PDB-7sbj: Crystal Structure of Ribulose-phosphate 3-epimerase from Stenotro...

ID or keywords:

Entry

Database: PDB / ID: 7sbj

Title

Crystal Structure of Ribulose-phosphate 3-epimerase from Stenotrophomonas maltophilia K279a

Components

Ribulose-phosphate 3-epimerase

Phosphopentose epimerase

Keywords

ISOMERASE / SSGCID / rpe /

Structural Genomics / Seattle Structural Genomics Center for Infectious Disease

Function / homology

Function and homology information

ribulose-phosphate 3-epimerase / D-ribulose-phosphate 3-epimerase activity / pentose catabolic process / pentose-phosphate shunt /

metal ion binding
Similarity search - Function

Biological species

Stenotrophomonas maltophilia (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.85 Å

Authors

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Funding support

United States, 1items

Citation

Journal: to be published
Title: Crystal Structure of Ribulose-phosphate 3-epimerase from Stenotrophomonas maltophilia K279a
Authors: Abendroth, J. / Lorimer, D.D. / Horanyi, P.S. / Edwards, T.E.

History

Deposition	Sep 25, 2021	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Oct 27, 2021	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	7sbj.cif.gz	341.7 KB	Display	PDBx/mmCIF format
PDB format	pdb7sbj.ent.gz	227.4 KB	Display	PDB format
PDBx/mmJSON format	7sbj.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/sb/7sbj ftp://data.pdbj.org/pub/pdb/validation_reports/sb/7sbj	HTTPS FTP

-
Related structure data

Related structure data	5umfS S: Starting model for refinement
Similar structure data	5umf-d 5wzh-d 5wzi-d 4xuq-d 4z64-2 5wzk-d 6i8w-d 6gwn-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

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#228 - Dec 2018 Directed Evolution of Enzymes similarity (1)

Deposited unit

A: Ribulose-phosphate 3-epimerase

B: Ribulose-phosphate 3-epimerase

C: Ribulose-phosphate 3-epimerase

hetero molecules

76.3 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	83.890, 136.480, 148.740
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	20
Space group name H-M	C222₁
Space group name Hall	C2c2
Symmetry operation	#1: x,y,z #2: x,-y,-z #3: -x,y,-z+1/2 #4: -x,-y,z+1/2 #5: x+1/2,y+1/2,z #6: x+1/2,-y+1/2,-z #7: -x+1/2,y+1/2,-z+1/2 #8: -x+1/2,-y+1/2,z+1/2

Components on special symmetry positions

ID	Model	Components
1	1	A-469- HOH
2	1	A-605- HOH
3	1	B-572- HOH
4	1	C-560- HOH

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
d_1	ens_1	(chain "A" and (resid 4 through 8 or resid 10...
d_2	ens_1	(chain "B" and (resid 4 through 8 or resid 10...
d_3	ens_1	(chain "C" and (resid 4 through 8 or resid 10...

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	CYS	PRO	A	1 - 5
d_1	2	ens_1	ILE	ASP	A	7 - 20
d_1	3	ens_1	VAL	CYS	A	22 - 50
d_1	4	ens_1	ALA	PRO	A	52 - 70
d_1	5	ens_1	ASP	ALA	A	72 - 79
d_1	6	ens_1	ALA	ILE	A	81 - 100
d_1	7	ens_1	LEU	CYS	A	102 - 108
d_1	8	ens_1	PRO	ILE	A	110 - 169
d_1	9	ens_1	LEU	GLY	A	171 - 196
d_1	10	ens_1	ALA	TYR	A	198 - 206
d_1	11	ens_1	VAL	ALA	A	209 - 211
d_1	12	ens_1	MET	ARG	A	213 - 221
d_1	13	ens_1	ZN	ZN	B
d_1	14	ens_1	SO4	SO4	C
d_1	15	ens_1	SO4	SO4	D
d_1	16	ens_1	CL	CL	E
d_1	17	ens_1	CL	CL	F
d_2	1	ens_1	CYS	PRO	H	1 - 5
d_2	2	ens_1	ILE	ASP	H	7 - 20
d_2	3	ens_1	VAL	CYS	H	22 - 50
d_2	4	ens_1	ALA	PRO	H	52 - 70
d_2	5	ens_1	ASP	ALA	H	72 - 79
d_2	6	ens_1	ALA	ILE	H	81 - 100
d_2	7	ens_1	LEU	CYS	H	102 - 108
d_2	8	ens_1	PRO	ILE	H	110 - 169
d_2	9	ens_1	LEU	GLY	H	171 - 196
d_2	10	ens_1	ALA	TYR	H	198 - 206
d_2	11	ens_1	VAL	ALA	H	209 - 211
d_2	12	ens_1	MET	ARG	H	213 - 221
d_2	13	ens_1	ZN	ZN	I
d_2	14	ens_1	SO4	SO4	J
d_2	15	ens_1	SO4	SO4	K
d_2	16	ens_1	CL	CL	L
d_2	17	ens_1	CL	CL	M
d_3	1	ens_1	CYS	PRO	O	1 - 5
d_3	2	ens_1	ILE	ASP	O	7 - 20
d_3	3	ens_1	VAL	CYS	O	22 - 50
d_3	4	ens_1	ALA	PRO	O	52 - 70
d_3	5	ens_1	ASP	ALA	O	72 - 79
d_3	6	ens_1	ALA	ILE	O	81 - 100
d_3	7	ens_1	LEU	CYS	O	102 - 108
d_3	8	ens_1	PRO	ILE	O	110 - 169
d_3	9	ens_1	LEU	GLY	O	171 - 196
d_3	10	ens_1	ALA	TYR	O	198 - 206
d_3	11	ens_1	VAL	ALA	O	209 - 211
d_3	12	ens_1	MET	ARG	O	213 - 221
d_3	13	ens_1	ZN	ZN	P
d_3	14	ens_1	SO4	SO4	Q
d_3	15	ens_1	SO4	SO4	R
d_3	16	ens_1	CL	CL	S
d_3	17	ens_1	CL	CL	T

NCS oper:

ID	Code	Matrix	Vector
1	given	(-0.999915194321, -0.00121472785076, 0.0129664413508), (-0.0106537603086, -0.496329700463, -0.868068733356), (0.0074900972185, -0.868133257556, 0.496274667467)	0.315372223462, -101.972904399, -59.1527406029
2	given	(0.999848361014, -0.00992306058816, -0.0143104104382), (0.00723101662763, -0.510995304121, 0.859553088276), (-0.0158419499077, -0.859526225333, -0.510846063495)	-0.948302270626, -38.2073314423, -96.3653432979

-
Protein , 1 types, 3 molecules ABC

#1: Protein	Ribulose-phosphate 3-epimerase / Phosphopentose epimerase Mass: 25070.846 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Stenotrophomonas maltophilia (strain K279a) (bacteria) Strain: K279a / Gene: rpe, Smlt4316 / Plasmid: StmaA.18616.a.B1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: B2FKL8, ribulose-phosphate 3-epimerase

#1: Protein

Ribulose-phosphate 3-epimerase /

Phosphopentose epimerase

Mass: 25070.846 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Stenotrophomonas maltophilia (strain K279a) (bacteria)
Strain: K279a / Gene: rpe, Smlt4316 / Plasmid: StmaA.18616.a.B1 / Production host:

Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: B2FKL8,

ribulose-phosphate 3-epimerase

-
Non-polymers , 5 types, 824 molecules

#2: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#3: Chemical	ChemComp-SO4 / SULFATE ION / Sulfate Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO₄
#4: Chemical	ChemComp-CL / CHLORIDE ION / Chloride Mass: 35.453 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Cl
#5: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 805 / Source method: isolated from a natural source / Formula: H₂O

-
Details

Has ligand of interest	N

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.84 Å³/Da / Density % sol: 56.7 %
Crystal grow	Temperature: 287 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: Anatrace/Calibre MCSG1 screen, condition e7: 200mM ammonium iodide, 20% (w/V) PEG 3350: StmaA.18161.a.B1.PS38644 at 18.6mg/ml, tray: 321485e7, puck: pxu9-1: cryo: 20% EG

-
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: Sep 16, 2021 / 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: 1.85→50 Å / Num. obs: 72940 / % possible obs: 100 % / Redundancy: 7.446 % / B_iso Wilson estimate: 22.713 Å² / CC_1/2: 0.998 / R_merge(I) obs: 0.095 / R_rim(I) all: 0.102 / Χ²: 0.922 / Net I/σ(I): 17.49

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
1.85-1.9	7.456	0.496	4.37	5361	0.927	0.533	99.9
1.9-1.95	7.467	0.427	5.08	5209	0.94	0.459	100
1.95-2.01	7.469	0.366	5.89	5079	0.956	0.393	100
2.01-2.07	7.48	0.303	7.08	4893	0.97	0.325	100
2.07-2.14	7.485	0.253	8.42	4779	0.981	0.271	100
2.14-2.21	7.486	0.208	10.04	4617	0.984	0.224	100
2.21-2.29	7.492	0.179	11.52	4456	0.988	0.193	99.9
2.29-2.39	7.489	0.155	13.02	4296	0.99	0.167	100
2.39-2.49	7.493	0.139	14.69	4138	0.992	0.149	100
2.49-2.62	7.493	0.116	17.04	3957	0.994	0.124	100
2.62-2.76	7.486	0.105	18.56	3782	0.995	0.113	100
2.76-2.93	7.482	0.088	21.39	3546	0.997	0.095	100
2.93-3.13	7.465	0.072	25.78	3372	0.998	0.078	100
3.13-3.38	7.449	0.058	30.66	3133	0.998	0.062	100
3.38-3.7	7.449	0.046	36.41	2887	0.999	0.05	100
3.7-4.14	7.388	0.04	40.71	2641	0.999	0.043	100
4.14-4.78	7.344	0.035	44.33	2334	0.999	0.038	100
4.78-5.85	7.3	0.036	43.03	1984	0.999	0.039	100
5.85-8.27	7.14	0.037	41.7	1569	0.999	0.04	100
8.27-50	6.547	0.03	47.98	907	0.998	0.033	99

-
Processing

Software

Name	Version	Classification
XDS		data reduction
XSCALE		data scaling
PHENIX	1.19 dev 4359	refinement
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 5umf as per Morda

5umf

Resolution: 1.85→40.74 Å / SU ML: 0.1398 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 16.8033
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.1788	2050	2.81 %	0
R_work	0.1478	70877	-	-
obs	0.1486	72927	99.96 %	-

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso mean: 19.15 Å²

Refinement step

Cycle: LAST / Resolution: 1.85→40.74 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4961	0	43	805	5809

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0084	5267
X-RAY DIFFRACTION	f_angle_d	0.8804	7230
X-RAY DIFFRACTION	f_chiral_restr	0.0664	847
X-RAY DIFFRACTION	f_plane_restr	0.0075	956
X-RAY DIFFRACTION	f_dihedral_angle_d	12.3575	1931

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	0.298619147944
ens_1	d_3	A	X-RAY DIFFRACTION	Torsion NCS	0.286279224531

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 (%)
1.85-1.89	0.2085	143	0.174	4651	X-RAY DIFFRACTION	99.9
1.89-1.94	0.2106	121	0.1654	4710	X-RAY DIFFRACTION	99.96
1.94-1.99	0.1893	126	0.1656	4665	X-RAY DIFFRACTION	99.94
1.99-2.05	0.234	114	0.1567	4728	X-RAY DIFFRACTION	99.96
2.05-2.12	0.2022	142	0.1553	4671	X-RAY DIFFRACTION	99.96
2.12-2.19	0.1897	151	0.1459	4667	X-RAY DIFFRACTION	99.98
2.19-2.28	0.201	122	0.1456	4726	X-RAY DIFFRACTION	99.96
2.28-2.38	0.1503	161	0.1415	4655	X-RAY DIFFRACTION	100
2.39-2.51	0.175	133	0.1458	4727	X-RAY DIFFRACTION	99.98
2.51-2.67	0.1995	126	0.1468	4721	X-RAY DIFFRACTION	100
2.67-2.87	0.1985	150	0.1591	4709	X-RAY DIFFRACTION	100
2.87-3.16	0.2012	128	0.1493	4744	X-RAY DIFFRACTION	99.98
3.16-3.62	0.1626	141	0.1378	4767	X-RAY DIFFRACTION	100
3.62-4.56	0.1223	144	0.1258	4775	X-RAY DIFFRACTION	100
4.56-40.74	0.1907	148	0.1582	4961	X-RAY DIFFRACTION	99.86

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	2.40360321564	1.01713011206	-0.462007802493	3.95117169416	-0.605842042598	1.22582380221	-0.00191003621301	0.0718090755978	0.122050209156	-0.27766906535	-0.0083686451705	0.211404718836	-0.0853120663383	-0.0518310206112	0.0186540430072	0.107230870653	0.0378730903151	-0.0326786108333	0.0716836532997	-0.0178526055864	0.143108624167	-22.9449392085	-20.0703877872	-41.2091222795
2	7.30047105136	-0.792421161755	3.29148667251	3.41206906205	2.25980400267	4.46312735189	-0.0462313375831	-0.209862229274	-0.128319133426	-0.0632649236082	-0.169336914762	0.572542717276	0.0876339734868	-0.368714686674	0.118754223361	0.153942865697	0.0397182738514	-0.0273220571821	0.0745872028713	-0.00237758725013	0.226997516327	-26.0559703216	-10.9010029991	-42.4757777624
3	0.526820536993	-0.148361717619	-0.224373293796	1.22449646334	0.869610157055	1.34686007117	-0.00703805562246	0.132836301281	-0.0349721004413	-0.0935762732495	0.00205807197758	0.0278432724124	-0.00643399800512	-0.0160814663466	0.00637167858155	0.0821806447018	0.000613126164774	0.00245660952354	0.095976203012	-0.00741182168025	0.0733463711525	8.66160435612	-61.8419966451	-60.4238157216
4	1.91496594222	0.531324360027	0.0910193011824	1.86181563229	-0.246985188574	1.43333163132	-0.0226541826706	-0.0820136190428	-0.0268637175116	0.0854040054128	0.0230605262724	0.0222968669167	-0.0455949015367	-0.00710386211792	-0.00725945111652	0.0656019620388	0.0165269184386	0.0028008624455	0.0688866472245	-0.000441131328041	0.0594607846727	14.010888067	-60.2942031908	-43.5920253062
5	2.69625790339	0.948608354738	-1.78810118094	3.30258664544	0.724147941979	1.87037735074	0.117149162034	0.231771149346	0.161973789525	-0.474246443432	0.0109712990706	0.226060940106	0.0272496842661	-0.138283746807	-0.0808016944269	0.0694948350244	-0.0285115242769	-0.0176551392464	0.0993473279705	-0.0189441819504	0.0975882014578	19.1809830305	-52.2423465466	-52.7886176531
6	3.58669764899	-2.48948663433	1.92352533652	4.19116719096	-1.2959527822	3.44205145164	0.0365553146547	-0.00023098016956	0.132378688306	-0.0592637206551	-0.117198017723	-0.618275546206	-0.292114342556	0.595733645853	0.0669094484369	0.0599109802761	-0.0413407502216	0.0169499849918	0.185120064356	-0.000110073744518	0.165003420797	31.0543611966	-52.7236808978	-50.9121298275
7	2.73333737378	0.394464478456	1.0687550908	1.52902366616	0.769838401034	3.9776364947	-0.0683955680711	0.28072055697	0.111356379167	-0.294011851406	0.0841470908498	-0.14699207491	-0.215614179561	0.202864811708	-0.00727178994997	0.11863650853	-0.0114016660194	0.0404899246316	0.122508343125	-0.0167574620361	0.0987836560804	22.9792085431	-56.07887332	-62.2736418641
8	4.37332344852	1.38195921708	-1.64754491939	4.89053792079	0.569044299299	1.63125535707	-0.152802050255	-0.0398391178344	-0.0165705856216	-0.313047475957	0.273028216306	-0.719045964361	-0.272955558713	0.472083531515	-0.203917070465	0.152149520897	-0.0338143818054	0.0789530038703	0.272422706705	-0.0456172030961	0.162110692746	25.3428034556	-59.3065665617	-71.5602783479
9	7.27338321178	-1.84926810739	0.467855273299	1.89647720615	0.0104794327255	2.56418414319	-0.0472780177255	0.0313706339291	-0.0510213256798	-0.0980217546665	0.0296934324206	0.051268849155	0.0900673144603	-0.0152477990444	0.0173906978602	0.112412143168	-0.0303549059149	0.00026400563131	0.0892428286168	-0.0381438214941	0.0863493219792	-10.57161852	-64.7921231135	-66.0059508812
10	0.657811495957	-0.0527829191775	0.208033905567	0.355702560387	0.331240902997	2.01914451931	-0.00582426615868	0.104938968741	-0.0548542710073	-0.0607261481664	-0.0369234665193	-0.00582142781247	-0.0174754083766	-0.0434353742465	0.033797403706	0.0792933995516	0.00413406311686	-0.0144340470606	0.0891924700974	-0.0109218582057	0.0742998967289	-8.23507322401	-55.9489685828	-59.7940810173
11	1.80448338433	0.414765762032	-0.871596099401	1.13280224234	-0.502441487576	1.02020123262	0.0156776757834	0.0525606396766	0.129732367233	0.00970494935477	-0.0222291141855	0.0103224248065	-0.0865297465107	-0.0629506564109	-0.00417508583086	0.0961076077909	0.0125019300244	-0.0286516179088	0.0857192081086	-0.0109927912108	0.087984768422	-14.556446236	-45.2029147311	-52.1052157198
12	2.17310153347	1.01573986338	0.502901971929	3.83310964888	-1.57510163032	3.61438921563	0.127044604742	0.00863996388305	-0.209126225349	-0.307156918989	-0.11379543822	-0.124901712368	0.306090605559	0.1224908979	-0.021860461941	0.0787935207665	0.00209695364766	0.0143765957839	0.13084233696	-0.0255784523041	0.0872123798179	-19.3908773122	-57.0679253556	-49.8109314744
13	3.75800431197	-2.7115759208	1.7847516388	3.3251565257	-3.49150208626	4.48846697021	0.0179688166929	-0.034607548194	-0.126246133245	0.017796288886	0.125791850628	0.574162124427	-0.00752920625428	-0.455600052739	-0.17429087322	0.0808705021085	-0.0091999257391	-0.0056176350135	0.178385965153	-0.0370593035339	0.144836217064	-31.2409043692	-55.1213564714	-49.1425234143
14	4.05850782228	-1.03519312078	-0.704581011361	3.94542641395	1.48977690779	2.88727069687	-0.087216606111	0.139062529418	-0.175722849901	-0.0939863912704	-0.0667612078184	0.0718768464128	0.169390746529	-0.356593295827	0.123093335145	0.0843132297703	-0.0116199615894	-0.0200362128146	0.153427116908	-0.0276299173912	0.0534570001092	-26.2842100098	-60.5877395752	-55.9418381666
15	1.6758420379	1.42457670244	-0.406781442988	2.42902321108	0.83805058591	2.85762210692	-0.111482523435	0.190576380062	-0.242881487432	-0.0871156648992	-0.0796764116153	0.173523517172	0.307898284551	-0.34781953892	0.125811323303	0.140742213027	-0.0445356218611	-0.0236010246334	0.172812656019	-0.0388797355019	0.117573290814	-22.7051679627	-68.9491436264	-63.0508186695
16	2.18880155944	-1.07677435777	-2.22749065741	1.37835861881	0.452666977903	3.52181068859	0.000413296109911	0.032354213991	0.0897088299439	-0.0222699086638	-0.0479516330904	-0.13205074218	-0.240346048515	0.068521277242	0.0461097212721	0.138460334598	0.0251350017886	-0.041540284853	0.0825327785699	0.0155368808982	0.155593534132	-10.3572214749	-12.6785736582	-38.1960814517
17	0.542301028308	0.0680615974592	-0.00646305895135	0.553734988479	-0.196770513731	0.6741079184	-0.0108433310051	-0.0487541484065	0.0204471547498	0.0300860286075	-0.00144052287492	0.0100640702381	0.00127387703793	0.0311580145254	0.0141085599662	0.095667668339	0.0172387929113	-0.0178272474434	0.0793046379763	-0.0098184099187	0.110935724419	-11.5597943568	-29.2206552711	-30.5437701673
18	2.02210113426	-0.394153717221	-0.683567013709	1.9496251785	-0.173558510241	4.85983504521	0.0399847262823	0.0464958667818	-0.0144726839753	-0.0734959942328	-0.0172769464118	0.129479157116	-0.12777564618	-0.10515843102	-0.0322248315418	0.0911769968605	0.0111261437283	-0.0272685446858	0.0456383837169	-0.0152860834732	0.152187656462	-24.5591570583	-30.8363697405	-39.1146978868

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 169 through 208 )	A	A	169 - 208	166 - 205
2	2	chain 'A' and (resid 209 through 224 )	A	A	209 - 224	206 - 221
3	3	chain 'B' and (resid 4 through 70 )	B	H	4 - 70	1 - 67
4	4	chain 'B' and (resid 71 through 129 )	B	H	71 - 129	68 - 126
5	5	chain 'B' and (resid 130 through 151 )	B	H	130 - 151	127 - 148
6	6	chain 'B' and (resid 152 through 168 )	B	H	152 - 168	149 - 165
7	7	chain 'B' and (resid 169 through 208 )	B	H	169 - 208	166 - 205
8	8	chain 'B' and (resid 209 through 224 )	B	H	209 - 224	206 - 221
9	9	chain 'C' and (resid 4 through 27 )	C	O	4 - 27	1 - 24
10	10	chain 'C' and (resid 28 through 70 )	C	O	28 - 70	25 - 67
11	11	chain 'C' and (resid 71 through 129 )	C	O	71 - 129	68 - 126
12	12	chain 'C' and (resid 130 through 151 )	C	O	130 - 151	127 - 148
13	13	chain 'C' and (resid 152 through 168 )	C	O	152 - 168	149 - 165
14	14	chain 'C' and (resid 169 through 191 )	C	O	169 - 191	166 - 188
15	15	chain 'C' and (resid 192 through 224 )	C	O	192 - 224	189 - 221
16	16	chain 'A' and (resid 4 through 27 )	A	A	4 - 27	1 - 24
17	17	chain 'A' and (resid 28 through 129 )	A	A	28 - 129	25 - 126
18	18	chain 'A' and (resid 130 through 168 )	A	A	130 - 168	127 - 165

-
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

-
Protein , 1 types, 3 molecules ABC

-
Non-polymers , 5 types, 824 molecules

-
Details

-
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

-Protein , 1 types, 3 molecules ABC

-Non-polymers , 5 types, 824 molecules

-Details

-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

-
Protein , 1 types, 3 molecules ABC

-
Non-polymers , 5 types, 824 molecules

-
Details

-
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