PDB-5dqv: The crystal structure of Bacillus subtilis YpgQ

ID or keywords:

Entry

Database: PDB / ID: 5dqv

Title

The crystal structure of Bacillus subtilis YpgQ

Components

Uncharacterized protein

Keywords

HYDROLASE /

HD domain

Function / homology

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 / NICKEL (II) ION / :

Function and homology information

Biological species

Bacillus subtilis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2 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	Mar 20, 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 / citation / database_2 / 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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PDBx/mmCIF format	5dqv.cif.gz	164.6 KB	Display	PDBx/mmCIF format
PDB format	pdb5dqv.ent.gz	130.2 KB	Display	PDB format
PDBx/mmJSON format	5dqv.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/5dqv ftp://data.pdbj.org/pub/pdb/validation_reports/dq/5dqv	HTTPS FTP

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Related structure data

Related structure data	5dqwC 5ihyC C: citing same article (ref.)
Similar structure data	5dqw-d 5gqe-2 1it0-2 2d1z-2 2d22-1 1it0-3 2d23-2 2d24-2 1log-d 2p11-d 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

47.4 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)	47.061, 53.432, 82.610
Angle α, β, γ (deg.)	90.00, 94.13, 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

NCS domain segments:

Refine code: 5

Dom-ID	Component-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	1	MET	MET	THR	THR	A	A	1 - 19	7 - 25
2	2	1	MET	MET	LEU	LEU	B	B	1 - 18	7 - 24
1	1	2	ASP	ASP	PRO	PRO	A	A	26 - 66	32 - 72
2	2	2	ASP	ASP	PRO	PRO	B	B	26 - 66	32 - 72
1	1	3	ASP	ASP	SER	SER	A	A	67 - 101	73 - 107
2	2	3	THR	THR	ARG	ARG	B	B	68 - 105	74 - 111
1	1	4	PRO	PRO	HIS	HIS	A	A	112 - 146	118 - 152
2	2	4	LEU	LEU	HIS	HIS	B	B	113 - 146	119 - 152
1	1	5	GLY	GLY	ASP	ASP	A	A	147 - 201	153 - 207
2	2	5	GLY	GLY	ASP	ASP	B	B	147 - 201	153 - 207

NCS ensembles :

ID
1
2
3
4
5

#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-NI / NICKEL (II) ION / Nickel Mass: 58.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ni
#3: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 117 / 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: 2.19 Å³/Da / Density % sol: 43.82 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 38% PEG 600, 0.1 M MES

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.97956 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 8, 2013
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97956 Å / Relative weight: 1
Reflection	Resolution: 2→20 Å / Num. obs: 27729 / % possible obs: 99.3 % / Redundancy: 3.6 % / Net I/σ(I): 30.4
Reflection shell	Resolution: 2→2.07 Å / Redundancy: 3.7 % / R_merge(I) obs: 0.507 / Mean I/σ(I) obs: 3.2 / % possible all: 98.9

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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:

SAD / Resolution: 2→20 Å / Cor.coef. F_o:F_c: 0.955 / Cor.coef. F_o:F_c free: 0.936 / Cross valid method: THROUGHOUT / ESU R: 0.179 / ESU R Free: 0.158 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.22753	1385	5 %	RANDOM
R_work	0.18822	-	-	-
obs	0.19026	26237	99.15 %	-

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: 43.9 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-1.83 Å²	0 Å²	-0.37 Å²
2-	-	0.2 Å²	0 Å²
3-	-	-	1.57 Å²

Refinement step

Cycle: 1 / Resolution: 2→20 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2899	0	2	117	3018

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.016	0.022	2973
X-RAY DIFFRACTION	r_bond_other_d	0	0.02	1935
X-RAY DIFFRACTION	r_angle_refined_deg	1.376	1.945	4026
X-RAY DIFFRACTION	r_angle_other_deg	4.305	3	4720
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	4.78	5	375
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	36.396	24.255	141
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.807	15	506
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	23.751	15	19
X-RAY DIFFRACTION	r_chiral_restr	0.085	0.2	470
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	3321
X-RAY DIFFRACTION	r_gen_planes_other	0.009	0.02	606
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	0.776	1.5	1858
X-RAY DIFFRACTION	r_mcbond_other	0	1.5	767
X-RAY DIFFRACTION	r_mcangle_it	1.35	2	2968
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	2.31	3	1115
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it	3.668	4.5	1054
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	107	MEDIUM POSITIONAL	0.25	0.5
1	122	LOOSE POSITIONAL	0.42	5
1	107	MEDIUM THERMAL	0.52	2
1	122	LOOSE THERMAL	0.78	10
2	244	MEDIUM POSITIONAL	0.21	0.5
2	269	LOOSE POSITIONAL	0.44	5
2	244	MEDIUM THERMAL	0.76	2
2	269	LOOSE THERMAL	1.06	10
3	198	MEDIUM POSITIONAL	0.2	0.5
3	180	LOOSE POSITIONAL	0.33	5
3	198	MEDIUM THERMAL	0.65	2
3	180	LOOSE THERMAL	0.99	10
4	197	MEDIUM POSITIONAL	0.22	0.5
4	196	LOOSE POSITIONAL	0.24	5
4	197	MEDIUM THERMAL	1.19	2
4	196	LOOSE THERMAL	1.06	10
5	324	MEDIUM POSITIONAL	0.23	0.5
5	402	LOOSE POSITIONAL	0.52	5
5	324	MEDIUM THERMAL	0.73	2
5	402	LOOSE THERMAL	1.29	10

LS refinement shell

Resolution: 2→2.051 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.264	99	-
R_work	0.246	1930	-
obs	-	-	98.88 %

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	11.6375	-4.2703	1.0908	11.34	-0.0125	7.8905	-0.0223	-0.5009	0.9441	0.0528	0.1555	-0.2655	-0.404	-0.1135	-0.1332	0.046	-0.0086	0.0498	0.1983	-0.0553	0.1471	-9.134	-4.961	14.546
2	4.1051	2.0048	0.0391	4.7047	-0.7389	1.8306	0.1115	-0.2386	-0.136	0.1602	-0.1744	-0.0248	-0.0222	0.0291	0.0628	0.0622	0.01	0.0518	0.1385	0.0056	0.0641	1.807	-3.794	10.749
3	3.6919	-0.5609	0.5531	6.293	-0.0921	3.1143	-0.0315	0.1257	0.1653	-0.4916	0.0966	-0.063	0.064	-0.0418	-0.0651	0.1004	-0.0022	0.04	0.1364	-0.0239	0.0489	-7.368	-9.101	2.317
4	5.3832	-4.3089	3.6163	4.4506	-3.0009	2.6324	0.4177	0.1443	-0.3082	-0.4776	-0.1313	0.3078	0.4356	0.0265	-0.2864	0.2188	-0.0104	-0.0008	0.1717	0.0318	0.1631	11.689	-9.238	9.889
5	4.8103	-3.1928	1.8774	3.1504	-1.5049	2.0819	0.1071	0.2141	0.1738	-0.2158	-0.2544	-0.1701	0.2896	0.2311	0.1474	0.1223	0.0011	0.0687	0.2114	0.0671	0.0823	24.163	-9.605	12.576
6	17.148	-6.7734	-8.2753	9.513	-6.0503	17.2657	-0.1748	1.0243	-0.1098	-1.9366	-1.3472	-1.2391	2.3984	1.0855	1.5221	1.0803	0.2398	0.4577	0.6813	0.0991	0.7596	37.494	-37.807	25.18
7	2.4765	-1.8119	2.3838	13.362	-0.8158	7.781	0.0178	-0.2653	-0.111	-0.0226	-0.0226	-0.7094	0.2137	0.1016	0.0049	0.2495	0.0576	0.0274	0.3469	0.1481	0.2482	33.82	-28.489	31.194
8	10.9102	-4.1365	-0.5585	11.2086	0.6908	5.6252	-0.1407	-0.0192	-1.0824	0.1802	0.0738	0.0888	0.6154	-0.338	0.067	0.5837	0.0162	0.0589	0.4387	0.2083	0.3322	30.146	-39.754	36.91
9	6.5969	-4.3091	2.9321	6.2714	-3.0289	3.0554	-0.3737	-0.9607	-0.5595	0.7955	0.5575	0.1483	0.0228	-0.3499	-0.1838	0.2867	0.05	0.0457	0.367	0.1402	0.14	24.332	-21.501	31.569
10	11.6182	-5.3558	5.2766	7.7541	-4.2095	4.6041	-0.9585	-1.3621	0.5048	1.2511	0.7706	-0.2674	-0.5697	-0.6809	0.1878	0.4043	0.1686	0.0104	0.4614	-0.0646	0.0451	20.66	-10.412	31.942

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	26 - 66
3	X-RAY DIFFRACTION	3	A	67 - 101
4	X-RAY DIFFRACTION	4	A	112 - 146
5	X-RAY DIFFRACTION	5	A	147 - 204
6	X-RAY DIFFRACTION	6	B	1 - 18
7	X-RAY DIFFRACTION	7	B	26 - 66
8	X-RAY DIFFRACTION	8	B	68 - 105
9	X-RAY DIFFRACTION	9	B	113 - 146
10	X-RAY DIFFRACTION	10	B	147 - 201

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