PDB-10xk: Bifidobacterium primatium DnaA DI

ID or keywords:

Entry

Database: PDB / ID: 10xk

Title

Bifidobacterium primatium DnaA DI

Components

Chromosomal replication initiator protein DnaA

Keywords

DNA BINDING PROTEIN / Initiator

Function / homology

Function and homology information

regulation of DNA replication / DNA replication origin binding / DNA replication initiation / lipid binding / ATP binding / plasma membrane / cytoplasm
Similarity search - Function

Biological species

Bifidobacterium primatium (bacteria)

Method

X-RAY DIFFRACTION /

MOLECULAR REPLACEMENT / Resolution: 2.4 Å

Authors

Ellis, P.K. / Schumacher, M.A.

Funding support

United States, 2items

Organization	Grant number	Country
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	R35GM130290	United States
National Science Foundation (NSF, United States)	DGE 2139754	United States

Citation

Journal: To Be Published
Title: Structures reveal DnaA domain I dimer conserved across Actinomycetes: implications for replication initiation
Authors: Ellis, P.K. / Schumacher, M.A.

History

Deposition	Feb 11, 2026	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jun 3, 2026	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	10xk.cif.gz	324.1 KB	Display	PDBx/mmCIF format
PDB format	pdb10xk.ent.gz	234.5 KB	Display	PDB format
PDBx/mmJSON format	10xk.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/0x/10xk ftp://data.pdbj.org/pub/pdb/validation_reports/0x/10xk	HTTPS FTP

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Related structure data

Related structure data	10wyC 10wzC 10xaC 10xbC 10xcC 10xdC 10xeC 10xfC 10xgC 10xhC 10xlC 10xoC 10xpC 10yoC C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#168 - Dec 2013 DNA Helicase similarity (10)

Deposited unit

A: Chromosomal replication initiator protein DnaA

B: Chromosomal replication initiator protein DnaA

C: Chromosomal replication initiator protein DnaA

D: Chromosomal replication initiator protein DnaA

E: Chromosomal replication initiator protein DnaA

F: Chromosomal replication initiator protein DnaA

G: Chromosomal replication initiator protein DnaA

H: Chromosomal replication initiator protein DnaA

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

1

E: Chromosomal replication initiator protein DnaA

A: Chromosomal replication initiator protein DnaA

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

2

B: Chromosomal replication initiator protein DnaA

D: Chromosomal replication initiator protein DnaA

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

3

C: Chromosomal replication initiator protein DnaA

F: Chromosomal replication initiator protein DnaA

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

4

G: Chromosomal replication initiator protein DnaA

H: Chromosomal replication initiator protein DnaA

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

Unit cell

Length a, b, c (Å)	55.927, 124.131, 63.747
Angle α, β, γ (deg.)	90.000, 97.700, 90.000
Int Tables number	4
Space group name H-M	P12₁1
Space group name Hall	P2yb
Symmetry operation	#1: x,y,z #2: -x,y+1/2,-z

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details (eV)
d_1	ens_1	(chain "A" and (resid 4 through 7 or (resid 8...
d_2	ens_1	(chain "B" and (resid 4 through 7 or (resid 8...
d_3	ens_1	(chain "C" and (resid 4 through 7 or (resid 8...
d_4	ens_1	(chain "D" and (resid 4 through 7 or (resid 8...
d_5	ens_1	(chain "E" and (resid 4 through 7 or (resid 8...
d_6	ens_1	(chain "F" and (resid 4 through 7 or (resid 8...
d_7	ens_1	(chain "G" and (resid 4 through 10 or resid 13...
d_8	ens_1	(chain "H" and (resid 4 through 7 or (resid 8...

NCS domain segments:

Ens-ID: ens_1

Dom-ID	Component-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
d_1	1	ALA	ALA	ALA	ALA	A	A	4 - 10	7 - 13
d_1	2	ILE	ILE	ALA	ALA	A	A	13 - 17	16 - 20
d_1	3	ASP	ASP	LEU	LEU	A	A	19 - 21	22 - 24
d_1	4	THR	THR	PRO	PRO	A	A	26 - 29	29 - 32
d_1	5	ASP	ASP	ASP	ASP	A	A	31	34
d_1	6	SER	SER	VAL	VAL	A	A	33 - 35	36 - 38
d_1	7	ASP	ASP	VAL	VAL	A	A	37 - 43	40 - 46
d_1	8	ASP	ASP	SER	SER	A	A	45 - 46	48 - 49
d_1	9	ILE	ILE	ASN	ASN	A	A	48 - 54	51 - 57
d_1	10	ILE	ILE	ASN	ASN	A	A	56 - 63	59 - 66
d_1	11	ALA	ALA	LEU	LEU	A	A	66 - 68	69 - 71
d_1	12	ALA	ALA	GLY	GLY	A	A	70 - 77	73 - 80
d_1	13	PRO	PRO	ILE	ILE	A	A	79 - 84	82 - 87
d_1	14	ILE	ILE	VAL	VAL	A	A	86 - 87	89 - 90
d_2	1	ALA	ALA	ALA	ALA	B	B	4 - 10	7 - 13
d_2	2	ILE	ILE	ALA	ALA	B	B	13 - 17	16 - 20
d_2	3	ASP	ASP	LEU	LEU	B	B	19 - 21	22 - 24
d_2	4	THR	THR	PRO	PRO	B	B	26 - 29	29 - 32
d_2	5	ASP	ASP	ASP	ASP	B	B	31	34
d_2	6	SER	SER	VAL	VAL	B	B	33 - 35	36 - 38
d_2	7	ASP	ASP	VAL	VAL	B	B	37 - 43	40 - 46
d_2	8	ASP	ASP	SER	SER	B	B	45 - 46	48 - 49
d_2	9	ILE	ILE	ASN	ASN	B	B	48 - 54	51 - 57
d_2	10	ILE	ILE	ASN	ASN	B	B	56 - 63	59 - 66
d_2	11	ALA	ALA	LEU	LEU	B	B	66 - 68	69 - 71
d_2	12	ALA	ALA	GLY	GLY	B	B	70 - 77	73 - 80
d_2	13	PRO	PRO	ILE	ILE	B	B	79 - 84	82 - 87
d_2	14	ILE	ILE	VAL	VAL	B	B	86 - 87	89 - 90
d_3	1	ALA	ALA	ALA	ALA	C	C	4 - 10	7 - 13
d_3	2	ILE	ILE	ALA	ALA	C	C	13 - 17	16 - 20
d_3	3	ASP	ASP	LEU	LEU	C	C	19 - 21	22 - 24
d_3	4	THR	THR	PRO	PRO	C	C	26 - 29	29 - 32
d_3	5	ASP	ASP	ASP	ASP	C	C	31	34
d_3	6	SER	SER	VAL	VAL	C	C	33 - 35	36 - 38
d_3	7	ASP	ASP	VAL	VAL	C	C	37 - 43	40 - 46
d_3	8	ASP	ASP	SER	SER	C	C	45 - 46	48 - 49
d_3	9	ILE	ILE	ASN	ASN	C	C	48 - 54	51 - 57
d_3	10	ILE	ILE	ASN	ASN	C	C	56 - 63	59 - 66
d_3	11	ALA	ALA	LEU	LEU	C	C	66 - 68	69 - 71
d_3	12	ALA	ALA	GLY	GLY	C	C	70 - 77	73 - 80
d_3	13	PRO	PRO	ILE	ILE	C	C	79 - 84	82 - 87
d_3	14	ILE	ILE	VAL	VAL	C	C	86 - 87	89 - 90
d_4	1	ALA	ALA	ALA	ALA	D	D	4 - 10	7 - 13
d_4	2	ILE	ILE	ALA	ALA	D	D	13 - 17	16 - 20
d_4	3	ASP	ASP	LEU	LEU	D	D	19 - 21	22 - 24
d_4	4	THR	THR	PRO	PRO	D	D	26 - 29	29 - 32
d_4	5	ASP	ASP	ASP	ASP	D	D	31	34
d_4	6	SER	SER	VAL	VAL	D	D	33 - 35	36 - 38
d_4	7	ASP	ASP	VAL	VAL	D	D	37 - 43	40 - 46
d_4	8	ASP	ASP	SER	SER	D	D	45 - 46	48 - 49
d_4	9	ILE	ILE	ASN	ASN	D	D	48 - 54	51 - 57
d_4	10	ILE	ILE	ASN	ASN	D	D	56 - 63	59 - 66
d_4	11	ALA	ALA	LEU	LEU	D	D	66 - 68	69 - 71
d_4	12	ALA	ALA	GLY	GLY	D	D	70 - 77	73 - 80
d_4	13	PRO	PRO	ILE	ILE	D	D	79 - 84	82 - 87
d_4	14	ILE	ILE	VAL	VAL	D	D	86 - 87	89 - 90
d_5	1	ALA	ALA	ALA	ALA	E	E	4 - 10	7 - 13
d_5	2	ILE	ILE	ALA	ALA	E	E	13 - 17	16 - 20
d_5	3	ASP	ASP	LEU	LEU	E	E	19 - 21	22 - 24
d_5	4	THR	THR	PRO	PRO	E	E	26 - 29	29 - 32
d_5	5	ASP	ASP	ASP	ASP	E	E	31	34
d_5	6	SER	SER	VAL	VAL	E	E	33 - 35	36 - 38
d_5	7	ASP	ASP	VAL	VAL	E	E	37 - 43	40 - 46
d_5	8	ASP	ASP	SER	SER	E	E	45 - 46	48 - 49
d_5	9	ILE	ILE	ASN	ASN	E	E	48 - 54	51 - 57
d_5	10	ILE	ILE	ASN	ASN	E	E	56 - 63	59 - 66
d_5	11	ALA	ALA	LEU	LEU	E	E	66 - 68	69 - 71
d_5	12	ALA	ALA	GLY	GLY	E	E	70 - 77	73 - 80
d_5	13	PRO	PRO	ILE	ILE	E	E	79 - 84	82 - 87
d_5	14	ILE	ILE	VAL	VAL	E	E	86 - 87	89 - 90
d_6	1	ALA	ALA	ALA	ALA	F	F	4 - 10	7 - 13
d_6	2	ILE	ILE	ALA	ALA	F	F	13 - 17	16 - 20
d_6	3	ASP	ASP	LEU	LEU	F	F	19 - 21	22 - 24
d_6	4	THR	THR	PRO	PRO	F	F	26 - 29	29 - 32
d_6	5	ASP	ASP	ASP	ASP	F	F	31	34
d_6	6	SER	SER	VAL	VAL	F	F	33 - 35	36 - 38
d_6	7	ASP	ASP	VAL	VAL	F	F	37 - 43	40 - 46
d_6	8	ASP	ASP	SER	SER	F	F	45 - 46	48 - 49
d_6	9	ILE	ILE	ASN	ASN	F	F	48 - 54	51 - 57
d_6	10	ILE	ILE	ASN	ASN	F	F	56 - 63	59 - 66
d_6	11	ALA	ALA	LEU	LEU	F	F	66 - 68	69 - 71
d_6	12	ALA	ALA	GLY	GLY	F	F	70 - 77	73 - 80
d_6	13	PRO	PRO	ILE	ILE	F	F	79 - 84	82 - 87
d_6	14	ILE	ILE	VAL	VAL	F	F	86 - 87	89 - 90
d_7	1	ALA	ALA	ALA	ALA	G	G	4 - 10	7 - 13
d_7	2	ILE	ILE	ALA	ALA	G	G	13 - 17	16 - 20
d_7	3	ASP	ASP	LEU	LEU	G	G	19 - 21	22 - 24
d_7	4	THR	THR	PRO	PRO	G	G	26 - 29	29 - 32
d_7	5	ASP	ASP	ASP	ASP	G	G	31	34
d_7	6	SER	SER	VAL	VAL	G	G	33 - 35	36 - 38
d_7	7	ASP	ASP	VAL	VAL	G	G	37 - 43	40 - 46
d_7	8	ASP	ASP	SER	SER	G	G	45 - 46	48 - 49
d_7	9	ILE	ILE	ASN	ASN	G	G	48 - 54	51 - 57
d_7	10	ILE	ILE	ASN	ASN	G	G	56 - 63	59 - 66
d_7	11	ALA	ALA	LEU	LEU	G	G	66 - 68	69 - 71
d_7	12	ALA	ALA	GLY	GLY	G	G	70 - 77	73 - 80
d_7	13	PRO	PRO	ILE	ILE	G	G	79 - 84	82 - 87
d_7	14	ILE	ILE	VAL	VAL	G	G	86 - 87	89 - 90
d_8	1	ALA	ALA	ALA	ALA	H	H	4 - 10	7 - 13
d_8	2	ILE	ILE	ALA	ALA	H	H	13 - 17	16 - 20
d_8	3	ASP	ASP	LEU	LEU	H	H	19 - 21	22 - 24
d_8	4	THR	THR	PRO	PRO	H	H	26 - 29	29 - 32
d_8	5	ASP	ASP	ASP	ASP	H	H	31	34
d_8	6	SER	SER	VAL	VAL	H	H	33 - 35	36 - 38
d_8	7	ASP	ASP	VAL	VAL	H	H	37 - 43	40 - 46
d_8	8	ASP	ASP	SER	SER	H	H	45 - 46	48 - 49
d_8	9	ILE	ILE	ASN	ASN	H	H	48 - 54	51 - 57
d_8	10	ILE	ILE	ASN	ASN	H	H	56 - 63	59 - 66
d_8	11	ALA	ALA	LEU	LEU	H	H	66 - 68	69 - 71
d_8	12	ALA	ALA	GLY	GLY	H	H	70 - 77	73 - 80
d_8	13	PRO	PRO	ILE	ILE	H	H	79 - 84	82 - 87
d_8	14	ILE	ILE	VAL	VAL	H	H	86 - 87	89 - 90

NCS oper:

ID	Code	Matrix	Vector
1	given	(-0.494724213134, 0.151415291936, 0.855757770813), (0.199291748676, -0.938696576291, 0.281303282187), (0.845890508191, 0.30971300752, 0.434220106771)	47.8149384765, 3.88072089929, 4.0499173015
2	given	(0.863361920619, 0.495542071603, 0.0951012581193), (-0.491035688388, 0.868504365818, -0.0677061244152), (-0.116147091024, 0.0117567778656, 0.993162439594)	-5.41007579304, 29.9735540499, -7.26092423702
3	given	(-0.884020663454, -0.460003828929, -0.0830899750706), (-0.44748686764, 0.884183302422, -0.134072334979), (0.135140556, -0.0813410418422, -0.987481982132)	44.5919218992, 30.6785148809, 5.47432530456
4	given	(-0.34945108403, -0.326619866389, 0.878181873389), (0.370921892668, -0.908924634657, -0.190454608908), (0.860407397347, 0.259182313043, 0.438775157907)	46.0935415053, 36.8287414213, -4.54927767867
5	given	(0.467660335556, -0.187950518396, -0.86369462959), (0.200065886421, -0.929265042288, 0.310548099772), (-0.860968902829, -0.318026860212, -0.39697791443)	46.0688668566, 3.29648457538, -4.32379374076
6	given	(0.513989100444, -0.63586633261, -0.575750997982), (-0.000531578542946, -0.671433468426, 0.74106464961), (-0.8577965505, -0.380593095747, -0.345447497343)	36.1982556, 38.188550302, 50.0451478059
7	given	(0.454149532744, 0.890522239698, 0.0268019124704), (-0.860763674355, 0.446337357227, -0.244681140373), (-0.229856691917, 0.0880517129138, 0.969233097368)	7.12675656224, 58.8642125879, -13.0876904062

#1: Protein	Chromosomal replication initiator protein DnaA Mass: 9770.034 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bifidobacterium primatium (bacteria) / Gene: dnaA, CS006_03610 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A2M9HC27
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 360 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	N

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.81 Å³/Da / Density % sol: 56.16 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop Details: 9% (w/v) PEG 8000; 50 mM Sodium cacodylate/HCl, pH 6.5; 100 mM Calcium Acetate; 12.5% glycerol

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SEALED TUBE / Type: RIGAKU PhotonJet-S / Wavelength: 1.54184 Å
Detector	Type: RIGAKU HyPix-6000HE / Detector: PIXEL / Date: Dec 4, 2025
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.54184 Å / Relative weight: 1
Reflection	Resolution: 2.4→22.45 Å / Num. obs: 33680 / % possible obs: 99.8 % / Redundancy: 12 % / B_iso Wilson estimate: 37.75 Å² / CC_1/2: 0.999 / R_pim(I) all: 0.017 / R_rim(I) all: 0.064 / Net I/σ(I): 25.4
Reflection shell	Resolution: 2.4→2.49 Å / Mean I/σ(I) obs: 5.2 / Num. unique obs: 3544 / CC_1/2: 0.953 / R_pim(I) all: 0.119 / R_rim(I) all: 0.405

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Processing

Software

Name	Version	Classification
PHENIX	1.20.1_4487	refinement
CrysalisPro		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.4→22.45 Å / SU ML: 0.315 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 27.2545
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.2364	2000	6.04 %
R_work	0.1933	31106	-
obs	0.1959	33106	98.33 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso mean: 59.82 Å²

Refinement step

Cycle: LAST / Resolution: 2.4→22.45 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5175	0	0	360	5535

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0055	5306
X-RAY DIFFRACTION	f_angle_d	0.8634	7267
X-RAY DIFFRACTION	f_chiral_restr	0.0545	900
X-RAY DIFFRACTION	f_plane_restr	0.0069	952
X-RAY DIFFRACTION	f_dihedral_angle_d	13.3122	1937

Refine LS restraints NCS

Ens-ID	Dom-ID	Asym-ID	Auth asym-ID	Refine-ID	Type	Rms dev position (Å)
ens_1	d_2	A	A	X-RAY DIFFRACTION	Torsion NCS	0.450130201895
ens_1	d_3	A	A	X-RAY DIFFRACTION	Torsion NCS	0.523446848101
ens_1	d_4	A	A	X-RAY DIFFRACTION	Torsion NCS	0.510116015454
ens_1	d_5	A	A	X-RAY DIFFRACTION	Torsion NCS	0.379345325702
ens_1	d_6	A	A	X-RAY DIFFRACTION	Torsion NCS	0.663987742787
ens_1	d_7	A	A	X-RAY DIFFRACTION	Torsion NCS	0.623663573966
ens_1	d_8	A	A	X-RAY DIFFRACTION	Torsion NCS	0.647046042889

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
2.4-2.46	0.3494	141	0.3044	2200	X-RAY DIFFRACTION	97.26
2.46-2.53	0.3357	142	0.2644	2204	X-RAY DIFFRACTION	97.83
2.53-2.6	0.3222	139	0.2659	2165	X-RAY DIFFRACTION	97.83
2.6-2.68	0.3222	140	0.2602	2184	X-RAY DIFFRACTION	96.11
2.68-2.78	0.2718	142	0.2571	2199	X-RAY DIFFRACTION	97.14
2.78-2.89	0.2864	142	0.2348	2199	X-RAY DIFFRACTION	97.58
2.89-3.02	0.3081	141	0.2307	2200	X-RAY DIFFRACTION	97.83
3.02-3.18	0.2835	142	0.226	2213	X-RAY DIFFRACTION	98.12
3.18-3.38	0.2586	142	0.2122	2205	X-RAY DIFFRACTION	98.82
3.38-3.64	0.2168	145	0.1736	2264	X-RAY DIFFRACTION	99.79
3.64-4	0.2324	147	0.1642	2285	X-RAY DIFFRACTION	99.67
4.01-4.58	0.1704	145	0.1419	2236	X-RAY DIFFRACTION	99.42
4.58-5.75	0.1906	146	0.1574	2268	X-RAY DIFFRACTION	99.71
5.75-22.45	0.1945	146	0.1704	2284	X-RAY DIFFRACTION	99.55

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	6.58267270785	-2.22300840302	1.59066218048	2.04723603506	0.0615135638974	5.11576989132	0.23537854031	-0.0428439237221	-0.0794272821727	-0.556798034259	-0.00502851386249	-0.992322470602	-0.174374226575	0.876270099785	-0.0491237014079	0.205454995646	-0.0261008893465	0.0575864647627	0.331366736017	-0.0212407966531	0.811667026362	23.3958486665	0.710554236241	6.24028026796
2	2.00450978835	0.399631518306	1.66720748952	3.16953581941	0.0970929100667	6.649405383	-0.274836186025	-1.21093484433	0.501639171216	0.0507946508697	0.233188957815	-0.238126943526	-0.339781685836	0.163972896249	0.113777633516	0.267111173019	-0.00535250614802	-0.0450927026322	0.425445072427	-0.114017878546	0.454212314181	9.10258714082	7.93791369077	12.9420949529
3	5.50566153343	-5.2608000331	-5.09306137741	5.0176141115	4.83894619642	4.71747613405	-0.545726563059	-0.653896665551	-0.575073528998	0.303636581892	0.254777051754	0.00167045088145	0.269141714516	-0.57487315573	0.283794344578	0.320004929579	-0.00393520112564	-0.00243116528325	0.397436937908	0.00657329559724	0.336864507934	9.6538128942	-2.84818773517	14.295631859
4	5.2641847647	2.78808934639	-0.487512682138	8.58560504533	-2.22578758849	4.55395921513	-0.318177815846	0.136291952545	-0.156804847221	-0.661893022213	0.0274673806586	-0.393926369618	0.520671154485	-0.265286479594	0.28824457578	0.35789319216	-0.061840565137	0.069446957739	0.223302213274	-0.108677465609	0.498677745798	13.6485673961	-6.69308547191	2.91110848418
5	2.76644807251	1.27519095577	-1.70725234438	8.38659747394	-1.2674203367	4.11900620495	0.0312985261823	0.316032390542	0.136107309528	-0.359969568293	-0.0170368409656	-0.518897234121	-0.16946286305	0.153086931503	-0.120406899093	0.297410239345	-0.0264045132315	-0.0112877026153	0.214789754429	-0.0821004026706	0.441439978419	15.7724563974	5.72393415673	-0.277664186157
6	3.80422753102	0.301529737083	-0.680360603686	9.16298017576	0.449604510141	2.34845439958	-0.236416263974	-0.235146236785	-0.0767189976407	-0.517799690148	0.388112731485	-0.500159272834	0.764058853893	0.30475113143	0.0880600875117	0.427334682514	-0.00674948579565	-0.000821328780026	0.200200202396	-0.067016238365	0.355048505508	14.0840185297	-10.458993203	1.39045652827
7	2.57859480268	-0.775496530005	-4.03714684779	2.94237048773	1.81970270323	6.61217848131	0.00812284207943	-1.99847408399	0.272718582246	0.436233622772	0.429401636351	-0.0788377743091	-0.00939265017666	-0.290712491034	-0.149361933814	0.490747156719	0.0548958019014	0.0973724928048	1.01532172404	-0.0310391711082	0.239840953083	42.0309739319	9.29307332025	27.0236684147
8	7.43716656221	-1.41721004871	-0.707722554031	3.94457605212	2.06235148686	4.5570603718	-0.394533595897	-1.05575987751	0.420427417516	0.425856850806	0.602560722746	-1.5531959415	-0.12342754703	-0.00662235482778	-0.117881310733	0.229947189767	0.0248026089204	-0.0668176480975	0.457746478695	-0.0955876637258	0.42011073827	55.7046614681	8.27036517099	17.7372456804
9	7.67389833611	-1.83164046469	-1.31479911235	5.91336341979	-2.36968585772	6.89350155744	-0.0225567715709	-0.167450269672	-0.16529164603	-0.176077204519	0.102583190724	0.194601178327	0.438936040564	-0.384267848306	-0.0619039934475	0.240451311707	-0.0236692318877	-0.0295370696603	0.413400115205	-0.0995453954021	0.223457431487	41.9168099239	10.7620474362	15.9050967585
10	2.00092892059	-2.24438463533	0.352427813447	3.21957346428	-5.34493203902	2.00090702149	-0.771192147556	-1.17875871234	0.883216322307	-1.94251816813	-0.129462622269	-2.08116777456	1.00544491564	4.17495507908	0.251882341364	0.699879860425	0.00616936271428	0.62357495249	1.33243386313	-0.441338018629	0.917427885092	24.2994825684	11.4340812582	-14.0121204038
11	8.43753823195	0.537649083243	4.33803419275	5.89748831508	1.61962026678	5.46500347637	-0.35547324478	0.291451895754	0.222239589098	0.103589031384	0.648186977609	-0.120896740961	-0.0459833651988	0.682908173237	-0.233526240805	0.253195290269	0.110292107948	-0.00975413579885	0.333565496566	0.0250947773164	0.240488206819	14.9666954535	19.8633332539	-2.3268852147
12	4.40748690234	-1.38614395372	-1.86046295723	8.72345062222	2.51871387073	6.93844954269	-0.0626993368803	0.718356594483	0.252317622163	-0.211972512681	-0.0152962362396	-0.146315328044	-0.395807719606	-0.654016149908	0.0249573511688	0.198317630575	0.0668154870427	-0.0600415963436	0.399986605994	-0.0290635879713	0.236797836644	6.03368171134	20.0437120108	-2.30274955853
13	6.26179713939	1.40172051421	-1.21226738139	2.44262366883	0.155102264977	4.055451297	-0.309601440449	1.57957431456	0.56485421747	-0.55996923247	0.248367285465	0.55080901393	-0.26697408192	-1.279384289	0.12456257157	0.366492592577	0.140752600072	-0.0730838389714	0.652418960769	0.0214009064536	0.305594457752	3.82883549148	21.602901135	-6.11476334403
14	7.2758159771	4.19034761966	-1.12724321446	4.01276675102	-0.311359200323	2.22759822033	-0.227852099993	0.398734941057	0.525115982613	-0.436478824055	0.522486122231	0.697439203637	-0.164823055376	-0.698078612296	-0.188419426876	0.236136777902	0.0521754599008	-0.0944625070493	0.290786045329	-0.0577566563027	0.455748340708	22.612913994	20.3300416201	2.26479509943
15	4.17892553704	1.8511357886	-4.01696635336	2.11363283417	-1.5901451328	3.87568944865	-0.150369056758	1.28574313047	1.11417423998	-1.38703578844	-0.174424373317	-0.0373162964436	-0.405377668961	0.211319497318	0.229249930943	0.694159569582	-0.0480633220126	-0.115678196733	0.646337845494	0.15041626219	0.511946308821	35.3898880167	25.1721236789	-6.92333185373
16	5.3424038465	-2.21607956809	-1.68314869968	6.54630916998	1.21488798366	5.36087845381	-0.0347285987677	-0.669801737482	0.690965232819	-0.322398387673	-0.0117972765419	0.0633572543089	-0.606576793925	0.1340511888	0.00662519192681	0.205225881832	-0.00255534342032	-0.0587635340338	0.314012165173	-0.105757222249	0.375872425993	33.345701669	20.9354475075	5.99845226656
17	2.44164392516	2.33810398547	0.38031966985	2.3442795621	1.21541785606	6.80618045214	-0.838501342	-1.37312074217	0.377571764586	1.48175970518	0.978614862905	0.30004425242	0.194393831028	0.753348213294	-0.213827527849	0.920699673348	0.229691478677	0.170531893632	0.489699654012	0.0276953925406	0.318012004978	41.8216240742	44.0470564455	19.9865064014
18	8.53101417307	-3.87407991387	-0.223818756862	2.41627395134	1.55255406373	3.28812578664	-0.0968428571525	-0.457594068762	-0.124060845901	0.803254684293	0.252953699812	-1.06175100667	0.330060561001	0.239806801026	-0.257454385676	0.590313397306	0.187322606113	0.020592896863	0.376059601377	-0.00250826227666	0.428333667058	54.9457826197	36.9516974614	9.4252250845
19	8.29584224099	-1.52631651519	-1.6456340858	6.43490525099	-0.0957373900621	3.41890126855	0.124623188876	0.278179527696	0.530477848446	0.172425457426	0.0603520110404	0.188831570937	0.0549233771853	-0.170989655342	-0.106706980423	0.645982595447	0.127979970323	0.0869489923651	0.210096401654	0.00597599124361	0.311081282946	45.9659487123	47.5671179595	6.80036846514
20	6.8097973216	2.7084772524	-1.99914288432	2.9783792418	-2.76043513869	3.41580253181	-0.221149395411	0.245783536592	0.398943688509	-0.376316265877	0.558244428746	1.63192060304	0.236327084588	-0.261142615679	-0.243785670404	0.649216957964	0.150381191968	0.0654629474612	0.23969576393	-0.015912772493	0.575744858106	40.7822712421	41.4481749212	8.77180865148
21	0.309856445786	0.149850762668	0.300980933426	0.226369247168	0.0977069450993	0.307706316606	0.339656246666	0.495536355596	0.0153991354173	-0.263850840457	0.116957573262	-0.294477063734	-0.189059981726	-0.0162447737736	-0.254472833486	0.798555181061	-0.247189579427	0.345359639269	2.53543645344	-0.580196336602	1.10013565557	65.4377677204	11.3807390625	-33.5113119469
22	9.71052280287	4.76093423791	6.97319310977	2.81702439946	3.38908485005	5.04391733764	-0.071155208605	0.361663623177	-0.02612066057	-0.633468741548	-0.0618636796051	0.189449598369	0.321163762348	-0.419861922772	0.143254963871	0.684595258765	-0.143058711936	0.120640377427	1.46600072257	-0.272644073895	0.673449072092	50.0250779073	8.8857762498	-26.7807256848
23	3.89075670853	0.180031420059	-3.14938182367	6.35320541563	1.11929885802	2.83933238971	-1.00895931784	1.12135534526	-2.88755559651	-0.246160388904	-0.784174414166	-0.880224208596	0.440219309335	-1.70985076965	1.76525878602	1.2169784553	-0.593477025188	0.231166250158	1.65473499076	-0.426542205586	1.23139032556	36.448613944	2.91596580684	-17.4835594022
24	5.95786753012	-0.0845593317438	1.21416721811	4.03746400201	3.3354839833	7.26095460421	-0.918390075035	0.84570624911	-0.7846131956	0.0779949689063	0.403919607142	0.301997946406	-0.21141606448	-1.00818950193	-0.0384388292199	0.528448396781	0.0801300845145	-0.12867247253	1.50077293994	-0.271531386071	0.514341650429	48.9506116303	13.3109435193	-17.8623622313
25	4.3379817093	-2.27732361313	-1.29946593666	2.43041207107	2.29091602606	2.51299187139	-0.421871414076	0.330235885541	-0.228961641463	1.07289633847	-0.492196103924	0.986006539027	0.0968426353477	-1.86718974028	0.710612474611	0.718060157978	0.157307566567	-0.0047858746108	1.25692090745	-0.528293874102	0.496172372885	46.1035003543	12.3753864741	-10.2221037843
26	0.00552990138924	0.0185485041816	-0.0187598240841	0.0405564730191	-0.0515122170947	0.0704410285563	0.124179708052	-0.0282099416952	-0.250169469426	0.612393724271	0.109046844609	-0.217624680918	0.927250645362	0.0129153440071	0.162881229239	1.07520134161	-0.500329750104	0.27271770055	1.23590589581	-1.66478791439	1.40641521942	52.6336608681	1.12775221916	-19.4284860146
27	7.4527589634	2.73210297951	0.468631482646	2.42367056299	-1.80736252975	3.32094440939	-0.477180475069	0.793314723936	0.22475934716	0.196485379505	0.761505977877	-0.166686893451	-0.445514440156	-1.49387327031	0.0162363614251	0.494279768199	0.25034901682	-0.19669122119	1.04842933095	-0.258315578085	0.421103905896	53.1656577897	15.7103217446	-13.9017397356
28	7.5839956809	-2.51202114557	-3.8056012402	8.91532254493	3.74175230376	8.26144892915	0.297452154566	0.844945139156	0.0925458219815	-1.33237082648	-0.0561584290836	-0.578575708555	-0.349966983496	-0.0646466092652	-0.277819276033	1.08773224138	0.285642867104	0.237768608509	0.794018354314	-0.0116874944462	0.530950206218	43.0362777692	42.3776240222	27.8973790037
29	5.05780555796	2.98486455445	-1.79130568241	4.09444187753	-1.91602741705	8.67275748011	0.335129785593	0.457591600539	0.711796251886	-0.42029526795	-0.228918168679	0.207382874972	-0.052649248386	-0.699072240816	-0.147621902064	0.870258702241	0.240190870606	0.0834224457312	0.566333164996	-0.0917172112782	0.525282333968	41.4547127364	45.275331966	36.7147505724
30	6.80814544971	4.25236174525	4.6672614564	8.76966474633	6.22850175923	6.44054198021	-0.0329370426495	0.051145080037	-0.303717323362	0.217922761354	0.155879943918	-0.0480382019674	0.0868079324187	-0.775134490761	-0.200523191537	0.756923205598	0.194781164767	0.130354268241	0.584948811784	0.0514049456716	0.505170088	42.4580093283	41.5185651973	39.6535033526
31	6.43301312547	-1.37025895422	-1.21469283693	2.76878053574	2.39543396202	3.2933754664	0.190832531735	0.09733949598	0.951702010269	-0.341847581406	0.0410969331751	-1.43014305052	-0.547329909245	1.9650072689	-0.584380909257	0.612659372502	0.0393033979506	0.159452641466	0.735143531685	0.157748539368	0.939136671109	18.7463374412	38.108016812	-11.8578278299
32	2.37511530092	-1.60021703014	1.88608054848	2.50496121364	-0.838558220641	2.92619194607	-0.161297036827	-0.456198962409	0.801759773482	0.871555336662	-1.56454020391	0.17167821574	-0.941703700466	0.372581865624	1.62738464332	1.03542989185	0.0442239523951	-0.0380561729752	0.909541826372	-0.1611589582	0.86591553633	11.7300901483	47.0533566026	-1.47695126166
33	8.69783983276	0.396265380904	-3.43762549773	8.04110710742	1.66124718082	8.67891857918	0.481434130475	0.764532059825	1.51465365461	-0.546530011325	-0.351653289621	-0.623155865717	-0.867087376517	-0.434427985115	-0.186305990137	0.568513988651	0.206194461239	0.168106049735	0.530160421058	0.117649662922	0.752158960225	7.46193764709	43.3744342552	-14.0172524663
34	2.15993257462	3.36067674972	0.739596278661	5.94641658659	2.19639828733	2.3435576452	0.426085379705	0.238107441203	0.866424284946	-0.494896287784	-0.135458015836	-1.32299523039	-0.689822092149	0.824636656373	-0.151040445848	0.751483968094	-0.0451942269487	0.223098268426	0.705723441472	0.147509331896	1.25253891082	14.540023993	45.9974476541	-16.3289793633

Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

ID	Refine TLS-ID	Selection details	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	chain 'A' and (resid 3 through 22 )	A	A	3 - 22	1 - 20
2	2	chain 'A' and (resid 23 through 28 )	A	A	23 - 28	21 - 26
3	3	chain 'A' and (resid 29 through 37 )	A	A	29 - 37	27 - 35
4	4	chain 'A' and (resid 38 through 64 )	A	A	38 - 64	36 - 62
5	5	chain 'A' and (resid 65 through 80 )	A	A	65 - 80	63 - 78
6	6	chain 'A' and (resid 81 through 87 )	A	A	81 - 87	79 - 85
7	7	chain 'B' and (resid 2 through 23 )	B	B	2 - 23	1 - 22
8	8	chain 'B' and (resid 24 through 36 )	B	B	24 - 36	23 - 35
9	9	chain 'B' and (resid 37 through 87 )	B	B	37 - 87	36 - 86
10	10	chain 'C' and (resid 1 through 5 )	C	C	1 - 5	1 - 5
11	11	chain 'C' and (resid 6 through 23 )	C	C	6 - 23	6 - 23
12	12	chain 'C' and (resid 24 through 52 )	C	C	24 - 52	24 - 52
13	13	chain 'C' and (resid 53 through 87 )	C	C	53 - 87	53 - 87
14	14	chain 'D' and (resid 1 through 23 )	D	D	1 - 23	1 - 23
15	15	chain 'D' and (resid 24 through 37 )	D	D	24 - 37	24 - 37
16	16	chain 'D' and (resid 38 through 87 )	D	D	38 - 87	38 - 87
17	17	chain 'E' and (resid 0 through 23 )	E	E	0 - 23	1 - 24
18	18	chain 'E' and (resid 24 through 37 )	E	E	24 - 37	25 - 38
19	19	chain 'E' and (resid 38 through 64 )	E	E	38 - 64	39 - 65
20	20	chain 'E' and (resid 65 through 87 )	E	E	65 - 87	66 - 88
21	21	chain 'F' and (resid 1 through 5 )	F	F	1 - 5	1 - 5
22	22	chain 'F' and (resid 6 through 23 )	F	F	6 - 23	6 - 23
23	23	chain 'F' and (resid 24 through 28 )	F	F	24 - 28	24 - 28
24	24	chain 'F' and (resid 29 through 54 )	F	F	29 - 54	29 - 54
25	25	chain 'F' and (resid 55 through 64 )	F	F	55 - 64	55 - 64
26	26	chain 'F' and (resid 65 through 80 )	F	F	65 - 80	65 - 80
27	27	chain 'F' and (resid 81 through 87 )	F	F	81 - 87	81 - 87
28	28	chain 'G' and (resid 4 through 23 )	G	G	4 - 23	1 - 20
29	29	chain 'G' and (resid 24 through 52 )	G	G	24 - 52	21 - 49
30	30	chain 'G' and (resid 53 through 87 )	G	G	53 - 87	50 - 84
31	31	chain 'H' and (resid 3 through 24 )	H	H	3 - 24	1 - 22
32	32	chain 'H' and (resid 25 through 37 )	H	H	25 - 37	23 - 35
33	33	chain 'H' and (resid 38 through 64 )	H	H	38 - 64	36 - 62
34	34	chain 'H' and (resid 65 through 87 )	H	H	65 - 87	63 - 85

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-Yorodumi

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Movie

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Structure viewers

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Viewer log

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This page

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This web site

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Options

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Open data

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Validation report

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Links

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Assembly

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Experimental details

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Experiment

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Sample preparation

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Data collection

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About Yorodumi

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Feb 9, 2022. New format data for meta-information of EMDB entries

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Mar 5, 2020. Novel coronavirus structure data

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Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

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Jul 12, 2017. Major update of PDB

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Yorodumi