PDB-8d57: Crystal Structure of dihydrodipicolinate reductase from Acinetoba...

ID or keywords:

Entry

Database: PDB / ID: 8d57

Title

Crystal Structure of dihydrodipicolinate reductase from Acinetobacter baumannii

Components

4-hydroxy-tetrahydrodipicolinate reductase

Keywords

OXIDOREDUCTASE / SSGCID /

dihydrodipicolinate reductase /

4-hydroxy-tetrahydrodipicolinate reductase / dapB /

Acinetobacter baumannii /

Structural Genomics / Seattle Structural Genomics Center for Infectious Disease

Function / homology

Function and homology information

4-hydroxy-tetrahydrodipicolinate reductase / oxidoreductase activity, acting on CH or CH2 groups, NAD or NADP as acceptor /

4-hydroxy-tetrahydrodipicolinate reductase / diaminopimelate biosynthetic process / lysine biosynthetic process via diaminopimelate / NAD binding /

NADP binding /

cytoplasm
Similarity search - Function

Biological species

Acinetobacter baumannii (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.65 Å

Authors

Seattle Structural Genomics Center for Infectious Disease / Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Funding support

United States, 1items

Citation

Journal: to be published
Title: Crystal Structure of dihydrodipicolinate reductase from Acinetobacter baumannii
Authors: Abendroth, J. / Davies, D.R. / Lorimer, D.D. / Horanyi, P.S. / Edwards, T.E.

History

Deposition	Jun 4, 2022	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jun 22, 2022	Provider: repository / Type: Initial release
Revision 1.1	Oct 18, 2023	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	8d57.cif.gz	692.1 KB	Display	PDBx/mmCIF format
PDB format	pdb8d57.ent.gz	480.8 KB	Display	PDB format
PDBx/mmJSON format	8d57.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/d5/8d57 ftp://data.pdbj.org/pub/pdb/validation_reports/d5/8d57	HTTPS FTP

-
Related structure data

Related structure data	4ywjS S: Starting model for refinement
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

-
Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: 4-hydroxy-tetrahydrodipicolinate reductase

B: 4-hydroxy-tetrahydrodipicolinate reductase

C: 4-hydroxy-tetrahydrodipicolinate reductase

D: 4-hydroxy-tetrahydrodipicolinate reductase

E: 4-hydroxy-tetrahydrodipicolinate reductase

F: 4-hydroxy-tetrahydrodipicolinate reductase

hetero molecules

180 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: 4-hydroxy-tetrahydrodipicolinate reductase

B: 4-hydroxy-tetrahydrodipicolinate reductase

C: 4-hydroxy-tetrahydrodipicolinate reductase

D: 4-hydroxy-tetrahydrodipicolinate reductase

hetero molecules

defined by author
Evidence: gel filtration
120 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

E: 4-hydroxy-tetrahydrodipicolinate reductase

F: 4-hydroxy-tetrahydrodipicolinate reductase

hetero molecules

E: 4-hydroxy-tetrahydrodipicolinate reductase

F: 4-hydroxy-tetrahydrodipicolinate reductase

hetero molecules

defined by author
120 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	79.800, 79.800, 519.130
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	152
Space group name H-M	P3₁21
Space group name Hall	P3₁2"
Symmetry operation	#1: x,y,z #2: -y,x-y,z+1/3 #3: -x+y,-x,z+2/3 #4: x-y,-y,-z+2/3 #5: -x,-x+y,-z+1/3 #6: y,x,-z

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
d_1	ens_1	(chain "A" and (resid 5 or (resid 6 through 7...
d_2	ens_1	(chain "B" and (resid 5 through 6 or (resid 7...
d_3	ens_1	(chain "C" and (resid 5 or (resid 6 through 7...
d_4	ens_1	(chain "D" and (resid 5 through 6 or (resid 7...
d_5	ens_1	(chain "E" and (resid 5 through 34 or (resid 35...
d_6	ens_1	(chain "F" and (resid 5 or (resid 6 through 7...

NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Beg label comp-ID	End label comp-ID	Label asym-ID	Label seq-ID
d_1	1	ens_1	PRO	SER	A	2 - 131
d_1	2	ens_1	LYS	VAL	A	133 - 159
d_1	3	ens_1	ALA	ASN	A	161 - 266
d_1	4	ens_1	CIT	CIT	B
d_2	1	ens_1	PRO	SER	C	1 - 130
d_2	2	ens_1	LYS	VAL	C	132 - 158
d_2	3	ens_1	ALA	ASN	C	160 - 265
d_2	4	ens_1	CIT	CIT	D
d_3	1	ens_1	PRO	SER	E	2 - 131
d_3	2	ens_1	LYS	VAL	E	133 - 159
d_3	3	ens_1	ALA	ASN	E	161 - 266
d_3	4	ens_1	CIT	CIT	F
d_4	1	ens_1	PRO	SER	G	2 - 131
d_4	2	ens_1	LYS	VAL	G	133 - 159
d_4	3	ens_1	ALA	ASN	G	161 - 266
d_4	4	ens_1	CIT	CIT	H
d_5	1	ens_1	PRO	SER	I	2 - 131
d_5	2	ens_1	LYS	VAL	I	133 - 159
d_5	3	ens_1	ALA	ASN	I	161 - 266
d_5	4	ens_1	CIT	CIT	J
d_6	1	ens_1	PRO	SER	K	2 - 131
d_6	2	ens_1	LYS	VAL	K	133 - 159
d_6	3	ens_1	ALA	ASN	K	161 - 266
d_6	4	ens_1	CIT	CIT	L

NCS oper:

ID	Code	Matrix	Vector
1	given	(-0.842312544479, 0.410056553669, 0.349804517132), (0.412007960334, 0.0714170863123, 0.908377146566), (0.34750398276, 0.90925971129, -0.22910207199)	-77.4055600957, -32.3945638617, 73.1419974994
2	given	(0.763806164381, -0.644766204363, -0.0296088663253), (-0.644321806933, -0.764379436783, 0.0239475621835), (-0.0380729873383, 0.00078634263429, -0.999274651585)	0.790491741266, -3.93607056875, 115.146582846
3	given	(-0.908603312252, 0.255241450499, -0.330593138028), (0.252185134964, -0.295685878004, -0.92139704756), (-0.332930441185, -0.920555084444, 0.204293068498)	-38.5712399416, 72.5029915702, 45.0422076024
4	given	(-0.560266049828, -0.0111346064305, -0.828237872805), (-0.766543067306, 0.38586110605, 0.513344847839), (0.313868888829, 0.922489689578, -0.224720033035)	16.0710846222, -83.3528959469, 13.9352249279
5	given	(0.175740385015, -0.984377490602, 0.0107829991411), (0.98392455926, 0.175285226886, -0.034169444238), (0.0317455313234, 0.0166146089635, 0.999357881847)	-2.71762310263, 0.987246130741, -57.4389819684

#1: Protein	4-hydroxy-tetrahydrodipicolinate reductase / / HTPA reductase Mass: 29818.943 Da / Num. of mol.: 6 / Fragment: AcbaC.00189.a.B1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Acinetobacter baumannii (bacteria) Gene: dapB, AB945B12_02229, ABUW_0039, ACX61_00190, C6N18_01125, FDN00_01175, FGL68_08535, GNY86_11650, HB367_13645, NCTC13421_00044 Plasmid: AcbaC.00189.a.B1 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: A0A0D5YCZ0, 4-hydroxy-tetrahydrodipicolinate reductase
#2: Chemical	ChemComp-CIT / CITRIC ACID / Citric acid Mass: 192.124 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₆H₈O₇
#3: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 87 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.68 Å³/Da / Density % sol: 54.05 %
Crystal grow	Temperature: 287 K / Method: vapor diffusion, sitting drop / pH: 5.8 Details: RigakuReagents JCSG+ screen, condition a2, optimized: 100mM sodium citrate tribasic / citric acid pH 5.8, 22% (w/V) PEG 3000: AcbaC.00189.a.B1.PW38917 at 19mg/ml + 4mM NAD. Tray 324181 c6: ...Details: RigakuReagents JCSG+ screen, condition a2, optimized: 100mM sodium citrate tribasic / citric acid pH 5.8, 22% (w/V) PEG 3000: AcbaC.00189.a.B1.PW38917 at 19mg/ml + 4mM NAD. Tray 324181 c6: cryo: 20% EG with NAD: puck ybo0-10.

Crystal

Density Matthews: 2.68 Å³/Da / Density % sol: 54.05 %

Crystal grow

Temperature: 287 K / Method: vapor diffusion, sitting drop / pH: 5.8
Details: RigakuReagents JCSG+ screen, condition a2, optimized: 100mM sodium citrate tribasic / citric acid pH 5.8, 22% (w/V) PEG 3000: AcbaC.00189.a.B1.PW38917 at 19mg/ml + 4mM NAD. Tray 324181 c6: ...

-
Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 21-ID-F / Wavelength: 0.97872 Å

Detector

Type: RAYONIX MX-300 / Detector: CCD / Date: Mar 24, 2022 / Details: Beryllium Lenses

Radiation

Monochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.97872 Å / Relative weight: 1

Reflection

Resolution: 2.65→50 Å / Num. obs: 57256 / % possible obs: 99.1 % / Redundancy: 5.5 % / B_iso Wilson estimate: 71.999 Å² / CC_1/2: 0.998 / R_merge(I) obs: 0.072 / R_rim(I) all: 0.079 / Χ²: 0.927 / Net I/σ(I): 13.64

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. unique obs	CC_1/2	R_rim(I) all	% possible all
2.65-2.72	5.655	0.646	2.8	4068	0.899	0.712	98.8
2.72-2.79	5.647	0.493	3.53	4043	0.933	0.543	99
2.79-2.87	5.637	0.444	3.93	3982	0.926	0.489	99.1
2.87-2.96	5.652	0.322	5.1	3807	0.966	0.354	99.2
2.96-3.06	5.609	0.244	6.52	3751	0.978	0.269	99
3.06-3.17	5.588	0.189	8.17	3557	0.984	0.208	99.1
3.17-3.29	5.585	0.139	10.33	3493	0.993	0.153	99.4
3.29-3.42	5.579	0.112	12.86	3356	0.993	0.123	99.5
3.42-3.57	5.542	0.091	14.96	3234	0.996	0.1	99.4
3.57-3.75	5.534	0.076	17.26	3088	0.995	0.084	99.3
3.75-3.95	5.514	0.068	19.75	2995	0.996	0.075	99.3
3.95-4.19	5.491	0.062	21.19	2823	0.997	0.069	99.4
4.19-4.48	5.4	0.057	22.93	2638	0.996	0.063	99.7
4.48-4.84	5.418	0.054	24.19	2455	0.997	0.06	99.4
4.84-5.3	5.375	0.057	23.55	2363	0.997	0.063	99.5
5.3-5.93	5.31	0.058	23.77	2050	0.996	0.064	99.4
5.93-6.84	5.238	0.055	24.61	1892	0.997	0.061	99.2
6.84-8.38	5.142	0.051	26.63	1610	0.996	0.057	99.5
8.38-11.85	4.914	0.048	26.94	1307	0.997	0.053	99.5
11.85-50	4.298	0.054	24.14	744	0.995	0.062	90.7

-
Processing

Software

Name	Version	Classification
PHENIX	1.20.1	refinement
XDS		data reduction
XSCALE		data scaling
PDB_EXTRACT	3.27	data extraction
MoRDa		phasing
PHENIX		model building
Coot		model building

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: pdb entry 4ywj as per Morda

4ywj

Resolution: 2.65→41.51 Å / SU ML: 0.3633 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.1958
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2347	1975	3.46 %	0
R_work	0.2077	55188	-	-
obs	0.2087	57163	99.23 %	-

Solvent computation

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

Displacement parameters

B_iso mean: 86.74 Å²

Refinement step

Cycle: LAST / Resolution: 2.65→41.51 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	11127	0	78	87	11292

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0044	11356
X-RAY DIFFRACTION	f_angle_d	0.658	15471
X-RAY DIFFRACTION	f_chiral_restr	0.0467	1869
X-RAY DIFFRACTION	f_plane_restr	0.0053	2046
X-RAY DIFFRACTION	f_dihedral_angle_d	12.8306	3828

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Refine-ID	Type	Rms dev position (Å)
ens_1	d_2	A	X-RAY DIFFRACTION	Torsion NCS	0.424836462583
ens_1	d_3	A	X-RAY DIFFRACTION	Torsion NCS	0.34619716394
ens_1	d_4	A	X-RAY DIFFRACTION	Torsion NCS	0.518296546478
ens_1	d_5	A	X-RAY DIFFRACTION	Torsion NCS	0.65705776989
ens_1	d_6	A	X-RAY DIFFRACTION	Torsion NCS	0.318470719873

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 (%)
2.65-2.72	0.34	166	0.3144	3775	X-RAY DIFFRACTION	98.77
2.72-2.79	0.326	139	0.29	3833	X-RAY DIFFRACTION	98.93
2.79-2.87	0.2679	118	0.2775	3931	X-RAY DIFFRACTION	99.22
2.87-2.96	0.3051	134	0.2623	3867	X-RAY DIFFRACTION	99.16
2.96-3.07	0.2878	128	0.266	3927	X-RAY DIFFRACTION	99.17
3.07-3.19	0.3241	151	0.2657	3877	X-RAY DIFFRACTION	99.16
3.19-3.34	0.2999	149	0.257	3866	X-RAY DIFFRACTION	99.5
3.34-3.51	0.2776	135	0.2265	3908	X-RAY DIFFRACTION	99.48
3.51-3.73	0.3094	152	0.2225	3914	X-RAY DIFFRACTION	99.27
3.73-4.02	0.1963	126	0.1955	3947	X-RAY DIFFRACTION	99.39
4.02-4.43	0.1985	130	0.1808	4027	X-RAY DIFFRACTION	99.83
4.43-5.07	0.2117	140	0.1772	3998	X-RAY DIFFRACTION	99.69
5.07-6.38	0.2249	131	0.2111	4081	X-RAY DIFFRACTION	99.67
6.38-41.51	0.1858	176	0.1688	4237	X-RAY DIFFRACTION	98.02

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	4.45261322068	-2.28270489497	1.00160009265	2.52354537896	2.04694297046	5.39940047522	-0.174603280642	0.15442180343	0.16913132001	-0.0123694147414	0.0823765855899	-0.115869272747	-0.767551625546	0.200534944092	0.115638965568	0.551378580117	-0.194868409615	0.0724751574861	0.607859232452	0.0768000925892	0.511838180324	-2.56153932291	28.8827162109	79.9240744101
2	3.08428535238	1.8241392395	-1.08992183495	1.88049611566	-0.216769144481	0.62442855829	-0.576473860081	1.31746999585	0.715889467858	-0.799243057752	0.554646250162	-0.254918681516	-1.18331186578	1.57486438124	-0.0651592369172	0.876504212996	-0.351665176948	0.134552583794	1.28858541864	0.0788012058879	0.65950214579	5.24861538266	26.3060739769	64.9334247306
3	2.04626962226	0.056481081588	0.509995016915	1.961765228	0.322159179554	4.40590708583	0.083518455786	0.113919089982	0.169028549895	-0.439136525219	-0.0250539618015	-0.149254907306	-0.127991091459	0.246148599181	-0.0593323618521	0.510712845055	0.025645301194	0.131725881481	0.362407804683	0.0847693832582	0.511839290837	-17.4444305987	13.4119691528	49.6633691706
4	5.31827136248	1.81613170864	1.52018378573	4.75356593012	1.2575018404	5.93278722602	0.0253490636482	0.679207908088	-0.633194540574	-0.135502601819	0.12544527471	-0.451272310035	0.129862899458	1.06089262317	-0.111057941092	0.455007501024	-0.0124471219247	0.0978478249591	0.808923369656	-0.00963240109637	0.605279231652	1.15765846209	13.7686399868	66.4253464254
5	2.89352509655	0.106332461675	0.305731832554	1.84592638831	0.661678010396	0.278498302221	-0.152741894908	-1.86592508648	0.809807645556	0.770088072065	-0.724491462961	0.701029874552	-0.306600402018	-1.33449521244	0.397975761237	0.823814288702	0.262494945796	0.016948373069	1.74012646811	-0.612408803343	1.13635706733	-41.5959376039	35.993896266	81.9696284432
6	2.06530404193	-0.189837011271	0.302551182837	1.28075257536	-0.522334441275	2.96791898762	0.16607260697	-0.493870058112	0.0339868123072	0.265686078259	-0.155635432891	0.277334987301	0.583819498588	-0.812887228123	0.0125854871384	0.526040856382	-0.151562028943	0.0864448783181	0.695285185578	0.0618659055746	0.521433869736	-39.7393909367	6.52894161051	67.945046605
7	1.3543065251	-0.208035658718	-0.99440883382	3.13866351609	-1.84947566653	2.04710982298	0.105448431797	-0.748635712267	0.961431751119	-0.0609054821087	-0.453267152745	1.21601009613	-0.651660006747	-1.46583870254	0.152235999811	0.721947826843	0.273855764567	0.0113403375922	1.4843172926	-0.505193962244	1.071097486	-49.6425320186	28.7330262812	70.3192902498
8	0.611674603288	0.431551963816	-0.222515508171	1.20845768081	1.51119284749	3.41264887469	-0.249286978889	-0.103407080277	-0.4469622606	0.331852230566	0.0989674102714	-0.212262870061	1.29779991144	-0.0772661332492	0.0934462201827	1.19185939385	0.128705581094	0.167912907213	0.492590943245	0.114041002884	0.774011922408	-17.5497191493	-20.6065659334	45.1715393169
9	2.75055438528	0.195417139746	0.666853128716	2.94729644471	-0.17320252623	3.69931949046	0.319705767435	-0.423854376051	-0.299247039636	0.351609686072	-0.200210225923	0.15358370246	0.814568572168	-0.276421337535	-0.107259421561	0.638295153284	-0.0708319309238	0.0413677281878	0.439936152143	0.120667051528	0.468945043377	-24.7003311078	-1.99201137025	67.0999078505
10	2.71038328768	0.963793587386	0.474537534038	5.8987323518	1.38081673166	5.03180622302	-0.196113218119	-0.635647931957	-0.116775140306	0.0362297335764	0.368592485661	-0.946136127624	0.793824613125	0.745692479509	-0.123415217569	1.06026749866	0.362507876014	-0.00510862756373	0.63627677362	0.047548157619	0.814838519568	-9.50264362733	-13.5785387194	48.7829225904
11	6.81952720461	-0.598800591637	1.42030320108	4.80863814667	2.13555152484	4.15541205747	0.33600801568	0.89112256314	-0.523602156959	-1.11241822153	-0.870265334431	1.21554705206	0.109810947796	-0.686403892225	0.61703161239	0.954762791558	0.0618343604084	-0.234973998021	1.00849753695	-0.225149392208	1.11496947036	-56.411841899	-3.66337925737	33.6752093324
12	2.55916172455	0.251997302006	0.303733357554	3.9192886571	1.23437436099	2.68797937416	0.00719665599145	0.0440406191518	0.235677766424	-0.418434364466	-0.208638436737	0.610780867224	-0.234687859318	-0.547844194613	0.216580673982	0.480124575936	0.121044798754	-0.0215897223917	0.426468938973	0.0572054843598	0.478725276144	-41.6317376455	15.3597787733	47.1663808375
13	1.55710040396	-1.70329012875	0.653702510741	2.45841988912	-0.459826904687	2.47871137136	-0.309645098493	0.0912786608481	-0.0478149239073	0.948081179618	-0.0105207698862	0.370318562468	0.304477076619	-0.468059716615	0.377147245644	1.39281672386	-0.340406731406	0.525827980803	0.76710141419	-0.0410834026079	1.33115184355	-49.313092128	-29.0745792623	22.1223199374
14	5.43008545798	3.71672786586	3.1144645075	5.46150816748	-1.17528471665	5.58353229044	-0.615202077206	-1.34973401181	-0.964578366574	0.688916569249	0.0311761044221	0.228917939978	0.523415868673	-1.34374123323	0.566768998189	2.20439791345	-0.0920732605026	0.908598829281	1.0229480133	-0.0880071912885	1.50814018173	-45.4157022207	-40.7908353463	26.6196971415
15	2.86949623454	2.98879232029	0.159876893464	3.4301454153	-0.531652433426	1.60659500921	-0.0822198018598	-0.303104469656	-1.44276166436	0.608897809469	0.24665141956	-0.494337027398	0.361818272932	-0.470389268622	-0.226004019051	1.63137163614	-0.361279740921	0.93050996837	0.603893138545	0.190862442923	1.72831709673	-38.6411487717	-45.4672285996	24.1011067352
16	0.73600185438	0.316741439647	-0.257677947242	2.07143060749	0.377953569035	0.430498127526	-0.52230042581	0.279046022994	-0.471715485696	0.525244667827	0.0680974486836	0.206134746596	0.990151120421	-0.323191595817	0.363721337519	1.95925300443	-0.343725622127	0.704469068486	0.607030694847	-0.231660641912	1.05680322286	-18.3490608299	-39.1665966758	9.55210587324
17	0.238378587386	0.386993805611	0.153543888359	1.49001801323	0.586736823069	0.234636703708	-0.436173250046	0.0313399171047	-0.644146927125	0.859157898279	0.188889972027	0.00140760770844	1.40845652436	0.0220584960229	0.545790493355	1.98779716072	-0.312593368598	0.684634804929	0.713423147237	-0.240626074387	1.26456901011	-16.0124265562	-46.9258845734	13.1636719721
18	1.08026495154	0.992105169017	-0.325213617742	0.974727639164	-0.163206176031	1.43423522551	-0.831924586473	0.197340033414	-0.818579002697	0.946168714654	0.166425452603	0.450103563792	1.1659007188	-0.0130116870614	0.579065565665	1.59384253346	-0.221657286258	0.533739986587	0.645281761511	-0.140160526376	1.02824181441	-12.5086548256	-36.3646207033	8.17263993364
19	1.04490052064	-0.447191775824	-0.15714882248	1.52961459494	0.256244870384	2.89134989438	-0.0294443406015	0.0104998021597	-0.240330574601	0.0849666851533	0.0899309055836	0.313697882652	0.0132412517005	-0.147208232902	-0.219155207495	1.90982686041	-0.481339106104	1.12501883323	0.629875733755	-0.0520163906324	1.39270571309	-40.6992592597	-38.4033836277	13.1014243736
20	5.53732015194	2.32110381178	1.74657982165	3.78314031901	-1.60629808582	2.49975382419	0.0200750373577	-0.0238989436327	-0.840086668667	-0.553046271068	0.729301364978	-0.296985440636	0.0942279760035	-0.26872893828	-0.00369946183156	1.89829416107	-0.617396258459	1.05056391667	0.901544282586	-0.196278787625	1.64564938564	-39.0779561365	-48.7512116913	11.6885883439
21	6.80955475314	0.956932688643	-3.15693352899	5.59715592007	2.40277499567	9.93687985676	0.054000841538	0.228595923555	-0.0706437385363	0.100938470868	-0.526605997062	0.42335504192	-0.109715799433	-1.25645103671	0.399153542523	0.725816394792	0.0791335928892	0.0551602635732	0.645592644109	0.00701276522222	0.50652458178	-30.6786428237	0.919588521268	22.9682283471
22	3.29854825038	-0.6032833982	0.108896770223	4.35717887677	-1.76804008977	3.46543586764	-0.0411166180051	0.809460328536	0.310958697839	-1.39561546733	0.247854900439	0.350879343589	-1.69771224867	-1.31920861767	-0.178980987283	1.29801340786	0.1295721496	0.0781034435119	0.87680609164	0.172797412857	0.604030444659	-27.0477101208	8.70391212598	8.19657284793
23	1.88312359262	-0.386181872016	-0.559745506246	2.53199029386	0.690751760751	3.57147923107	-0.207388148446	0.811333247558	-0.354895677557	0.142773975194	-0.110980352068	0.351159615823	0.294591726436	-1.08841609892	0.327322977673	0.644805354158	-0.273822574286	0.135377256841	0.757575729812	-0.139401811351	0.595217956308	-18.2766176961	-15.5133495472	-8.25434674622
24	6.8387807429	-2.61186545524	-1.44861107277	3.95539478805	2.29098912301	7.74966212874	-0.0264718900894	0.648981861383	0.59215611681	-0.685673530746	0.242895916731	-0.728681216944	-0.862733040872	-0.0654707092233	-0.188634749275	0.858241899456	-0.0205300111675	0.134205727927	0.413639599016	0.0317639247546	0.507781626586	-15.3085318412	2.56219037379	9.12646328133

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 4 through 70 )	A	A	4 - 70	1 - 67
2	2	chain 'A' and (resid 71 through 128 )	A	A	71 - 128	68 - 125
3	3	chain 'A' and (resid 129 through 239 )	A	A	129 - 239	126 - 236
4	4	chain 'A' and (resid 240 through 270 )	A	A	240 - 270	237 - 267
5	5	chain 'B' and (resid 5 through 128 )	B	C	5 - 128	1 - 124
6	6	chain 'B' and (resid 129 through 239 )	B	C	129 - 239	125 - 235
7	7	chain 'B' and (resid 240 through 272 )	B	C	240 - 272	236 - 268
8	8	chain 'C' and (resid 4 through 148 )	C	E	4 - 148	1 - 145
9	9	chain 'C' and (resid 149 through 239 )	C	E	149 - 239	146 - 236
10	10	chain 'C' and (resid 240 through 270 )	C	E	240 - 270	237 - 267
11	11	chain 'D' and (resid 4 through 115 )	D	G	4 - 115	1 - 112
12	12	chain 'D' and (resid 116 through 269 )	D	G	116 - 269	113 - 266
13	13	chain 'E' and (resid 4 through 70 )	E	I	4 - 70	1 - 67
14	14	chain 'E' and (resid 71 through 93 )	E	I	71 - 93	68 - 90
15	15	chain 'E' and (resid 94 through 128 )	E	I	94 - 128	91 - 125
16	16	chain 'E' and (resid 129 through 166 )	E	I	129 - 166	126 - 163
17	17	chain 'E' and (resid 167 through 187 )	E	I	167 - 187	164 - 184
18	18	chain 'E' and (resid 188 through 239 )	E	I	188 - 239	185 - 236
19	19	chain 'E' and (resid 240 through 252 )	E	I	240 - 252	237 - 249
20	20	chain 'E' and (resid 253 through 270 )	E	I	253 - 270	250 - 267
21	21	chain 'F' and (resid 4 through 70 )	F	K	4 - 70	1 - 67
22	22	chain 'F' and (resid 71 through 128 )	F	K	71 - 128	68 - 125
23	23	chain 'F' and (resid 129 through 239 )	F	K	129 - 239	126 - 236
24	24	chain 'F' and (resid 240 through 270 )	F	K	240 - 270	237 - 267

-
News

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

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

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

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

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

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

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

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Processing

+About Yorodumi

-News

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

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

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

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

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

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

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

+
Jul 12, 2017. Major update of PDB

-
Yorodumi