PDB-4q86: YcaO with AMP Bound

ID or keywords:

Entry

Database: PDB / ID: 4q86

Title

YcaO with AMP Bound

Components

Ribosomal protein S12 methylthiotransferase accessory factor YcaO

Keywords

PROTEIN BINDING / YcaO ATP Binding Domain

Function / homology

Function and homology information

ATP diphosphatase activity / magnesium ion binding / cytosol
Similarity search - Function

Biological species

Escherichia coli (E. coli)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.25 Å

Authors

Chekan, J.R. / Nair, S.K.

Citation

Journal: Nat.Chem.Biol. / Year: 2014
Title: Discovery of a new ATP-binding motif involved in peptidic azoline biosynthesis.
Authors: Dunbar, K.L. / Chekan, J.R. / Cox, C.L. / Burkhart, B.J. / Nair, S.K. / Mitchell, D.A.

History

Deposition	Apr 25, 2014	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Aug 13, 2014	Provider: repository / Type: Initial release
Revision 1.1	Sep 3, 2014	Group: Database references
Revision 1.2	Oct 1, 2014	Group: Database references
Revision 1.3	Feb 28, 2024	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / software / struct_conn / struct_ncs_dom_lim / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _software.name / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _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	4q86.cif.gz	936.7 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	4q86_validation.pdf.gz	2.7 MB	Display	wwPDB validaton report
Full document	4q86_full_validation.pdf.gz	2.7 MB	Display
Data in XML	4q86_validation.xml.gz	177.4 KB	Display
Data in CIF	4q86_validation.cif.gz	249.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/q8/4q86 ftp://data.pdbj.org/pub/pdb/validation_reports/q8/4q86	HTTPS FTP

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Related structure data

Related structure data	4q84C 4q85C C: citing same article (ref.)
Similar structure data	4q85-1 4q85-2 4q85-3 4q84-d 4q85-4 3kd4-d 5dzt-d 3ztv-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) 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

4q84C

4q85C

C: citing same article (ref.)

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#129 - Sep 2010 Isocitrate Dehydrogenase similarity (1) #154 - Oct 2012 Citric Acid Cycle similarity (1) #24 - Dec 2001 Glycogen Phosphorylase similarity (1) #55 - Jul 2004 DNA Ligase similarity (1) #16 - Apr 2001 Aminoacyl-tRNA Synthetases similarity (1)

Deposited unit

A: Ribosomal protein S12 methylthiotransferase accessory factor YcaO

B: Ribosomal protein S12 methylthiotransferase accessory factor YcaO

C: Ribosomal protein S12 methylthiotransferase accessory factor YcaO

D: Ribosomal protein S12 methylthiotransferase accessory factor YcaO

E: Ribosomal protein S12 methylthiotransferase accessory factor YcaO

F: Ribosomal protein S12 methylthiotransferase accessory factor YcaO

G: Ribosomal protein S12 methylthiotransferase accessory factor YcaO

H: Ribosomal protein S12 methylthiotransferase accessory factor YcaO

hetero molecules

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

1

A: Ribosomal protein S12 methylthiotransferase accessory factor YcaO

B: Ribosomal protein S12 methylthiotransferase accessory factor YcaO

hetero molecules

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

2

C: Ribosomal protein S12 methylthiotransferase accessory factor YcaO

D: Ribosomal protein S12 methylthiotransferase accessory factor YcaO

hetero molecules

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

3

E: Ribosomal protein S12 methylthiotransferase accessory factor YcaO

F: Ribosomal protein S12 methylthiotransferase accessory factor YcaO

hetero molecules

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

4

G: Ribosomal protein S12 methylthiotransferase accessory factor YcaO

H: Ribosomal protein S12 methylthiotransferase accessory factor YcaO

hetero molecules

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

Unit cell

Length a, b, c (Å)	111.254, 112.949, 132.886
Angle α, β, γ (deg.)	89.94, 73.51, 77.23
Int Tables number	1
Space group name H-M	P1

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Component-ID: _ / Refine code: _

Dom-ID	Ens-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	THR	THR	ALA	ALA	A	A	2 - 582	2 - 582
2	1	THR	THR	ALA	ALA	B	B	2 - 582	2 - 582
1	2	ALA	ALA	LYS	LYS	A	A	12 - 580	12 - 580
2	2	ALA	ALA	LYS	LYS	C	C	12 - 580	12 - 580
1	3	THR	THR	PHE	PHE	A	A	2 - 583	2 - 583
2	3	THR	THR	PHE	PHE	D	D	2 - 583	2 - 583
1	4	THR	THR	LYS	LYS	A	A	4 - 580	4 - 580
2	4	THR	THR	LYS	LYS	E	E	4 - 580	4 - 580
1	5	GLY	GLY	LYS	LYS	A	A	8 - 580	8 - 580
2	5	GLY	GLY	LYS	LYS	F	F	8 - 580	8 - 580
1	6	PRO	PRO	LYS	LYS	A	A	7 - 580	7 - 580
2	6	PRO	PRO	LYS	LYS	G	G	7 - 580	7 - 580
1	7	THR	THR	ALA	ALA	A	A	2 - 582	2 - 582
2	7	THR	THR	ALA	ALA	H	H	2 - 582	2 - 582
1	8	ALA	ALA	LYS	LYS	B	B	12 - 580	12 - 580
2	8	ALA	ALA	LYS	LYS	C	C	12 - 580	12 - 580
1	9	THR	THR	ALA	ALA	B	B	2 - 582	2 - 582
2	9	THR	THR	ALA	ALA	D	D	2 - 582	2 - 582
1	10	THR	THR	LYS	LYS	B	B	4 - 580	4 - 580
2	10	THR	THR	LYS	LYS	E	E	4 - 580	4 - 580
1	11	GLY	GLY	LYS	LYS	B	B	8 - 580	8 - 580
2	11	GLY	GLY	LYS	LYS	F	F	8 - 580	8 - 580
1	12	PRO	PRO	LYS	LYS	B	B	7 - 580	7 - 580
2	12	PRO	PRO	LYS	LYS	G	G	7 - 580	7 - 580
1	13	THR	THR	TRP	TRP	B	B	2 - 584	2 - 584
2	13	THR	THR	TRP	TRP	H	H	2 - 584	2 - 584
1	14	ALA	ALA	LYS	LYS	C	C	12 - 580	12 - 580
2	14	ALA	ALA	LYS	LYS	D	D	12 - 580	12 - 580
1	15	ALA	ALA	LYS	LYS	C	C	12 - 580	12 - 580
2	15	ALA	ALA	LYS	LYS	E	E	12 - 580	12 - 580
1	16	ALA	ALA	LYS	LYS	C	C	12 - 580	12 - 580
2	16	ALA	ALA	LYS	LYS	F	F	12 - 580	12 - 580
1	17	ALA	ALA	LYS	LYS	C	C	12 - 580	12 - 580
2	17	ALA	ALA	LYS	LYS	G	G	12 - 580	12 - 580
1	18	ALA	ALA	LYS	LYS	C	C	12 - 580	12 - 580
2	18	ALA	ALA	LYS	LYS	H	H	12 - 580	12 - 580
1	19	THR	THR	LYS	LYS	D	D	4 - 580	4 - 580
2	19	THR	THR	LYS	LYS	E	E	4 - 580	4 - 580
1	20	GLY	GLY	LYS	LYS	D	D	8 - 580	8 - 580
2	20	GLY	GLY	LYS	LYS	F	F	8 - 580	8 - 580
1	21	PRO	PRO	LYS	LYS	D	D	7 - 580	7 - 580
2	21	PRO	PRO	LYS	LYS	G	G	7 - 580	7 - 580
1	22	THR	THR	ALA	ALA	D	D	2 - 582	2 - 582
2	22	THR	THR	ALA	ALA	H	H	2 - 582	2 - 582
1	23	GLY	GLY	LYS	LYS	E	E	8 - 580	8 - 580
2	23	GLY	GLY	LYS	LYS	F	F	8 - 580	8 - 580
1	24	PRO	PRO	LYS	LYS	E	E	7 - 580	7 - 580
2	24	PRO	PRO	LYS	LYS	G	G	7 - 580	7 - 580
1	25	THR	THR	LYS	LYS	E	E	4 - 580	4 - 580
2	25	THR	THR	LYS	LYS	H	H	4 - 580	4 - 580
1	26	GLY	GLY	LYS	LYS	F	F	8 - 580	8 - 580
2	26	GLY	GLY	LYS	LYS	G	G	8 - 580	8 - 580
1	27	GLY	GLY	LYS	LYS	F	F	8 - 580	8 - 580
2	27	GLY	GLY	LYS	LYS	H	H	8 - 580	8 - 580
1	28	PRO	PRO	LYS	LYS	G	G	7 - 580	7 - 580
2	28	PRO	PRO	LYS	LYS	H	H	7 - 580	7 - 580

NCS ensembles :

#1: Protein	Ribosomal protein S12 methylthiotransferase accessory factor YcaO Mass: 65702.109 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: ycaO, b0905, JW0888 / Production host: Escherichia coli (E. coli) / References: UniProt: P75838
#2: Chemical	ChemComp-AMP / ADENOSINE MONOPHOSPHATE Mass: 347.221 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C₁₀H₁₄N₅O₇P / Comment: AMP*YM
#3: Chemical	... ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 21 / Source method: obtained synthetically / Formula: Mg
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1987 / 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: 2.96 Å³/Da / Density % sol: 58.51 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 18% PEG 8,000 0.1 M magnesium acetate 0.1 M sodium cacodylate pH 6.5, 8 mg/mL protein, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
Detector	Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 18, 2013
Radiation	Monochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97872 Å / Relative weight: 1
Reflection	Resolution: 2.25→127.14 Å / Num. all: 264918 / Num. obs: 264918 / % possible obs: 93.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.8 % / R_sym value: 0.106 / Net I/σ(I): 10
Reflection shell	Resolution: 2.25→2.26 Å / Redundancy: 3.9 % / Mean I/σ(I) obs: 2 / Num. unique all: 1908 / R_sym value: 0.71 / % possible all: 66.1

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Processing

Software

Name	Version	Classification
HKL-2000		data collection
PHASER		phasing
REFMAC	5.8.0049	refinement
autoPROC		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.25→127.14 Å / Cor.coef. F_o:F_c: 0.923 / Cor.coef. F_o:F_c free: 0.902 / SU B: 7.856 / SU ML: 0.188 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.324 / ESU R Free: 0.231 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.24999	13386	5.1 %	RANDOM
R_work	0.21776	-	-	-
all	0.21937	270260	-	-
obs	0.21937	251531	93.07 %	-

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: 39.417 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.86 Å²	1.12 Å²	-0.47 Å²
2-	-	-0.63 Å²	0.28 Å²
3-	-	-	1.41 Å²

Refinement step

Cycle: LAST / Resolution: 2.25→127.14 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	36574	0	182	1987	38743

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.012	0.019	37656
X-RAY DIFFRACTION	r_bond_other_d	0.008	0.02	34197
X-RAY DIFFRACTION	r_angle_refined_deg	1.481	1.957	51250
X-RAY DIFFRACTION	r_angle_other_deg	1.488	3	78711
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.435	5	4619
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	38.107	24.792	1926
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.48	15	5889
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	20.854	15	192
X-RAY DIFFRACTION	r_chiral_restr	0.084	0.2	5510
X-RAY DIFFRACTION	r_gen_planes_refined	0.009	0.021	43524
X-RAY DIFFRACTION	r_gen_planes_other	0.007	0.02	8913
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
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	3.034	3.827	18500
X-RAY DIFFRACTION	r_mcbond_other	3.034	3.827	18499
X-RAY DIFFRACTION	r_mcangle_it	4.498	5.737	23111
X-RAY DIFFRACTION	r_mcangle_other	4.498	5.737	23112
X-RAY DIFFRACTION	r_scbond_it	3.356	4.104	19156
X-RAY DIFFRACTION	r_scbond_other	3.356	4.104	19157
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	5.212	6.043	28140
X-RAY DIFFRACTION	r_long_range_B_refined	7.581	31.059	45807
X-RAY DIFFRACTION	r_long_range_B_other	7.534	31.083	45090
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-ID	Dom-ID	Auth asym-ID	Number	Rms dev position (Å)
1	1	A	35247	0.07
1	2	B	35247	0.07
2	1	A	34567	0.07
2	2	C	34567	0.07
3	1	A	35361	0.07
3	2	D	35361	0.07
4	1	A	35095	0.07
4	2	E	35095	0.07
5	1	A	34132	0.08
5	2	F	34132	0.08
6	1	A	34921	0.07
6	2	G	34921	0.07
7	1	A	34905	0.08
7	2	H	34905	0.08
8	1	B	34347	0.08
8	2	C	34347	0.08
9	1	B	35226	0.07
9	2	D	35226	0.07
10	1	B	34808	0.08
10	2	E	34808	0.08
11	1	B	33996	0.09
11	2	F	33996	0.09
12	1	B	34588	0.08
12	2	G	34588	0.08
13	1	B	35155	0.08
13	2	H	35155	0.08
14	1	C	34452	0.07
14	2	D	34452	0.07
15	1	C	34554	0.07
15	2	E	34554	0.07
16	1	C	33826	0.09
16	2	F	33826	0.09
17	1	C	34227	0.08
17	2	G	34227	0.08
18	1	C	34401	0.07
18	2	H	34401	0.07
19	1	D	34816	0.08
19	2	E	34816	0.08
20	1	D	33928	0.09
20	2	F	33928	0.09
21	1	D	34614	0.08
21	2	G	34614	0.08
22	1	D	34784	0.08
22	2	H	34784	0.08
23	1	E	34040	0.09
23	2	F	34040	0.09
24	1	E	34439	0.08
24	2	G	34439	0.08
25	1	E	34510	0.08
25	2	H	34510	0.08
26	1	F	33785	0.09
26	2	G	33785	0.09
27	1	F	33777	0.1
27	2	H	33777	0.1
28	1	G	34410	0.08
28	2	H	34410	0.08

LS refinement shell

Resolution: 2.255→2.313 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.331	802	-
R_work	0.307	14266	-
obs	-	-	71.7 %

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