PDB-3h4v: Selective screening and design to identify inhibitors of leishman...

ID or keywords:

Entry

Database: PDB / ID: 3h4v

Title

Selective screening and design to identify inhibitors of leishmania major pteridine reductase 1

Components

Pteridine reductase 1

Keywords

OXIDOREDUCTASE / SHORT-CHAIN REDUCTASE / LEISHMANIA / TRYPANOSOMA / PTR1 / INHIBITOR / Methotrexate resistance / NADP

Function / homology

Function and homology information

pteridine reductase / 6,7-dihydropteridine reductase activity / pteridine reductase activity / tetrahydrobiopterin biosynthetic process / response to methotrexate / oxidoreductase activity / cytosol
Similarity search - Function

Biological species

Leishmania major (eukaryote)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.4 Å

Authors

Mcluskey, K. / Gibellini, F. / Hunter, W.N.

Citation

Journal: Proc.Natl.Acad.Sci.USA / Year: 2008
Title: Discovery of potent pteridine reductase inhibitors to guide antiparasite drug development
Authors: Cavazzuti, A. / Paglietti, G. / Hunter, W.N. / Gamarro, F. / Piras, S. / Loriga, M. / Allecca, S. / Corona, P. / McLuskey, K. / Tulloch, L. / Gibellini, F. / Ferrari, S. / Costi, M.P.

History

Deposition	Apr 21, 2009	Deposition site: RCSB / Processing site: PDBJ
Supersession	May 5, 2009	ID: 2P8K
Revision 1.0	May 5, 2009	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Version format compliance
Revision 1.2	Nov 1, 2017	Group: Refinement description / Category: software
Revision 1.3	Nov 1, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3h4v.cif.gz	442.2 KB	Display	PDBx/mmCIF format
PDB format	pdb3h4v.ent.gz	361.4 KB	Display	PDB format
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Validation report

Summary document	3h4v_validation.pdf.gz	4.9 MB	Display	wwPDB validaton report
Full document	3h4v_full_validation.pdf.gz	5 MB	Display
Data in XML	3h4v_validation.xml.gz	105.4 KB	Display
Data in CIF	3h4v_validation.cif.gz	136.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/h4/3h4v ftp://data.pdbj.org/pub/pdb/validation_reports/h4/3h4v	HTTPS FTP

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Related structure data

Related structure data	2qhxC 1e92S 1p33 1w0c 2bf7 2bfa 2bfm C: citing same article (ref.) S: Starting model for refinement
Similar structure data	1p33-d 1w0c-2 2bfa-d 2bf7-d 6rxc-d 1e92-d 1e7w-1 1w0c-1 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) 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	#90 - Jun 2007 Fatty Acid Synthase similarity (3) #77 - May 2006 Glucose Oxidase similarity (3) #188 - Aug 2015 Tetrahydrobiopterin Biosynthesis similarity (2) #216 - Dec 2017 Biodegradable Plastic similarity (2)

Deposited unit

A: Pteridine reductase 1

B: Pteridine reductase 1

C: Pteridine reductase 1

D: Pteridine reductase 1

E: Pteridine reductase 1

F: Pteridine reductase 1

G: Pteridine reductase 1

H: Pteridine reductase 1

hetero molecules

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

1

A: Pteridine reductase 1

B: Pteridine reductase 1

C: Pteridine reductase 1

D: Pteridine reductase 1

hetero molecules

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

2

E: Pteridine reductase 1

F: Pteridine reductase 1

G: Pteridine reductase 1

H: Pteridine reductase 1

hetero molecules

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

Unit cell

Length a, b, c (Å)	95.206, 103.492, 146.476
Angle α, β, γ (deg.)	90.00, 108.24, 90.00
Int Tables number	4
Space group name H-M	P12₁1

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B
3	1	C
4	1	D
5	1	E
6	1	F
1	2	A
2	2	B
3	2	C
4	2	D
5	2	E
6	2	F

NCS domain segments:

Refine code: 1

Dom-ID	Component-ID	Ens-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	1	PRO	PRO	ALA	ALA	A	A	7 - 15	7 - 15
2	1	1	PRO	PRO	ALA	ALA	B	B	7 - 15	7 - 15
3	1	1	PRO	PRO	ALA	ALA	C	C	7 - 15	7 - 15
4	1	1	PRO	PRO	ALA	ALA	D	D	7 - 15	7 - 15
5	1	1	PRO	PRO	ALA	ALA	E	E	7 - 15	7 - 15
6	1	1	PRO	PRO	ALA	ALA	F	F	7 - 15	7 - 15
1	2	1	ARG	ARG	ARG	ARG	A	A	17	17
2	2	1	ARG	ARG	ARG	ARG	B	B	17	17
3	2	1	ARG	ARG	ARG	ARG	C	C	17	17
4	2	1	ARG	ARG	ARG	ARG	D	D	17	17
5	2	1	ARG	ARG	ARG	ARG	E	E	17	17
6	2	1	ARG	ARG	ARG	ARG	F	F	17	17
1	3	1	GLY	GLY	GLY	GLY	A	A	19	19
2	3	1	GLY	GLY	GLY	GLY	B	B	19	19
3	3	1	GLY	GLY	GLY	GLY	C	C	19	19
4	3	1	GLY	GLY	GLY	GLY	D	D	19	19
5	3	1	GLY	GLY	GLY	GLY	E	E	19	19
6	3	1	GLY	GLY	GLY	GLY	F	F	19	19
1	4	1	SER	SER	LEU	LEU	A	A	21 - 35	21 - 35
2	4	1	SER	SER	LEU	LEU	B	B	21 - 35	21 - 35
3	4	1	SER	SER	LEU	LEU	C	C	21 - 35	21 - 35
4	4	1	SER	SER	LEU	LEU	D	D	21 - 35	21 - 35
5	4	1	SER	SER	LEU	LEU	E	E	21 - 35	21 - 35
6	4	1	SER	SER	LEU	LEU	F	F	21 - 35	21 - 35
1	5	1	TYR	TYR	HIS	HIS	A	A	37 - 38	37 - 38
2	5	1	TYR	TYR	HIS	HIS	B	B	37 - 38	37 - 38
3	5	1	TYR	TYR	HIS	HIS	C	C	37 - 38	37 - 38
4	5	1	TYR	TYR	HIS	HIS	D	D	37 - 38	37 - 38
5	5	1	TYR	TYR	HIS	HIS	E	E	37 - 38	37 - 38
6	5	1	TYR	TYR	HIS	HIS	F	F	37 - 38	37 - 38
1	6	1	SER	SER	ALA	ALA	A	A	40 - 42	40 - 42
2	6	1	SER	SER	ALA	ALA	B	B	40 - 42	40 - 42
3	6	1	SER	SER	ALA	ALA	C	C	40 - 42	40 - 42
4	6	1	SER	SER	ALA	ALA	D	D	40 - 42	40 - 42
5	6	1	SER	SER	ALA	ALA	E	E	40 - 42	40 - 42
6	6	1	SER	SER	ALA	ALA	F	F	40 - 42	40 - 42
1	7	1	ALA	ALA	ALA	ALA	A	A	44 - 53	44 - 53
2	7	1	ALA	ALA	ALA	ALA	B	B	44 - 53	44 - 53
3	7	1	ALA	ALA	ALA	ALA	C	C	44 - 53	44 - 53
4	7	1	ALA	ALA	ALA	ALA	D	D	44 - 53	44 - 53
5	7	1	ALA	ALA	ALA	ALA	E	E	44 - 53	44 - 53
6	7	1	ALA	ALA	ALA	ALA	F	F	44 - 53	44 - 53
1	8	1	ARG	ARG	ILE	ILE	A	A	55 - 60	55 - 60
2	8	1	ARG	ARG	ILE	ILE	B	B	55 - 60	55 - 60
3	8	1	ARG	ARG	ILE	ILE	C	C	55 - 60	55 - 60
4	8	1	ARG	ARG	ILE	ILE	D	D	55 - 60	55 - 60
5	8	1	ARG	ARG	ILE	ILE	E	E	55 - 60	55 - 60
6	8	1	ARG	ARG	ILE	ILE	F	F	55 - 60	55 - 60
1	9	1	GLN	GLN	VAL	VAL	A	A	63 - 69	63 - 69
2	9	1	GLN	GLN	VAL	VAL	B	B	63 - 69	63 - 69
3	9	1	GLN	GLN	VAL	VAL	C	C	63 - 69	63 - 69
4	9	1	GLN	GLN	VAL	VAL	D	D	63 - 69	63 - 69
5	9	1	GLN	GLN	VAL	VAL	E	E	63 - 69	63 - 69
6	9	1	GLN	GLN	VAL	VAL	F	F	63 - 69	63 - 69
1	10	1	PRO	PRO	PRO	PRO	A	A	82 - 117	82 - 117
2	10	1	PRO	PRO	PRO	PRO	B	B	82 - 117	82 - 117
3	10	1	PRO	PRO	PRO	PRO	C	C	82 - 117	82 - 117
4	10	1	PRO	PRO	PRO	PRO	D	D	82 - 117	82 - 117
5	10	1	PRO	PRO	PRO	PRO	E	E	82 - 117	82 - 117
6	10	1	PRO	PRO	PRO	PRO	F	F	82 - 117	82 - 117
1	11	1	THR	THR	ALA	ALA	A	A	138 - 159	138 - 159
2	11	1	THR	THR	ALA	ALA	B	B	138 - 159	138 - 159
3	11	1	THR	THR	ALA	ALA	C	C	138 - 159	138 - 159
4	11	1	THR	THR	ALA	ALA	D	D	138 - 159	138 - 159
5	11	1	THR	THR	ALA	ALA	E	E	138 - 159	138 - 159
6	11	1	THR	THR	ALA	ALA	F	F	138 - 159	138 - 159
1	12	1	VAL	VAL	ALA	ALA	A	A	162 - 167	162 - 167
2	12	1	VAL	VAL	ALA	ALA	B	B	162 - 167	162 - 167
3	12	1	VAL	VAL	ALA	ALA	C	C	162 - 167	162 - 167
4	12	1	VAL	VAL	ALA	ALA	D	D	162 - 167	162 - 167
5	12	1	VAL	VAL	ALA	ALA	E	E	162 - 167	162 - 167
6	12	1	VAL	VAL	ALA	ALA	F	F	162 - 167	162 - 167
1	13	1	ARG	ARG	SER	SER	A	A	170 - 227	170 - 227
2	13	1	ARG	ARG	SER	SER	B	B	170 - 227	170 - 227
3	13	1	ARG	ARG	SER	SER	C	C	170 - 227	170 - 227
4	13	1	ARG	ARG	SER	SER	D	D	170 - 227	170 - 227
5	13	1	ARG	ARG	SER	SER	E	E	170 - 227	170 - 227
6	13	1	ARG	ARG	SER	SER	F	F	170 - 227	170 - 227
1	14	1	TYR	TYR	SER	SER	A	A	248 - 267	248 - 267
2	14	1	TYR	TYR	SER	SER	B	B	248 - 267	248 - 267
3	14	1	TYR	TYR	SER	SER	C	C	248 - 267	248 - 267
4	14	1	TYR	TYR	SER	SER	D	D	248 - 267	248 - 267
5	14	1	TYR	TYR	SER	SER	E	E	248 - 267	248 - 267
6	14	1	TYR	TYR	SER	SER	F	F	248 - 267	248 - 267
1	15	1	ALA	ALA	ALA	ALA	A	A	269	269
2	15	1	ALA	ALA	ALA	ALA	B	B	269	269
3	15	1	ALA	ALA	ALA	ALA	C	C	269	269
4	15	1	ALA	ALA	ALA	ALA	D	D	269	269
5	15	1	ALA	ALA	ALA	ALA	E	E	269	269
6	15	1	ALA	ALA	ALA	ALA	F	F	269	269
1	16	1	TYR	TYR	VAL	VAL	A	A	271 - 277	271 - 277
2	16	1	TYR	TYR	VAL	VAL	B	B	271 - 277	271 - 277
3	16	1	TYR	TYR	VAL	VAL	C	C	271 - 277	271 - 277
4	16	1	TYR	TYR	VAL	VAL	D	D	271 - 277	271 - 277
5	16	1	TYR	TYR	VAL	VAL	E	E	271 - 277	271 - 277
6	16	1	TYR	TYR	VAL	VAL	F	F	271 - 277	271 - 277
1	17	1	VAL	VAL	ALA	ALA	A	A	279 - 288	279 - 288
2	17	1	VAL	VAL	ALA	ALA	B	B	279 - 288	279 - 288
3	17	1	VAL	VAL	ALA	ALA	C	C	279 - 288	279 - 288
4	17	1	VAL	VAL	ALA	ALA	D	D	279 - 288	279 - 288
5	17	1	VAL	VAL	ALA	ALA	E	E	279 - 288	279 - 288
6	17	1	VAL	VAL	ALA	ALA	F	F	279 - 288	279 - 288
1	1	2	NAP	NAP	DVP	DVP	A	I - J	300 - 301
2	1	2	NAP	NAP	DVP	DVP	B	K - L	300 - 301
3	1	2	NAP	NAP	DVP	DVP	C	M - N	300 - 301
4	1	2	NAP	NAP	DVP	DVP	D	O - P	300 - 301
5	1	2	NAP	NAP	DVP	DVP	E	Q - R	300 - 301
6	1	2	NAP	NAP	DVP	DVP	F	S - T	300 - 301

NCS ensembles :

ID
1
2

#1: Protein	Pteridine reductase 1 / H region methotrexate resistance protein Mass: 30440.580 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Leishmania major (eukaryote) / Gene: PTR1, HMTXR / Plasmid: PET15B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q01782, pteridine reductase
#2: Chemical	ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE Mass: 743.405 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C₂₁H₂₈N₇O₁₇P₃
#3: Chemical	ChemComp-DVP / METHYL 1-(4-{[(2,4-DIAMINOPTERIDIN-6-YL)METHYL]AMINO}BENZOYL)PIPERIDINE-4-CARBOXYLATE / 1-{4-[(2,4-DIAMINO-PTERIDIN-6-YLMETHYL)-AMINO]-BENZOYL}-PIPERIDINE-4-CARBOXYLIC ACID METHYL ESTER Mass: 436.467 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C₂₁H₂₄N₈O₃
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1098 / Source method: isolated from a natural source / Formula: H₂O
Sequence details	THERE IS CONFLICT BETWEEN THE REPORTED SEQUENCE AND THE DATABASE REFERENCE SEQUENCE AT THE POSITION. ...THERE IS CONFLICT BETWEEN THE REPORTED SEQUENCE AND THE DATABASE REFERENCE SEQUENCE AT THE POSITION. IT IS REFERRED TO REFERENCE 3 IN Q01782.

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.8 Å³/Da / Density % sol: 55.5 % / Description: THE FILE CONTAINS FRIEDEL PAIRS.
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 12% PEG 5000, 100MM SODIUM ACETATE, 100MM CALCIUM ACETATE, pH 5.50, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.939
Detector	Type: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 28, 2003 / Details: MIRRORS
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.939 Å / Relative weight: 1
Reflection	Resolution: 2.4→30 Å / Num. obs: 100504 / % possible obs: 95.5 % / Observed criterion σ(I): 2 / Redundancy: 2.7 % / B_iso Wilson estimate: 27 Å² / R_merge(I) obs: 0.25 / R_sym value: 0.12 / Net I/σ(I): 8.1
Reflection shell	Resolution: 2.4→2.49 Å / R_merge(I) obs: 0.609 / Mean I/σ(I) obs: 3.1 / % possible all: 89.5

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Processing

Software

Name	Version	Classification
AMoRE		phasing
REFMAC	5.2.0003	refinement
HKL-2000		data reduction
DENZO		data reduction
SCALEPACK		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1E92

1e92

Resolution: 2.4→30 Å / Cor.coef. F_o:F_c: 0.903 / Cor.coef. F_o:F_c free: 0.826 / SU B: 12.183 / SU ML: 0.292 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.576 / ESU R Free: 0.379 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: THE FRIEDEL PAIRS WERE USED FOR PHASING.

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.356	4985	5 %	RANDOM
R_work	0.276	-	-	-
obs	0.28	100504	95.2 %	-

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: 23.68 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.38 Å²	0 Å²	-0.39 Å²
2-	-	-0.08 Å²	0 Å²
3-	-	-	0.22 Å²

Refinement step

Cycle: LAST / Resolution: 2.4→30 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	15900	0	640	1098	17638

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.019	0.022	16892
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.852	1.991	23096
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.942	5	2101
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	34.928	22.596	624
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	17.559	15	2485
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	20.789	15	128
X-RAY DIFFRACTION	r_chiral_restr	0.117	0.2	2693
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.02	12580
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined	0.258	0.2	9589
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined	0.315	0.2	11405
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.248	0.2	1443
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.307	0.2	131
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.495	0.2	50
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	3.27	4	10879
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	5.108	8	16949
X-RAY DIFFRACTION	r_scbond_it	6.772	10	7030
X-RAY DIFFRACTION	r_scangle_it	7.7	10	6146
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-ID	Auth asym-ID	Number	Type	Rms dev position (Å)	Weight position
1	A	1534	TIGHT POSITIONAL	0.07	0.05
1	B	1534	TIGHT POSITIONAL	0.07	0.05
1	C	1534	TIGHT POSITIONAL	0.07	0.05
1	D	1534	TIGHT POSITIONAL	0.06	0.05
1	E	1534	TIGHT POSITIONAL	0.09	0.05
1	F	1534	TIGHT POSITIONAL	0.08	0.05
1	A	1534	TIGHT THERMAL	0.29	0.5
1	B	1534	TIGHT THERMAL	0.28	0.5
1	C	1534	TIGHT THERMAL	0.26	0.5
1	D	1534	TIGHT THERMAL	0.24	0.5
1	E	1534	TIGHT THERMAL	0.36	0.5
1	F	1534	TIGHT THERMAL	0.36	0.5
2	A	80	TIGHT POSITIONAL	0.06	0.05
2	B	80	TIGHT POSITIONAL	0.06	0.05
2	C	80	TIGHT POSITIONAL	0.05	0.05
2	D	80	TIGHT POSITIONAL	0.06	0.05
2	E	80	TIGHT POSITIONAL	0.06	0.05
2	F	80	TIGHT POSITIONAL	0.06	0.05
2	A	80	TIGHT THERMAL	0.28	0.5
2	B	80	TIGHT THERMAL	0.25	0.5
2	C	80	TIGHT THERMAL	0.27	0.5
2	D	80	TIGHT THERMAL	0.24	0.5
2	E	80	TIGHT THERMAL	0.3	0.5
2	F	80	TIGHT THERMAL	0.29	0.5

LS refinement shell

Resolution: 2.4→2.46 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.397	310	-
R_work	0.305	6292	-
obs	-	-	84.78 %

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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

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-Related structure data

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-Experimental details

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-Sample preparation

-Data collection

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+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

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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

+
Open data

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Basic information

-
Structure visualization

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Downloads & links

-
Download

-
Validation report

-
Related structure data

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Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

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Sample preparation

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Data collection

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Processing

+
About Yorodumi

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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

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Yorodumi