PDB-4q85: YcaO with Non-hydrolyzable ATP (AMPCPP) Bound

ID or keywords:

Entry

Database: PDB / ID: 4q85

Title

YcaO with Non-hydrolyzable ATP (AMPCPP) Bound

Components

Ribosomal protein S12 methylthiotransferase accessory factor YcaO

Ribosome

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: 3.29 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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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/q8/4q85 ftp://data.pdbj.org/pub/pdb/validation_reports/q8/4q85	HTTPS FTP

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Related structure data

Related structure data	4q84C 4q86C C: citing same article (ref.)
Similar structure data	4q86-2 4q86-3 4q86-1 4q84-d 4q86-4 3kd4-d 5ig5-d 4rpg-d 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

4q86C

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	#104 - Aug 2008 Selenocysteine Synthase similarity (1) #146 - Feb 2012 Aminoglycoside Antibiotics similarity (1) #226 - Oct 2018 Aminoglycoside Antibiotics and Resistance similarity (1) #251 - Nov 2020 Adenylyl Cyclase 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
133 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)	110.282, 112.402, 130.683
Angle α, β, γ (deg.)	89.40, 73.63, 77.62
Int Tables number	1
Space group name H-M	P1

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Component-ID: 0 / Refine code: 0

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	ALA	ALA	LYS	LYS	A	A	12 - 580	12 - 580
2	1	ALA	ALA	LYS	LYS	B	B	12 - 580	12 - 580
1	2	GLU	GLU	ALA	ALA	A	A	14 - 581	14 - 581
2	2	GLU	GLU	ALA	ALA	C	C	14 - 581	14 - 581
1	3	ALA	ALA	LYS	LYS	A	A	12 - 580	12 - 580
2	3	ALA	ALA	LYS	LYS	D	D	12 - 580	12 - 580
1	4	ALA	ALA	LYS	LYS	A	A	12 - 580	12 - 580
2	4	ALA	ALA	LYS	LYS	E	E	12 - 580	12 - 580
1	5	ALA	ALA	LYS	LYS	A	A	12 - 580	12 - 580
2	5	ALA	ALA	LYS	LYS	F	F	12 - 580	12 - 580
1	6	SER	SER	LYS	LYS	A	A	25 - 580	25 - 580
2	6	SER	SER	LYS	LYS	G	G	25 - 580	25 - 580
1	7	ALA	ALA	LYS	LYS	A	A	12 - 580	12 - 580
2	7	ALA	ALA	LYS	LYS	H	H	12 - 580	12 - 580
1	8	GLU	GLU	LYS	LYS	B	B	14 - 580	14 - 580
2	8	GLU	GLU	LYS	LYS	C	C	14 - 580	14 - 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	ALA	ALA	B	B	2 - 581	2 - 581
2	10	THR	THR	ALA	ALA	E	E	2 - 581	2 - 581
1	11	GLN	GLN	LYS	LYS	B	B	3 - 580	3 - 580
2	11	GLN	GLN	LYS	LYS	F	F	3 - 580	3 - 580
1	12	SER	SER	LYS	LYS	B	B	25 - 580	25 - 580
2	12	SER	SER	LYS	LYS	G	G	25 - 580	25 - 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	GLU	GLU	LYS	LYS	C	C	14 - 580	14 - 580
2	14	GLU	GLU	LYS	LYS	D	D	14 - 580	14 - 580
1	15	GLU	GLU	LYS	LYS	C	C	14 - 580	14 - 580
2	15	GLU	GLU	LYS	LYS	E	E	14 - 580	14 - 580
1	16	GLU	GLU	LYS	LYS	C	C	14 - 580	14 - 580
2	16	GLU	GLU	LYS	LYS	F	F	14 - 580	14 - 580
1	17	SER	SER	LYS	LYS	C	C	25 - 580	25 - 580
2	17	SER	SER	LYS	LYS	G	G	25 - 580	25 - 580
1	18	GLU	GLU	LYS	LYS	C	C	14 - 580	14 - 580
2	18	GLU	GLU	LYS	LYS	H	H	14 - 580	14 - 580
1	19	THR	THR	ALA	ALA	D	D	2 - 581	2 - 581
2	19	THR	THR	ALA	ALA	E	E	2 - 581	2 - 581
1	20	GLN	GLN	LYS	LYS	D	D	3 - 580	3 - 580
2	20	GLN	GLN	LYS	LYS	F	F	3 - 580	3 - 580
1	21	SER	SER	LYS	LYS	D	D	25 - 580	25 - 580
2	21	SER	SER	LYS	LYS	G	G	25 - 580	25 - 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	GLN	GLN	ALA	ALA	E	E	3 - 581	3 - 581
2	23	GLN	GLN	ALA	ALA	F	F	3 - 581	3 - 581
1	24	SER	SER	LYS	LYS	E	E	25 - 580	25 - 580
2	24	SER	SER	LYS	LYS	G	G	25 - 580	25 - 580
1	25	THR	THR	ALA	ALA	E	E	2 - 581	2 - 581
2	25	THR	THR	ALA	ALA	H	H	2 - 581	2 - 581
1	26	SER	SER	LYS	LYS	F	F	25 - 580	25 - 580
2	26	SER	SER	LYS	LYS	G	G	25 - 580	25 - 580
1	27	GLN	GLN	LYS	LYS	F	F	3 - 580	3 - 580
2	27	GLN	GLN	LYS	LYS	H	H	3 - 580	3 - 580
1	28	SER	SER	LYS	LYS	G	G	25 - 580	25 - 580
2	28	SER	SER	LYS	LYS	H	H	25 - 580	25 - 580

NCS ensembles :

#1: Protein	Ribosomal protein S12 methylthiotransferase accessory factor YcaO / Ribosome 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-APC / DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER / ALPHA,BETA-METHYLENEADENOSINE-5'-TRIPHOSPHATE Mass: 505.208 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C₁₁H₁₈N₅O₁₂P₃ / Comment: AMP-CPP, energy-carrying molecule analogue*YM
#3: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 19 / Source method: obtained synthetically / Formula: Mg
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 432 / 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: 2.88 Å³/Da / Density % sol: 57.35 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 20% PEG 8,000 0.1 M magnesium acetate 0.1 M sodium cacodylate pH 6.5 6 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-G / Wavelength: 0.97857 Å
Detector	Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 2, 2013
Radiation	Monochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97857 Å / Relative weight: 1
Reflection	Resolution: 3.29→125.2 Å / Num. all: 89486 / Num. obs: 88591 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.5 % / R_merge(I) obs: 0.176 / Net I/σ(I): 2.5
Reflection shell	Resolution: 3.29→3.3 Å / Redundancy: 2.5 % / Mean I/σ(I) obs: 2.1 / R_sym value: 0.593 / % possible all: 98.2

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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: 3.29→125.2 Å / Cor.coef. F_o:F_c: 0.92 / Cor.coef. F_o:F_c free: 0.861 / SU B: 26.163 / SU ML: 0.415 / Cross valid method: THROUGHOUT / ESU R Free: 0.528 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.23928	4442	5 %	RANDOM
R_work	0.19002	-	-	-
obs	0.19248	84143	99.04 %	-
all	-	84993	-	-

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: 63.451 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.8 Å²	1.38 Å²	-0.03 Å²
2-	-	0.4 Å²	-1.79 Å²
3-	-	-	-0.17 Å²

Refinement step

Cycle: LAST / Resolution: 3.29→125.2 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	35815	0	174	432	36421

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.011	0.019	36875
X-RAY DIFFRACTION	r_bond_other_d	0.008	0.02	33389
X-RAY DIFFRACTION	r_angle_refined_deg	1.507	1.955	50208
X-RAY DIFFRACTION	r_angle_other_deg	1.441	3	76850
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.915	5	4511
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	37.294	24.804	1890
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	17.818	15	5731
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	19.482	15	183
X-RAY DIFFRACTION	r_chiral_restr	0.083	0.2	5393
X-RAY DIFFRACTION	r_gen_planes_refined	0.008	0.021	42564
X-RAY DIFFRACTION	r_gen_planes_other	0.006	0.02	8726
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	4.894	6.244	18092
X-RAY DIFFRACTION	r_mcbond_other	4.893	6.245	18091
X-RAY DIFFRACTION	r_mcangle_it	7.758	9.367	22587
X-RAY DIFFRACTION	r_mcangle_other	7.824	9.406	22588
X-RAY DIFFRACTION	r_scbond_it	4.949	6.577	18783
X-RAY DIFFRACTION	r_scbond_other	4.994	6.603	18784
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	8.061	9.772	27622
X-RAY DIFFRACTION	r_long_range_B_refined	12.605	50.713	42832
X-RAY DIFFRACTION	r_long_range_B_other	12.605	50.752	42780
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	33762	0.06
1	2	B	33762	0.06
2	1	A	33359	0.07
2	2	C	33359	0.07
3	1	A	33665	0.07
3	2	D	33665	0.07
4	1	A	33928	0.06
4	2	E	33928	0.06
5	1	A	32479	0.09
5	2	F	32479	0.09
6	1	A	32141	0.07
6	2	G	32141	0.07
7	1	A	33835	0.06
7	2	H	33835	0.06
8	1	B	33348	0.07
8	2	C	33348	0.07
9	1	B	34648	0.07
9	2	D	34648	0.07
10	1	B	34486	0.06
10	2	E	34486	0.06
11	1	B	32579	0.1
11	2	F	32579	0.1
12	1	B	32103	0.07
12	2	G	32103	0.07
13	1	B	34900	0.06
13	2	H	34900	0.06
14	1	C	33203	0.07
14	2	D	33203	0.07
15	1	C	33816	0.07
15	2	E	33816	0.07
16	1	C	31955	0.1
16	2	F	31955	0.1
17	1	C	31980	0.07
17	2	G	31980	0.07
18	1	C	33405	0.07
18	2	H	33405	0.07
19	1	D	34281	0.07
19	2	E	34281	0.07
20	1	D	32469	0.1
20	2	F	32469	0.1
21	1	D	31926	0.08
21	2	G	31926	0.08
22	1	D	34383	0.07
22	2	H	34383	0.07
23	1	E	32891	0.09
23	2	F	32891	0.09
24	1	E	32114	0.07
24	2	G	32114	0.07
25	1	E	34341	0.07
25	2	H	34341	0.07
26	1	F	30992	0.1
26	2	G	30992	0.1
27	1	F	32563	0.1
27	2	H	32563	0.1
28	1	G	32198	0.07
28	2	H	32198	0.07

LS refinement shell

Resolution: 3.287→3.372 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.326	342	-
R_work	0.292	6161	-
obs	-	-	98.65 %

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