PDB-5dqw: The crystal structure of Bacillus subtilis YpgQ in complex with ADP

ID or keywords:

Entry

Database: PDB / ID: 5dqw

Title

The crystal structure of Bacillus subtilis YpgQ in complex with ADP

Components

Uncharacterized protein

Keywords

HYDROLASE / HD domain

Function / homology

Function and homology information

HD-domain/PDEase-like / Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #1910 / Cyclin A; domain 1 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Up-down Bundle / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology

Biological species

Bacillus subtilis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.15 Å

Authors

Jeon, Y.J. / Song, W.S. / Yoon, S.I.

Citation

Journal: J.Struct.Biol. / Year: 2016
Title: Structural and biochemical characterization of bacterial YpgQ protein reveals a metal-dependent nucleotide pyrophosphohydrolase
Authors: Jeon, Y.J. / Park, S.C. / Song, W.S. / Kim, O.H. / Oh, B.C. / Yoon, S.I.

History

Deposition	Sep 15, 2015	Deposition site: RCSB / Processing site: PDBJ
Revision 1.0	Apr 27, 2016	Provider: repository / Type: Initial release
Revision 1.1	Jun 15, 2016	Group: Database references
Revision 1.2	Nov 8, 2023	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 / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list / struct_conn / struct_ncs_dom_lim Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation / _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

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5dqw.cif.gz	163.5 KB	Display	PDBx/mmCIF format
PDB format	pdb5dqw.ent.gz	127.7 KB	Display	PDB format
PDBx/mmJSON format	5dqw.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/dq/5dqw ftp://data.pdbj.org/pub/pdb/validation_reports/dq/5dqw	HTTPS FTP

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Related structure data

Related structure data	5dqvSC 5ihyC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	2d22-1 5dqv-d 2d1z-2 2d20-2 5gqe-2 4qpl-1 1it0-2 3kcq-2 2d1z-1 1it0-3 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

A: Uncharacterized protein

B: Uncharacterized protein

hetero molecules

48.3 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)	46.865, 52.499, 82.322
Angle α, β, γ (deg.)	90.00, 93.33, 90.00
Int Tables number	4
Space group name H-M	P12₁1

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B
1	2	A
2	2	B
1	3	A
2	3	B
1	4	A
2	4	B
1	5	A
2	5	B
1	6	A
2	6	B

NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Refine code	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	1	MET	MET	THR	THR	5	A	A	1 - 19	7 - 25
2	2	1	GLN	GLN	GLU	GLU	5	B	B	6 - 21	12 - 27
1	1	2	GLY	GLY	PRO	PRO	5	A	A	24 - 66	30 - 72
2	2	2	SER	SER	PRO	PRO	5	B	B	22 - 66	28 - 72
1	1	3	ADP	ADP	ADP	ADP	4	A	C	301
2	2	3	ADP	ADP	ADP	ADP	4	B	E	301
1	1	4	ASP	ASP	SER	SER	5	A	A	67 - 101	73 - 107
2	2	4	ASP	ASP	ARG	ARG	5	B	B	67 - 105	73 - 111
1	1	5	PRO	PRO	HIS	HIS	5	A	A	112 - 146	118 - 152
2	2	5	ILE	ILE	HIS	HIS	5	B	B	115 - 146	121 - 152
1	1	6	GLY	GLY	ASP	ASP	5	A	A	147 - 201	153 - 207
2	2	6	GLY	GLY	ASP	ASP	5	B	B	147 - 201	153 - 207

NCS ensembles :

ID
1
2
3
4
5
6

#1: Protein	Uncharacterized protein / YpgQ Mass: 23656.828 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: BIS30_00575 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0D5CVW2
#2: Chemical	ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₀H₁₅N₅O₁₀P₂ / Comment: ADP, energy-carrying molecule*YM
#3: Chemical	ChemComp-NI / NICKEL (II) ION Mass: 58.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ni
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 46 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION

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Sample preparation

Crystal	Density Matthews: 2.14 Å³/Da / Density % sol: 42.44 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 40% PEG 600, 0.1 M sodium citrate

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 1.00004 Å
Detector	Type: ADSC QUANTUM 270 / Detector: CCD / Date: Apr 8, 2014
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.00004 Å / Relative weight: 1
Reflection	Resolution: 2.15→30 Å / Num. obs: 22139 / % possible obs: 99.6 % / Redundancy: 3.7 % / Net I/σ(I): 34
Reflection shell	Resolution: 2.15→2.23 Å / Redundancy: 3.7 % / R_merge(I) obs: 0.441 / Mean I/σ(I) obs: 3.7 / % possible all: 100

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Processing

Software

Name	Version	Classification
REFMAC	5.5.0109	refinement
HKL-2000		data reduction
HKL-2000		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 5DQV

5dqv

Resolution: 2.15→30 Å / Cor.coef. F_o:F_c: 0.948 / Cor.coef. F_o:F_c free: 0.92 / Cross valid method: THROUGHOUT / ESU R: 0.263 / ESU R Free: 0.216 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.26134	1118	5.1 %	RANDOM
R_work	0.20939	-	-	-
obs	0.21209	20727	99.5 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 53.5 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-2.04 Å²	0 Å²	-1.63 Å²
2-	-	3.19 Å²	0 Å²
3-	-	-	-1.34 Å²

Refinement step

Cycle: 1 / Resolution: 2.15→30 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2836	0	56	46	2938

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.014	0.021	2941
X-RAY DIFFRACTION	r_bond_other_d	0	0.02	1867
X-RAY DIFFRACTION	r_angle_refined_deg	1.342	1.963	3995
X-RAY DIFFRACTION	r_angle_other_deg	4.35	3	4537
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.289	5	365
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	35.262	23.926	135
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.609	15	461
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	22.924	15	19
X-RAY DIFFRACTION	r_chiral_restr	0.081	0.2	461
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.02	3283
X-RAY DIFFRACTION	r_gen_planes_other	0.007	0.02	614
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	0.611	1.5	1830
X-RAY DIFFRACTION	r_mcbond_other	0	1.5	759
X-RAY DIFFRACTION	r_mcangle_it	1.087	2	2901
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	1.966	3	1111
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it	3.117	4.5	1094
X-RAY DIFFRACTION	r_scangle_other
X-RAY DIFFRACTION	r_long_range_B_refined
X-RAY DIFFRACTION	r_long_range_B_other
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Refine-ID: X-RAY DIFFRACTION

Ens-ID	Number	Type	Rms dev position (Å)	Weight position
1	65	MEDIUM POSITIONAL	0.2	0.5
1	65	LOOSE POSITIONAL	0.35	5
1	65	MEDIUM THERMAL	0.41	2
1	65	LOOSE THERMAL	0.57	10
2	255	MEDIUM POSITIONAL	0.25	0.5
2	270	LOOSE POSITIONAL	0.45	5
2	255	MEDIUM THERMAL	0.66	2
2	270	LOOSE THERMAL	0.86	10
3	37	MEDIUM POSITIONAL	0.36	0.5
3	37	MEDIUM THERMAL	0.88	2
4	208	MEDIUM POSITIONAL	0.25	0.5
4	190	LOOSE POSITIONAL	0.53	5
4	208	MEDIUM THERMAL	0.59	2
4	190	LOOSE THERMAL	0.76	10
5	187	MEDIUM POSITIONAL	0.14	0.5
5	177	LOOSE POSITIONAL	0.48	5
5	187	MEDIUM THERMAL	0.66	2
5	177	LOOSE THERMAL	0.75	10
6	326	MEDIUM POSITIONAL	0.17	0.5
6	411	LOOSE POSITIONAL	0.61	5
6	326	MEDIUM THERMAL	0.87	2
6	411	LOOSE THERMAL	1	10

LS refinement shell

Resolution: 2.15→2.206 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.331	77	-
R_work	0.259	1541	-
obs	-	-	99.94 %

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	12.3222	-7.3904	1.7727	21.4231	-2.2043	7.5969	0.0523	-0.5295	0.8568	0.3719	0.0907	-0.3529	-0.407	0.196	-0.1429	0.078	-0.0341	0.1353	0.184	-0.0597	0.3468	-8.882	-4.623	14.61
2	6.4276	3.2106	0.5435	5.2657	-1.8502	2.6859	0.1859	-0.4672	-0.2776	0.3017	-0.1366	0.0276	-0.1199	0.0677	-0.0494	0.0933	-0.0048	0.1348	0.154	-0.0075	0.2841	2.032	-4.03	10.91
3	5.8796	-0.28	0.8332	7.8772	1.1919	3.2457	-0.1019	0.1629	0.245	-0.5806	0.397	-0.3118	0.0893	-0.1182	-0.2952	0.1341	-0.0489	0.1247	0.084	-0.0266	0.2824	-7.061	-9.108	2.605
4	5.7451	-3.8635	4.2161	4.6256	-4.025	4.7574	0.389	0.0983	-0.2289	-0.4544	-0.1268	0.2106	0.5788	0.0371	-0.2623	0.1583	-0.0253	0.0843	0.0851	0.024	0.2383	11.83	-8.957	9.889
5	6.3312	-4.4535	2.8967	5.0347	-2.0605	3.3509	0.1923	0.2899	0.4382	-0.3079	-0.3889	-0.3853	0.3993	0.3561	0.1966	0.163	0.0065	0.1401	0.1924	0.0603	0.2821	24.152	-8.599	12.83
6	38.1884	-30.844	-6.8929	35.9038	3.0478	1.8435	1.0086	0.0345	-1.1625	-2.9606	-1.2301	1.5071	0.3564	0.3267	0.2215	0.9614	0.0056	0.2871	0.813	0.2466	1.0263	34.272	-37.109	24.008
7	6.2939	-1.4864	3.7159	10.5546	-0.8799	7.6441	-0.0748	-0.7558	-0.2204	-0.4034	0.1042	0.1826	0.1612	-0.1578	-0.0293	0.3028	0.046	0.1443	0.3814	0.2153	0.4852	33.483	-28.544	30.574
8	10.2716	-3.9946	-3.2601	6.6008	1.6263	7.6564	-0.0661	-0.551	-1.3726	-0.3053	0.2132	-0.1561	0.6492	-0.0946	-0.147	0.4278	-0.0416	0.1212	0.5312	0.3837	0.749	30.889	-39.45	36.801
9	11.1021	-2.8605	4.2949	3.2989	-1.8317	4.4597	-0.2588	-1.5694	-0.9632	0.3038	0.5995	0.2287	0.3218	-0.6297	-0.3406	0.2475	-0.0077	0.1269	0.3179	0.1597	0.3068	24.128	-21.129	30.292
10	7.4833	-3.0225	2.2287	4.6257	-2.8587	6.5034	-0.4906	-1.1415	0.2291	0.7501	0.5263	-0.0369	-0.1379	-0.4115	-0.0358	0.2877	0.07	0.1165	0.3889	-0.0722	0.2167	20.824	-10.381	31.931

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	1 - 19
2	X-RAY DIFFRACTION	2	A	24 - 66
3	X-RAY DIFFRACTION	3	A	67 - 101
4	X-RAY DIFFRACTION	4	A	112 - 146
5	X-RAY DIFFRACTION	5	A	147 - 202
6	X-RAY DIFFRACTION	6	B	6 - 22
7	X-RAY DIFFRACTION	7	B	23 - 66
8	X-RAY DIFFRACTION	8	B	67 - 105
9	X-RAY DIFFRACTION	9	B	115 - 146
10	X-RAY DIFFRACTION	10	B	147 - 201

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