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- PDB-6xu1: Crystal structure of tetrameric human H215A-SAMHD1 (residues 109-... -

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Basic information

Entry
Database: PDB / ID: 6xu1
TitleCrystal structure of tetrameric human H215A-SAMHD1 (residues 109-626) with GTP, dAMPNPP and Mg
ComponentsDeoxynucleoside triphosphate triphosphohydrolase SAMHD1
KeywordsHYDROLASE / triphosphohydrolase / metallo-enzyme / binuclear / HD
Function / homology
Function and homology information


Nucleotide catabolism / Hydrolases; Acting on ester bonds; Triphosphoric-monoester hydrolases / deoxynucleoside triphosphate hydrolase activity / dGTP binding / dATP catabolic process / deoxyribonucleotide catabolic process / tetraspanin-enriched microdomain / dGTPase activity / dGTP catabolic process / DNA strand resection involved in replication fork processing ...Nucleotide catabolism / Hydrolases; Acting on ester bonds; Triphosphoric-monoester hydrolases / deoxynucleoside triphosphate hydrolase activity / dGTP binding / dATP catabolic process / deoxyribonucleotide catabolic process / tetraspanin-enriched microdomain / dGTPase activity / dGTP catabolic process / DNA strand resection involved in replication fork processing / negative regulation of type I interferon-mediated signaling pathway / regulation of innate immune response / RNA nuclease activity / somatic hypermutation of immunoglobulin genes / double-strand break repair via homologous recombination / Interferon alpha/beta signaling / single-stranded DNA binding / site of double-strand break / protein homotetramerization / defense response to virus / nucleic acid binding / immune response / innate immune response / DNA damage response / GTP binding / RNA binding / zinc ion binding / nucleoplasm / identical protein binding / nucleus / plasma membrane
Similarity search - Function
: / HD domain profile. / HD domain / HD domain / SAM domain (Sterile alpha motif) / SAM domain profile. / Metal dependent phosphohydrolases with conserved 'HD' motif. / Sterile alpha motif. / HD/PDEase domain / Sterile alpha motif domain / Sterile alpha motif/pointed domain superfamily
Similarity search - Domain/homology
Chem-DZ4 / : / GUANOSINE-5'-TRIPHOSPHATE / Deoxynucleoside triphosphate triphosphohydrolase SAMHD1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2 Å
AuthorsMorris, E.R. / Kunzelmann, S. / Caswell, S.J. / Arnold, L.H. / Purkiss, A.G. / Kelly, G. / Taylor, I.A.
Funding support United Kingdom, 4items
OrganizationGrant numberCountry
Wellcome Trust108014/Z/15/Z United Kingdom
Wellcome TrustFC001029 United Kingdom
Medical Research Council (MRC, United Kingdom)FC001029 United Kingdom
Cancer Research UKFC001029 United Kingdom
CitationJournal: Nat Commun / Year: 2020
Title: Crystal structures of SAMHD1 inhibitor complexes reveal the mechanism of water-mediated dNTP hydrolysis.
Authors: Morris, E.R. / Caswell, S.J. / Kunzelmann, S. / Arnold, L.H. / Purkiss, A.G. / Kelly, G. / Taylor, I.A.
History
DepositionJan 17, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 24, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 8, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jan 24, 2024Group: 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 / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Deoxynucleoside triphosphate triphosphohydrolase SAMHD1
B: Deoxynucleoside triphosphate triphosphohydrolase SAMHD1
C: Deoxynucleoside triphosphate triphosphohydrolase SAMHD1
D: Deoxynucleoside triphosphate triphosphohydrolase SAMHD1
E: Deoxynucleoside triphosphate triphosphohydrolase SAMHD1
F: Deoxynucleoside triphosphate triphosphohydrolase SAMHD1
G: Deoxynucleoside triphosphate triphosphohydrolase SAMHD1
H: Deoxynucleoside triphosphate triphosphohydrolase SAMHD1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)494,21765
Polymers481,1348
Non-polymers13,08357
Water14,340796
1
A: Deoxynucleoside triphosphate triphosphohydrolase SAMHD1
B: Deoxynucleoside triphosphate triphosphohydrolase SAMHD1
C: Deoxynucleoside triphosphate triphosphohydrolase SAMHD1
D: Deoxynucleoside triphosphate triphosphohydrolase SAMHD1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)247,12133
Polymers240,5674
Non-polymers6,55429
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area24700 Å2
ΔGint-211 kcal/mol
Surface area67500 Å2
MethodPISA
2
E: Deoxynucleoside triphosphate triphosphohydrolase SAMHD1
F: Deoxynucleoside triphosphate triphosphohydrolase SAMHD1
G: Deoxynucleoside triphosphate triphosphohydrolase SAMHD1
H: Deoxynucleoside triphosphate triphosphohydrolase SAMHD1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)247,09632
Polymers240,5674
Non-polymers6,52928
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area24300 Å2
ΔGint-208 kcal/mol
Surface area67290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)137.369, 171.860, 179.572
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14A
24E
15A
25F
16A
26G
17A
27H
18B
28C
19B
29D
110B
210E
111B
211F
112B
212G
113B
213H
114C
214D
115C
215E
116C
216F
117C
217G
118C
218H
119D
219E
120D
220F
121D
221G
122D
222H
123E
223F
124E
224G
125E
225H
126F
226G
127F
227H
128G
228H

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASPASPGLUGLUAA113 - 5977 - 491
21ASPASPGLUGLUBB113 - 5977 - 491
12ASPASPTRPTRPAA113 - 5987 - 492
22ASPASPTRPTRPCC113 - 5987 - 492
13THRTHRGLUGLUAA114 - 5978 - 491
23THRTHRGLUGLUDD114 - 5978 - 491
14ASPASPGLNGLNAA113 - 5827 - 476
24ASPASPGLNGLNEE113 - 5827 - 476
15THRTHRTRPTRPAA114 - 5988 - 492
25THRTHRTRPTRPFF114 - 5988 - 492
16THRTHRTRPTRPAA114 - 5988 - 492
26THRTHRTRPTRPGG114 - 5988 - 492
17THRTHRGLUGLUAA114 - 5978 - 491
27THRTHRGLUGLUHH114 - 5978 - 491
18ASPASPTRPTRPBB113 - 5987 - 492
28ASPASPTRPTRPCC113 - 5987 - 492
19THRTHRGLUGLUBB114 - 5978 - 491
29THRTHRGLUGLUDD114 - 5978 - 491
110ASPASPGLNGLNBB113 - 5827 - 476
210ASPASPGLNGLNEE113 - 5827 - 476
111THRTHRGLUGLUBB114 - 5978 - 491
211THRTHRGLUGLUFF114 - 5978 - 491
112THRTHRGLUGLUBB114 - 5978 - 491
212THRTHRGLUGLUGG114 - 5978 - 491
113THRTHRGLUGLUBB114 - 5978 - 491
213THRTHRGLUGLUHH114 - 5978 - 491
114THRTHRTRPTRPCC114 - 5988 - 492
214THRTHRTRPTRPDD114 - 5988 - 492
115ASPASPGLNGLNCC113 - 5827 - 476
215ASPASPGLNGLNEE113 - 5827 - 476
116THRTHRGLUGLUCC114 - 5978 - 491
216THRTHRGLUGLUFF114 - 5978 - 491
117THRTHRGLUGLUCC114 - 5978 - 491
217THRTHRGLUGLUGG114 - 5978 - 491
118THRTHRTRPTRPCC114 - 5988 - 492
218THRTHRTRPTRPHH114 - 5988 - 492
119THRTHRGLNGLNDD114 - 5828 - 476
219THRTHRGLNGLNEE114 - 5828 - 476
120THRTHRGLUGLUDD114 - 5978 - 491
220THRTHRGLUGLUFF114 - 5978 - 491
121THRTHRGLUGLUDD114 - 5978 - 491
221THRTHRGLUGLUGG114 - 5978 - 491
122THRTHRTRPTRPDD114 - 5988 - 492
222THRTHRTRPTRPHH114 - 5988 - 492
123THRTHRGLNGLNEE114 - 5828 - 476
223THRTHRGLNGLNFF114 - 5828 - 476
124THRTHRGLNGLNEE114 - 5828 - 476
224THRTHRGLNGLNGG114 - 5828 - 476
125THRTHRGLNGLNEE114 - 5828 - 476
225THRTHRGLNGLNHH114 - 5828 - 476
126THRTHRTRPTRPFF114 - 5988 - 492
226THRTHRTRPTRPGG114 - 5988 - 492
127THRTHRGLUGLUFF114 - 5978 - 491
227THRTHRGLUGLUHH114 - 5978 - 491
128THRTHRGLUGLUGG114 - 5978 - 491
228THRTHRGLUGLUHH114 - 5978 - 491

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28

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Components

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Protein , 1 types, 8 molecules ABCDEFGH

#1: Protein
Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 / dNTPase / Dendritic cell-derived IFNG-induced protein / DCIP / Monocyte protein 5 / MOP-5 / SAM ...dNTPase / Dendritic cell-derived IFNG-induced protein / DCIP / Monocyte protein 5 / MOP-5 / SAM domain and HD domain-containing protein 1 / hSAMHD1


Mass: 60141.738 Da / Num. of mol.: 8 / Mutation: H215A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SAMHD1, MOP5 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta2
References: UniProt: Q9Y3Z3, Hydrolases; Acting on ester bonds; Triphosphoric-monoester hydrolases

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Non-polymers , 5 types, 853 molecules

#2: Chemical
ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 25 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-DZ4 / 2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]adenosine


Mass: 490.197 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C10H17N6O11P3 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: GTP, energy-carrying molecule*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 796 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.2 Å3/Da / Density % sol: 44.22 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 0.1 M Bistris methane-HCl pH 6, 15% (w/v) PEG 3350, 0.1 M MgCl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97624 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 24, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97624 Å / Relative weight: 1
ReflectionResolution: 2.2→107.3 Å / Num. obs: 212120 / % possible obs: 98.67 % / Redundancy: 6.87 % / Biso Wilson estimate: 24.4 Å2 / CC1/2: 0.988 / Rmerge(I) obs: 0.181 / Rpim(I) all: 0.074 / Rrim(I) all: 0.197 / Net I/σ(I): 8.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.2-2.244.751.0471.586980.5170.5251.17981.74
5.97-107.437.090.06618112930.9970.0260.071100

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation6.9 Å107.3 Å
Translation6.9 Å107.3 Å

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
Aimless0.7.4data scaling
PHASER2.7.17phasing
REFMAC5.8.0158refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6TX0

6tx0


Resolution: 2.2→107.3 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.94 / SU B: 11.984 / SU ML: 0.142 / SU R Cruickshank DPI: 0.2666 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.267 / ESU R Free: 0.183
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2024 10526 5 %RANDOM
Rwork0.1763 ---
obs0.1776 201458 98.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 111.08 Å2 / Biso mean: 30.718 Å2 / Biso min: 6.79 Å2
Baniso -1Baniso -2Baniso -3
1--0.91 Å20 Å2-0 Å2
2--0.59 Å20 Å2
3---0.33 Å2
Refinement stepCycle: final / Resolution: 2.2→107.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms30873 0 769 796 32438
Biso mean--17.98 23.67 -
Num. residues----3816
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.01932389
X-RAY DIFFRACTIONr_bond_other_d0.0020.0229505
X-RAY DIFFRACTIONr_angle_refined_deg2.0921.96643966
X-RAY DIFFRACTIONr_angle_other_deg1.1112.99268464
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.44753800
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.69523.9271566
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.394155560
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.31415212
X-RAY DIFFRACTIONr_chiral_restr0.1260.24715
X-RAY DIFFRACTIONr_gen_planes_refined0.010.02135396
X-RAY DIFFRACTIONr_gen_planes_other0.0020.026652
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A320900.06
12B320900.06
21A325160.03
22C325160.03
31A320600.06
32D320600.06
41A314580.04
42E314580.04
51A322300.06
52F322300.06
61A325180.03
62G325180.03
71A320140.05
72H320140.05
81B322140.06
82C322140.06
91B322080.04
92D322080.04
101B313280.06
102E313280.06
111B323640.04
112F323640.04
121B321680.05
122G321680.05
131B323180.03
132H323180.03
141C321680.05
142D321680.05
151C314280.03
152E314280.03
161C319800.06
162F319800.06
171C323560.03
172G323560.03
181C322500.05
182H322500.05
191D312460.05
192E312460.05
201D323640.04
202F323640.04
211D320380.05
212G320380.05
221D323840.03
222H323840.03
231E311360.06
232F311360.06
241E314720.03
242G314720.03
251E312360.05
252H312360.05
261F322400.06
262G322400.06
271F322000.04
272H322000.04
281G321540.05
282H321540.05
LS refinement shellResolution: 2.2→2.257 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.299 617 -
Rwork0.271 12595 -
obs--83.92 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°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)
10.17180.0126-0.02260.0952-0.0180.06150.0024-0.02120.03320.02050.02560.0038-0.0410.0347-0.0280.038-0.01560.02360.039-0.00160.08597.6697-7.511236.4061
20.18430.0026-0.02790.0866-0.0340.0573-0.0018-0.0433-0.02420.02170.03670.04080.0063-0.0063-0.03490.0179-0.00330.00760.06490.03420.0757-4.8518-39.395345.5197
30.1857-0.03060.05180.023-0.00430.11240.02830.0151-0.0218-0.01850.0182-0.00720.04480.01-0.04650.0515-0.0039-0.0240.04950.00290.05916.0719-48.92728.9039
40.1483-0.0336-0.03930.19590.02850.02860.02580.03080.0267-0.0479-0.02050.0146-0.0093-0.0314-0.00530.03450.0024-0.00530.05960.04190.0659-7.6105-17.05031.3305
50.1964-0.1621-0.02990.39940.06680.017-0.1466-0.0149-0.0020.20220.11210.09520.02620.00690.03440.15740.05330.01020.04990.01330.054355.5662-39.947882.8853
60.2799-0.11440.06650.1147-0.01840.0969-0.01310.02860.09420.0008-0.0225-0.06970.0027-0.01410.03560.01520.0005-0.00760.03360.01430.098571.036-35.655251.38
70.3298-0.1845-0.00530.1796-0.02920.06580.02530.061-0.09710.0034-0.0460.07490.00590.02880.02060.0270.01860.00610.0322-0.01540.097266.3697-74.633649.3962
80.4323-0.30970.01560.29810.00130.0041-0.1933-0.1117-0.03920.19460.1794-0.00450.00530.01420.01390.14830.12020.01760.1344-0.01080.032677.259-73.459983.1805
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A113 - 599
2X-RAY DIFFRACTION2B113 - 598
3X-RAY DIFFRACTION3C113 - 598
4X-RAY DIFFRACTION4D114 - 598
5X-RAY DIFFRACTION5E113 - 583
6X-RAY DIFFRACTION6F114 - 600
7X-RAY DIFFRACTION7G114 - 599
8X-RAY DIFFRACTION8H114 - 598

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  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

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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

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