	0.902	1,2	100

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Phasing

Phasing	Method: MAD

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Processing

Software

Name	Version	Classification
DENZO		data reduction
SCALEPACK		data scaling
SHELX		phasing
SHELX		model building
REFMAC	5.4.0067	refinement
PDB_EXTRACT	3.005	data extraction
SHELXD		phasing

Refinement

Method to determine structure:

MAD / Resolution: 2.9→44.63 Å / Cor.coef. F_o:F_c: 0.891 / Cor.coef. F_o:F_c free: 0.88 / SU B: 34.563 / SU ML: 0.321 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.811 / ESU R Free: 0.413 / Stereochemistry target values: MAXIMUM LIKELIHOOD

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.312	477	4.7 %	RANDOM
R_work	0.274	-	-	-
obs	0.276	10107	99.11 %	-

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: 8.772 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.02 Å²	0 Å²	0 Å²
2-	-	0.02 Å²	0 Å²
3-	-	-	-0.05 Å²

Refinement step

Cycle: LAST / Resolution: 2.9→44.63 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1866	0	32	6	1904

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.011	0.021	1938
X-RAY DIFFRACTION	r_angle_refined_deg	1.645	1.977	2597
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	24.29	5	238
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	26.251	22.526	95
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	16.263	15	324
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	15.55	15	24
X-RAY DIFFRACTION	r_chiral_restr	0.112	0.2	285
X-RAY DIFFRACTION	r_gen_planes_refined	0.008	0.021	1465
X-RAY DIFFRACTION	r_mcbond_it	0.272	1.5	1201
X-RAY DIFFRACTION	r_mcangle_it	0.532	2	1891
X-RAY DIFFRACTION	r_scbond_it	0.82	3	737
X-RAY DIFFRACTION	r_scangle_it	1.383	4.5	706

LS refinement shell

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

	R_factor	Num. reflection	% reflection
R_free	0.33	35	-
R_work	0.309	620	-
all	-	655	-
obs	-	-	89.6 %

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	12.3598	-3.9152	3.669	14.8512	7.8213	7.0321	0.4026	0.0869	0.6097	1.5576	-1.0945	-3.3728	-1.2598	1.3972	0.6919	0.5555	-0.2422	0.0056	0.5256	0.1221	0.5291	43.658	7.68	14.303
2	4.2686	1.3971	-0.3764	1.8257	0.788	5.7019	0.1049	0.0256	-0.1166	0.0519	-0.1026	0.4744	0.1577	-0.3986	-0.0023	0.3379	-0.0287	-0.0334	0.26	-0.0674	0.3657	29.389	-9.885	14.087
3	18.1971	3.6067	-9.0026	12.2929	-0.7535	16.4267	0.1542	-1.1613	-0.4254	1.0386	-0.4421	1.6378	-1.8276	-1.1446	0.2879	0.6404	0.0509	0.0009	0.4361	0.0698	0.5809	33.396	8.135	6.106
4	2.6771	6.6233	1.6741	22.109	-3.0965	10.2034	-0.714	-1.7524	2.292	0.3909	0.6409	3.2827	0.8396	-1.3433	0.0731	0.2842	-0.1133	-0.0116	0.4214	0.0203	0.8331	21.927	-11.222	24.087
5	4.3489	8.3249	-0.9246	22.029	-3.7058	14.4846	-0.2517	0.4569	1.065	1.2432	0.909	1.4374	-1.4392	-1.0535	-0.6573	0.4899	0.063	0.0001	0.1839	0.0306	0.506	32.28	7.378	17.269
6	9.4383	3.9034	-3.1262	25.0845	10.7214	10.3623	-0.3629	0.2099	-1.2631	0.7472	-0.1504	-2.3726	2.5027	0.5227	0.5133	0.8087	0.1441	0.0286	0.3433	0.0858	0.5273	40.785	-9.995	-6.639
7	4.7785	-3.4104	0.1716	6.5051	-1.7504	4.5681	0.1162	0.0064	0.3406	0.216	0.0956	0.2787	-0.6502	-0.2543	-0.2119	0.4384	-0.0112	0.032	0.2136	-0.0711	0.345	32.565	11.585	-6.852
8	7.5852	-3.8547	3.9145	4.1891	-3.219	14.3913	-0.2503	0.1188	-0.5848	-0.0952	0.1364	0.3674	0.6931	-1.1341	0.1139	0.5499	-0.0425	-0.0118	0.3726	0.0226	0.5091	32.932	-7.29	1.578
9	55.3682	-13.9074	18.3855	48.6304	-4.5252	6.6354	0.3572	0.0214	-2.7492	-0.8088	1.3783	2.8589	-0.2899	-3.5433	-1.7355	0.2726	0.0511	0.0067	0.4749	0.032	0.5281	27.207	14.988	-16.61
10	2.4877	-2.3289	-1.3558	15.4322	-8.8523	9.8959	-0.5996	0.2731	-0.9987	-1.4048	1.3389	1.3355	1.3785	-1.2041	-0.7393	0.4581	-0.1382	-0.0258	0.2077	-0.0094	0.4894	30.411	-6.654	-10.384

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	B	A	17 - 33	17 - 33
2	X-RAY DIFFRACTION	2	B	A	34 - 88	34 - 88
3	X-RAY DIFFRACTION	3	B	A	89 - 102	89 - 102
4	X-RAY DIFFRACTION	4	B	A	114 - 125	114 - 125
5	X-RAY DIFFRACTION	5	B	A	126 - 147	126 - 147
6	X-RAY DIFFRACTION	6	D	B	21 - 33	21 - 33
7	X-RAY DIFFRACTION	7	D	B	34 - 87	34 - 87
8	X-RAY DIFFRACTION	8	D	B	88 - 103	88 - 103
9	X-RAY DIFFRACTION	9	D	B	115 - 125	115 - 125
10	X-RAY DIFFRACTION	10	D	B	126 - 150	126 - 150

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