PDB-2db4: Crystal structure of rotor ring with DCCD of the V- ATPase from E...

ID or keywords:

Entry

Database: PDB / ID: 2db4

Title

Crystal structure of rotor ring with DCCD of the V- ATPase from Enterococcus hirae

Components

V-Type Sodium ATPase Subunit K

Keywords

HYDROLASE / NtpK /

V-ATPase / Na(+)-ATPase / DCCD /

Proteolipid /

Enterococcus hirae /

Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI

Function / homology

Function and homology information

proton-transporting V-type ATPase, V0 domain / sodium ion transport / proton-transporting ATPase activity, rotational mechanism / identical protein binding /

plasma membrane
Similarity search - Function

Biological species

Enterococcus hirae (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.4 Å

Authors

Murata, T. / Yamato, I. / Kakinuma, Y. / Shirouzu, M. / Walker, J.E. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Citation

Journal: Proc.Natl.Acad.Sci.USA / Year: 2011
Title: Structure of the rotor ring modified with N,N'-dicyclohexylcarbodiimide of the Na+-transporting vacuolar ATPase.
Authors: Mizutani, K. / Yamamoto, M. / Suzuki, K. / Yamato, I. / Kakinuma, Y. / Shirouzu, M. / Walker, J.E. / Yokoyama, S. / Iwata, S. / Murata, T.

History

Deposition	Dec 15, 2005	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Dec 5, 2006	Provider: repository / Type: Initial release
Revision 1.1	Apr 30, 2008	Group: Version format compliance
Revision 1.2	Jul 13, 2011	Group: Advisory / Version format compliance
Revision 1.3	Sep 28, 2011	Group: Database references
Revision 1.4	May 23, 2012	Group: Non-polymer description

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	2db4.cif.gz	312.8 KB	Display	PDBx/mmCIF format
PDB format	pdb2db4.ent.gz	272.5 KB	Display	PDB format
PDBx/mmJSON format	2db4.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/db/2db4 ftp://data.pdbj.org/pub/pdb/validation_reports/db/2db4	HTTPS FTP

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Related structure data

Related structure data	3aouC 2bl2 2cyd C: citing same article (ref.)
Similar structure data	2cyd-d 2bl2-d 5j09-d 4y4m-d 5mx5-2 3aou-d 5mx5-1 5frq-d Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search
Other databases	TargetDB: ar_001000494.1

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#72 - Dec 2005 ATP Synthase similarity (4) #219 - Mar 2018 Vacuolar ATPase similarity (4) #244 - Apr 2020 Photosynthetic Supercomplexes similarity (1) #22 - Oct 2001 Photosystem I similarity (1) #59 - Nov 2004 Photosystem II similarity (1) #66 - Jun 2005 Carotenoid Oxygenase similarity (1)

Deposited unit

A: V-Type Sodium ATPase Subunit K

B: V-Type Sodium ATPase Subunit K

C: V-Type Sodium ATPase Subunit K

D: V-Type Sodium ATPase Subunit K

E: V-Type Sodium ATPase Subunit K

F: V-Type Sodium ATPase Subunit K

G: V-Type Sodium ATPase Subunit K

H: V-Type Sodium ATPase Subunit K

I: V-Type Sodium ATPase Subunit K

J: V-Type Sodium ATPase Subunit K

hetero molecules

182 kDa, 10 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)	120.214, 125.229, 211.577
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Refine code: 1

Dom-ID	Component-ID	Ens-ID	Beg label comp-ID	End label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	1	MET	ALA	A	A	1 - 156	1 - 156
2	1	1	MET	ALA	B	B	1 - 156	1 - 156
3	1	1	MET	ALA	G	G	1 - 156	1 - 156
4	1	1	MET	ALA	D	D	1 - 156	1 - 156
5	1	1	MET	ALA	E	E	1 - 156	1 - 156
6	1	1	MET	ALA	H	H	1 - 156	1 - 156
1	1	2	MET	PRO	A	A	1 - 49	1 - 49
2	1	2	MET	PRO	C	C	1 - 49	1 - 49
3	1	2	MET	PRO	F	F	1 - 49	1 - 49
4	2	2	LYS	ALA	A	A	51 - 156	51 - 156
5	2	2	LYS	ALA	C	C	51 - 156	51 - 156
6	2	2	LYS	ALA	F	F	51 - 156	51 - 156
1	1	3	MET	TYR	A	A	1 - 4	1 - 4
2	1	3	MET	TYR	I	I	1 - 4	1 - 4
3	2	3	VAL	GLN	A	A	13 - 48	13 - 48
4	2	3	VAL	GLN	I	I	13 - 48	13 - 48
5	3	3	ALA	PHE	A	A	55 - 77	55 - 77
6	3	3	ALA	PHE	I	I	55 - 77	55 - 77
7	4	3	VAL	PRO	A	A	86 - 125	86 - 125
8	4	3	VAL	PRO	I	I	86 - 125	86 - 125
9	5	3	HIS	LEU	A	A	127 - 154	127 - 154
10	5	3	HIS	LEU	I	I	127 - 154	127 - 154
11	6	3	NA	LHG	A	K - V	557 - 559	1
12	6	3	NA	LHG	I	S - LA	8157 - 8159	1
1	1	4	VAL	ILE	A	A	13 - 78	13 - 78
2	1	4	VAL	ILE	J	J	13 - 78	13 - 78
3	2	4	GLY	ALA	A	A	89 - 156	89 - 156
4	2	4	GLY	ALA	J	J	89 - 156	89 - 156

NCS ensembles :

ID
1
2
3
4

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Protein , 1 types, 10 molecules ABCDEFGHIJ

#1: Protein	V-Type Sodium ATPase Subunit K / Na+ / - translocating ATPase subunit K / Sodium ATPase proteolipid component Mass: 16043.918 Da / Num. of mol.: 10 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterococcus hirae (bacteria) / Production host: Enterococcus hirae (bacteria) / Strain (production host): 25D References: UniProt: P43457, H+-transporting two-sector ATPase

#1: Protein

V-Type Sodium ATPase Subunit K / Na+ / - translocating ATPase subunit K / Sodium ATPase proteolipid component

Mass: 16043.918 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Enterococcus hirae (bacteria) / Production host:

Enterococcus hirae (bacteria) / Strain (production host): 25D
References: UniProt: P43457,

H+-transporting two-sector ATPase

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Non-polymers , 5 types, 295 molecules

#2: Chemical	ChemComp-DCW / DICYCLOHEXYLUREA / Dicyclohexylurea Mass: 224.342 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C₁₃H₂₄N₂O
#3: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Na
#4: Chemical	ChemComp-LHG / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / Phosphatidylglycerol Mass: 722.970 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: C₃₈H₇₅O₁₀P / Comment: phospholipid*YM
#5: Chemical	ChemComp-UMQ / UNDECYL-MALTOSIDE / UNDECYL-BETA-D-MALTOPYRANOSIDE Mass: 496.589 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C₂₃H₄₄O₁₁ / Comment: detergent*YM
#6: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 245 / 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: 4.9 Å³/Da / Density % sol: 74.89 %
Crystal grow	Temperature: 296 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 32% PEG 400, 240mM Sodium citrate, 100mM Tris-HCl (pH 7.5), 4% Glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 296K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å
Detector	Type: RIGAKU / Detector: IMAGE PLATE / Date: Jun 1, 2005
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2.4→107.83 Å / Num. all: 125160 / Num. obs: 124723 / Observed criterion σ(I): 0 / Redundancy: 4.7 % / B_iso Wilson estimate: 57.321 Å² / R_merge(I) obs: 0.091 / Net I/σ(I): 11.2
Reflection shell	Resolution: 2.4→2.462 Å / Redundancy: 3.7 % / R_merge(I) obs: 0.605 / Mean I/σ(I) obs: 1.8 / Num. unique all: 8579

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Processing

Software

Name	Version	Classification
REFMAC	5.2.0005	refinement
MOSFLM		data reduction
CCP4	(SCALA)	data scaling
AMoRE		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.4→107.83 Å / Cor.coef. F_o:F_c: 0.921 / Cor.coef. F_o:F_c free: 0.919 / SU B: 10.704 / SU ML: 0.143 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 1.8 / ESU R: 0.242 / ESU R Free: 0.186 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.23094	6272	5 %	RANDOM
R_work	0.22499	-	-	-
obs	0.22529	118450	99.65 %	-
all	-	124797	-	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK

Displacement parameters

B_iso mean: 57.321 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-3.32 Å²	0 Å²	0 Å²
2-	-	2.75 Å²	0 Å²
3-	-	-	0.56 Å²

Refinement step

Cycle: LAST / Resolution: 2.4→107.83 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	11270	0	1134	245	12649

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.009	0.022	12839
X-RAY DIFFRACTION	r_angle_refined_deg	1.199	2.055	17091
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	4.705	5	1550
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	40.302	25.652	368
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.521	15	1995
X-RAY DIFFRACTION	r_chiral_restr	0.089	0.2	2006
X-RAY DIFFRACTION	r_gen_planes_refined	0.004	0.02	8622
X-RAY DIFFRACTION	r_nbd_refined	0.194	0.2	7257
X-RAY DIFFRACTION	r_nbtor_refined	0.3	0.2	8905
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.127	0.2	517
X-RAY DIFFRACTION	r_metal_ion_refined	0.019	0.2	2
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.182	0.2	29
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.173	0.2	7
X-RAY DIFFRACTION	r_mcbond_it	0.403	1.5	7660
X-RAY DIFFRACTION	r_mcangle_it	0.742	2	12229
X-RAY DIFFRACTION	r_scbond_it	0.943	3	5209
X-RAY DIFFRACTION	r_scangle_it	1.624	4.5	4862

Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-ID	Dom-ID	Auth asym-ID	Number	Type	Rms dev position (Å)	Weight position
1	1	A	1251	tight positional	0.02	0.05
1	2	B	1251	tight positional	0.02	0.05
1	3	G	1251	tight positional	0.02	0.05
1	4	D	1251	tight positional	0.02	0.05
1	5	E	1251	tight positional	0.02	0.05
1	6	H	1251	tight positional	0.02	0.05
2	1	A	1242	tight positional	0.02	0.05
2	2	C	1242	tight positional	0.02	0.05
2	3	F	1242	tight positional	0.02	0.05
3	1	A	1054	tight positional	0.04	0.05
4	1	A	1082	tight positional	0.03	0.05
1	1	A	1251	tight thermal	0.08	0.5
1	2	B	1251	tight thermal	0.05	0.5
1	3	G	1251	tight thermal	0.05	0.5
1	4	D	1251	tight thermal	0.04	0.5
1	5	E	1251	tight thermal	0.04	0.5
1	6	H	1251	tight thermal	0.06	0.5
2	1	A	1242	tight thermal	0.07	0.5
2	2	C	1242	tight thermal	0.05	0.5
2	3	F	1242	tight thermal	0.05	0.5
3	1	A	1054	tight thermal	0.11	0.5
4	1	A	1082	tight thermal	0.17	0.5

LS refinement shell

Resolution: 2.4→2.462 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.294	509	-
R_work	0.281	8579	-
obs	-	-	99.11 %

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	2.5598	-0.5527	0.1491	1.0373	0.314	1.5822	0.23	0.0459	0.4561	-0.0717	0.0247	-0.1574	-0.3788	0.2511	-0.2547	-0.0256	-0.0685	0.0931	-0.1639	-0.0655	0.0388	36.2306	58.7011	21.2007
2	2.1223	-0.4038	-0.0674	1.0687	0.1532	1.4429	0.1871	-0.159	0.3609	0.1678	0.0219	-0.102	-0.3661	0.3441	-0.2089	0.0525	-0.1028	0.0939	-0.0909	-0.1939	0.0257	34.2503	61.1297	38.846
3	1.1735	-0.4877	-0.765	1.3236	-0.1247	1.3255	0.1718	-0.4251	0.1581	0.3484	-0.0072	-0.0826	-0.2494	0.4516	-0.1647	0.0928	-0.088	0.0503	0.0708	-0.225	-0.0265	32.3237	52.7203	54.5862
4	2.7613	-0.507	-0.4887	1.637	0.1427	0.9852	0.0256	-0.7092	0.1284	0.4831	0.0692	-0.1179	-0.012	0.4588	-0.0947	0.1408	-0.0112	-0.0079	0.2179	-0.0651	-0.075	31.1189	36.6555	62.4186
5	2.9388	-0.4421	-0.6049	1.5428	0.258	0.9677	0.004	-0.6168	0.0564	0.4784	0.0386	-0.1291	0.1737	0.4337	-0.0426	0.1282	0.0728	0.0119	0.1468	0.1416	-0.0769	31.1218	19.0224	59.2715
6	2.183	0.1869	-0.8554	0.9962	0.1343	1.2345	-0.0543	-0.3562	-0.1608	0.2307	0.0055	-0.0788	0.296	0.3711	0.0488	0.0567	0.109	0.0496	-0.0383	0.2087	-0.0205	32.3608	6.5772	46.3721
7	2.1179	0.7354	-0.4924	0.9102	-0.2182	1.3343	-0.0249	-0.2243	-0.4215	0.0606	-0.0586	-0.0578	0.3049	0.2262	0.0836	-0.0395	0.0911	0.0533	-0.1563	0.1167	0.0095	34.365	4.0152	28.7323
8	2.636	0.5515	0.4478	0.7901	0.0107	1.4332	-0.0136	0.016	-0.4225	-0.0553	-0.0253	-0.0415	0.1999	0.178	0.0388	-0.1232	0.0522	0.0291	-0.1674	0.0229	-0.1002	36.4076	12.4371	13.0571
9	3.5002	-0.0421	0.5415	0.3547	-0.2041	0.726	0.0418	0.0779	-0.121	-0.0943	-0.0103	-0.0143	-0.0252	0.0853	-0.0315	-0.1866	0.0069	0.0149	-0.1262	-0.0029	-0.2097	37.6093	28.4971	5.281

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	A	A	1 - 156	1 - 156
2	X-RAY DIFFRACTION	2	B	B	1 - 156	1 - 156
3	X-RAY DIFFRACTION	3	C	C	1 - 156	1 - 156
4	X-RAY DIFFRACTION	4	D	D	1 - 156	1 - 156
5	X-RAY DIFFRACTION	5	E	E	1 - 156	1 - 156
6	X-RAY DIFFRACTION	6	F	F	1 - 156	1 - 156
7	X-RAY DIFFRACTION	7	G	G	1 - 156	1 - 156
8	X-RAY DIFFRACTION	8	H	H	1 - 156	1 - 156
9	X-RAY DIFFRACTION	9	I	I	1 - 156	1 - 156

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