[English] 日本語
Yorodumi
- PDB-4zvz: Co-crystal structures of PP5 in complex with 5-methyl-7-oxabicycl... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4zvz
TitleCo-crystal structures of PP5 in complex with 5-methyl-7-oxabicyclo[2.2.1]heptane-2,3-dicarboxylic acid
ComponentsSerine/threonine-protein phosphatase 5
KeywordsHydrolase/Hydrolase Inhibitor / Protein phosphatase 5 / Hydrolase-Hydrolase Inhibitor complex
Function / homology
Function and homology information


response to arachidonic acid / peptidyl-serine dephosphorylation / peptidyl-threonine dephosphorylation / response to morphine / protein folding chaperone complex / myosin phosphatase activity / protein serine/threonine phosphatase activity / protein-serine/threonine phosphatase / phosphatase activity / phosphoprotein phosphatase activity ...response to arachidonic acid / peptidyl-serine dephosphorylation / peptidyl-threonine dephosphorylation / response to morphine / protein folding chaperone complex / myosin phosphatase activity / protein serine/threonine phosphatase activity / protein-serine/threonine phosphatase / phosphatase activity / phosphoprotein phosphatase activity / protein dephosphorylation / ESR-mediated signaling / response to lead ion / Hsp90 protein binding / tau protein binding / ADP binding / Negative regulation of MAPK pathway / MAPK cascade / double-strand break repair / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / mitotic cell cycle / positive regulation of canonical NF-kappaB signal transduction / intracellular membrane-bounded organelle / DNA-templated transcription / lipid binding / protein-containing complex / RNA binding / nucleoplasm / ATP binding / identical protein binding / metal ion binding / nucleus / plasma membrane / cytosol
Similarity search - Function
PPP domain / PP5, C-terminal metallophosphatase domain / PPP5 TPR repeat region / Serine/threonine specific protein phosphatases signature. / Protein phosphatase 2A homologues, catalytic domain. / Serine/threonine-specific protein phosphatase/bis(5-nucleosyl)-tetraphosphatase / Metallo-dependent phosphatases / Purple Acid Phosphatase; chain A, domain 2 / Tetratricopeptide repeat 1 / Tetratricopeptide repeat ...PPP domain / PP5, C-terminal metallophosphatase domain / PPP5 TPR repeat region / Serine/threonine specific protein phosphatases signature. / Protein phosphatase 2A homologues, catalytic domain. / Serine/threonine-specific protein phosphatase/bis(5-nucleosyl)-tetraphosphatase / Metallo-dependent phosphatases / Purple Acid Phosphatase; chain A, domain 2 / Tetratricopeptide repeat 1 / Tetratricopeptide repeat / Calcineurin-like phosphoesterase domain, ApaH type / Calcineurin-like phosphoesterase / Metallo-dependent phosphatase-like / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / 4-Layer Sandwich / Tetratricopeptide-like helical domain superfamily / Alpha Beta
Similarity search - Domain/homology
Chem-4TF / : / DI(HYDROXYETHYL)ETHER / Serine/threonine-protein phosphatase 5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å
AuthorsChattopadhyay, D. / Swingle, M.R. / Salter, E.A. / Wierzbicki, A. / Honkanen, R.E.
Citation
Journal: Biochem. Pharmacol. / Year: 2016
Title: Crystal structures and mutagenesis of PPP-family ser/thr protein phosphatases elucidate the selectivity of cantharidin and novel norcantharidin-based inhibitors of PP5C.
Authors: Chattopadhyay, D. / Swingle, M.R. / Salter, E.A. / Wood, E. / D'Arcy, B. / Zivanov, C. / Abney, K. / Musiyenko, A. / Rusin, S.F. / Kettenbach, A. / Yet, L. / Schroeder, C.E. / Golden, J.E. / ...Authors: Chattopadhyay, D. / Swingle, M.R. / Salter, E.A. / Wood, E. / D'Arcy, B. / Zivanov, C. / Abney, K. / Musiyenko, A. / Rusin, S.F. / Kettenbach, A. / Yet, L. / Schroeder, C.E. / Golden, J.E. / Dunham, W.H. / Gingras, A.C. / Banerjee, S. / Forbes, D. / Wierzbicki, A. / Honkanen, R.E.
#1: Journal: J.Biol.Chem. / Year: 2004
Title: Structural basis for the catalytic activity of human serine/threonine protein phosphatase-5.
Authors: Swingle, M.R. / Honkanen, R.E. / Ciszak, E.M.
History
DepositionMay 18, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 27, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 8, 2017Group: Database references
Revision 1.2Sep 27, 2023Group: 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_conn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_conn.ptnr2_symmetry / _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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Serine/threonine-protein phosphatase 5
B: Serine/threonine-protein phosphatase 5
C: Serine/threonine-protein phosphatase 5
D: Serine/threonine-protein phosphatase 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)153,25619
Polymers151,5484
Non-polymers1,70815
Water5,098283
1
A: Serine/threonine-protein phosphatase 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,2554
Polymers37,8871
Non-polymers3683
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Serine/threonine-protein phosphatase 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,2554
Polymers37,8871
Non-polymers3683
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Serine/threonine-protein phosphatase 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,3846
Polymers37,8871
Non-polymers4975
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Serine/threonine-protein phosphatase 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,3615
Polymers37,8871
Non-polymers4744
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)40.858, 80.520, 91.165
Angle α, β, γ (deg.)88.15, 87.33, 86.71
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: 0 / Refine code: 0

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11TYRTYRPROPROAA176 - 48610 - 320
21TYRTYRPROPROBB176 - 48610 - 320
12PROPROPROPROAA179 - 48613 - 320
22PROPROPROPROCC179 - 48613 - 320
13GLYGLYPROPROAA178 - 48612 - 320
23GLYGLYPROPRODD178 - 48612 - 320
14PROPROTYRTYRBB179 - 48913 - 323
24PROPROTYRTYRCC179 - 48913 - 323
15GLYGLYALAALABB178 - 48812 - 322
25GLYGLYALAALADD178 - 48812 - 322
16PROPROTYRTYRCC179 - 48913 - 323
26PROPROTYRTYRDD179 - 48913 - 323

NCS ensembles :
ID
1
2
3
4
5
6

-
Components

-
Protein , 1 types, 4 molecules ABCD

#1: Protein
Serine/threonine-protein phosphatase 5 / PP5 / Protein phosphatase T / PPT


Mass: 37887.020 Da / Num. of mol.: 4 / Fragment: UNP residues 169-499
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PPP5C, PPP5 / Plasmid: pMal2cE / Production host: Escherichia coli (E. coli)
References: UniProt: P53041, protein-serine/threonine phosphatase

-
Non-polymers , 5 types, 298 molecules

#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mn
#3: Chemical
ChemComp-4TF / (1R,2S,3R,4S,5S)-5-(propoxymethyl)-7-oxabicyclo[2.2.1]heptane-2,3-dicarboxylic acid


Mass: 258.268 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C12H18O6
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 283 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.97 Å3/Da / Density % sol: 37.65 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 25% MPD, 6% PEG, 10 mM Tris, pH 8.0

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 9, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2→91.03 Å / Num. obs: 76635 / % possible obs: 97.9 % / Redundancy: 2.4 % / CC1/2: 0.986 / Rmerge(I) obs: 0.086 / Rpim(I) all: 0.074 / Net I/σ(I): 11.7 / Num. measured all: 183306
Reflection shell

Diffraction-ID: 1 / Redundancy: 2.4 % / Rejects: 0

Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
2-2.110.5052.126687110830.640.42196.8
6.32-91.030.0437.5578324330.9910.03798.1

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
Aimless0.1.27data scaling
PHENIXphasing
PDB_EXTRACT3.15data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1s95
Resolution: 2→91.03 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.93 / SU B: 9.914 / SU ML: 0.142 / Cross valid method: THROUGHOUT / ESU R: 0.243 / ESU R Free: 0.182 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.23517 3848 5 %RANDOM
Rwork0.20438 ---
obs0.20593 72774 97.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.285 Å2
Baniso -1Baniso -2Baniso -3
1--0.38 Å2-0.74 Å20.54 Å2
2--1.56 Å20.01 Å2
3----1.15 Å2
Refinement stepCycle: LAST / Resolution: 2→91.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10032 0 95 283 10410
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0210395
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0941.96314059
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.60251248
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.0724.715509
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.614151790
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.3541544
X-RAY DIFFRACTIONr_chiral_restr0.0750.21504
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0217940
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A4290.05
12B4290.05
21A4310.04
22C4310.04
31A4380.02
32D4380.02
41B4200.04
42C4200.04
51B4290.04
52D4290.04
61C4340.02
62D4340.02
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.315 276 -
Rwork0.284 5362 -
obs--96.67 %
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
118.6119-2.4747.15430.4098-1.40645.53950.1971-0.0148-0.1001-0.2355-0.10530.07011.34550.3532-0.09170.7160.0073-0.02690.2913-0.17150.420321.3284-10.936815.2607
23.46340.20220.24853.8348-0.99855.7484-0.04770.3358-0.3375-0.1876-0.00050.03910.584-0.20570.04810.1514-0.05690.03870.1944-0.08930.147426.9737-4.163116.4842
31.68290.24990.7420.98630.17515.27470.05420.0091-0.38320.08670.03820.06930.5751-0.5448-0.09250.1161-0.06280.02010.19790.0060.185821.1628-2.42134.4711
414.1216-19.7315-0.298729.885-4.584311.69150.2393-0.1305-0.7393-0.7351-0.70730.64811.79162.08440.4680.81010.2508-0.25190.43560.14280.460342.4111-7.176142.0575
53.6471-0.9478-0.39252.889-0.8635.229-0.11180.052-0.2490.00260.0610.01930.240.18110.05080.0188-0.00560.02460.0534-0.02710.098237.44182.381225.8128
62.85440.1623-0.54280.89580.82725.275-0.06880.1456-0.23030.0612-0.02730.04370.0745-0.16170.0960.0073-0.00330.01480.0419-0.01440.063228.88293.595429.4615
73.85941.10460.94341.0507-1.43174.2795-0.08440.01450.36510.12810.12380.1621-0.3985-0.5258-0.03940.0760.10530.00650.4428-0.01070.144917.353111.464523.5776
82.26151.0625-0.84980.69590.59236.15370.0836-0.18420.04420.0848-0.07950.0679-0.14720.1066-0.00410.14150.02150.06540.05650.01140.11728.97578.306843.1909
99.97383.40791.70011.22431.38411.2282-0.0647-0.3085-0.1066-0.0279-0.128-0.0141-0.2406-0.21170.19270.12130.02640.03010.08980.01810.066924.80049.403652.5162
100.2914-0.0554-0.68592.52851.18683.90040.2599-0.09230.18160.1077-0.19660.1696-0.8418-0.3308-0.06340.2963-0.02440.09810.2101-0.09190.226925.896218.318743.2654
112.577-0.75531.2973.538-0.08446.34980.1031-0.11550.5829-0.0699-0.06570.0598-0.94040.2021-0.03740.2991-0.08230.04860.193-0.05280.202833.164522.307346.2434
122.1689-0.5777-1.55981.5733-0.33595.3810.1431-0.3360.16820.1427-0.0612-0.1798-0.57210.8047-0.08190.1211-0.088-0.02590.2104-0.03810.142739.686913.479342.8778
133.54950.77190.49112.66771.50380.853-0.0134-0.38410.07310.02320.0722-0.097-0.01480.0598-0.05870.1845-0.13090.01770.18550.02160.122541.014914.245436.8928
143.3074-0.13050.86752.9716-1.18797.43430.0341-0.16480.04630.21270.016-0.1263-0.29730.5971-0.05010.0324-0.02080.03050.1801-0.0320.148743.70388.734630.5139
1529.7962-31.6676-15.837737.273118.61849.3073-0.15640.79370.28070.4249-0.67661.56480.1543-0.39060.8330.54950.02970.04530.48210.01330.973730.99615.650712.849
166.37590.08692.78721.24290.19291.26330.12510.11050.1785-0.1349-0.2660.2078-0.0688-0.03840.14090.53660.0271-0.01970.34940.05630.315116.29223.41658.8406
172.38160.3346-0.82441.3807-0.28413.85050.00950.05310.395-0.1007-0.02360.1196-0.45230.07360.0140.22360.0133-0.02540.10320.03640.158615.42517.693463.5021
180.0292-0.15870.22322.7706-0.39674.44650.021-0.03870.0150.1651-0.14760.1626-0.43110.06870.12660.3202-0.09870.02110.2889-0.06480.199810.647714.659385.6725
193.69950.7658-1.96512.38610.53496.4381-0.0947-0.02360.01650.04230.04450.23870.0388-0.55850.05020.08510.0088-0.02310.10580.01160.10195.81274.596570.8142
205.3423-0.2533-0.31481.0507-0.75083.73010.0655-0.07080.2573-0.0789-0.08810.1811-0.1761-0.40210.02260.1159-0.0046-0.00550.1427-0.00670.12295.75017.671872.9013
211.51370.4885-0.42392.0787-1.05743.94820.015-0.17660.14760.1839-0.11630.0294-0.3417-0.06260.10130.0894-0.0055-0.01460.09930.00630.09712.869110.351773.5747
220.5157-0.5622-1.5231.49570.89076.9172-0.1455-0.1893-0.09470.1783-0.1548-0.31670.22710.75080.30030.04930.04210.0390.33640.16390.310326.13793.598468.6744
231.70732.266-1.39073.0563-1.59143.89130.2315-0.2633-0.03310.3139-0.2865-0.1015-0.31390.51830.0550.1212-0.0366-0.03520.2848-0.00390.176219.43848.750780.5398
242.42510.8729-0.97921.4748-0.2284.84080.0865-0.32030.09510.4358-0.1488-0.11710.1543-0.07190.06230.2552-0.05680.01270.21470.01380.121711.1304-2.465391.7028
252.80280.7104-0.0981.5172-0.80621.81610.0984-0.3322-0.11070.4513-0.2465-0.27270.08030.30970.14810.2662-0.044-0.02260.29610.06020.165118.2634-1.757989.8478
265.38150.5551-2.82783.9033-1.01711.691-0.1249-0.1008-0.57250.2567-0.2211-0.34550.18420.14290.3460.46370.0175-0.02630.30620.05340.200513.2139-12.171990.4253
271.2708-0.6594-0.27041.6233-0.97386.62420.0878-0.1841-0.13410.1913-0.08930.15940.2477-0.36990.00150.1754-0.08290.02910.18080.01410.17344.5-5.056685.9446
280.59751.2031-1.44744.7479-6.57699.37560.1931-0.24480.00560.13450.05160.21680.0558-0.2238-0.24470.2611-0.07470.05470.25820.02510.16973.2851-6.728881.6992
292.67740.0955-1.06663.77851.13616.2526-0.1374-0.3196-0.3957-0.0935-0.06150.28630.3639-0.20850.19890.1249-0.0919-0.03590.22010.02890.15262.6688-2.785572.2197
302.80730.2994-1.78432.584-0.23242.7431-0.1822-0.204-0.0081-0.08660.01810.10760.3645-0.16680.16410.1797-0.0309-0.02990.2222-0.01250.15855.656-1.290167.996
3110.9524-0.71134.142423.9084-9.633715.6330.4073-0.23680.49890.5672-0.597-0.4847-0.08250.43830.18980.2833-0.02260.10660.1583-0.13860.35762.47463.827927.1405
323.70680.4979-1.05841.5186-0.20123.35140.1866-0.49050.37640.2662-0.1219-0.0449-0.2953-0.0729-0.06460.2158-0.03780.00860.1696-0.09660.2361.601355.443828.8861
331.7301-0.0717-1.46462.70460.87573.32390.14930.32650.5482-0.35210.02820.1319-0.35950.1796-0.17750.24680.0272-0.01780.23030.0870.31181.357252.94367.3171
343.80011.0232-1.83322.0083-0.78014.9260.2014-0.0266-0.07960.0899-0.0964-0.26490.07060.3593-0.10510.14570.032-0.06770.0917-0.00790.189710.101442.055618.6253
354.33480.3108-0.64821.76510.26533.35040.21390.17230.14410.3561-0.0321-0.3654-0.0730.3113-0.18180.13710.0242-0.03580.0736-0.00140.18969.813345.073117.9956
364.38741.32620.69763.09270.91663.23080.2018-0.18740.10320.1097-0.22930.1720.099-0.1730.02750.06390.02510.00480.0527-0.02950.1248-1.950544.944718.7427
375.0785-1.28422.047.343-3.39422.68680.137-0.33930.1146-0.0181-0.0290.741-0.0198-0.5135-0.1080.14340.00120.06310.2995-0.11550.2567-12.468348.450926.4316
382.67450.9105-0.31811.88130.06762.57940.08450.41250.1584-0.2617-0.04340.0341-0.13030.0947-0.04120.10120.0406-0.03330.1431-0.01240.1223-0.525444.06877.5798
393.6047-4.8555-0.599411.3271-0.63973.3562-0.00910.61210.2387-0.69090.07380.6581-0.0548-0.1482-0.06470.3992-0.0328-0.18640.49270.10880.3556-3.925539.84-4.6141
403.55980.2511.78010.76761.07442.14420.25380.5027-0.2817-0.2173-0.38080.2858-0.1026-0.29470.1270.26140.1047-0.15490.3257-0.10870.3447-9.479238.42445.5336
412.8760.2269-0.78292.98531.16893.4208-0.0660.2353-0.3431-0.18330.06820.25710.6418-0.0401-0.00220.33280.0606-0.05560.2319-0.09370.31-1.192625.06711.5799
422.3421.32130.47082.2519-1.37036.64980.0640.4071-0.3666-0.2306-0.0996-0.21410.51510.39260.03560.21540.1022-0.03520.1511-0.07690.27567.616331.76595.227
432.3505-0.6895-1.0124.15443.416211.81890.1440.3422-0.2818-0.1119-0.2213-0.26810.0670.11840.07730.15060.0895-0.06610.1151-0.03220.29948.696529.917910.9128
444.04110.3279-1.02984.81440.39693.4449-0.09010.1406-0.46340.03220.0289-0.17560.5690.03240.06120.22110.0831-0.13790.1425-0.02330.279410.237832.831318.0941
452.41380.8122-0.2272.0549-0.45024.2080.1374-0.3455-0.33970.3816-0.1080.11820.2246-0.0487-0.02940.30350.025-0.07830.10750.02680.28545.315635.092626.5193
466.27791.8157-0.248.7151.9420.51790.1917-0.2066-0.54250.8764-0.1719-0.25410.2796-0.0026-0.01990.5950.1145-0.05710.38140.06380.430232.75529.784671.5881
471.3003-0.13430.52610.85-0.34845.21470.1173-0.0754-0.20540.00210.0136-0.04250.49010.4414-0.13090.20230.0791-0.00160.18370.02050.220329.884438.356865.4387
482.7904-0.06951.29231.96971.66867.3481-0.0059-0.2347-0.139-0.08-0.0058-0.02780.1982-0.58350.01160.05150.02120.03390.11720.04190.156617.643145.4563.8561
493.18210.66221.12472.0524-0.36136.15320.0055-0.0479-0.2009-0.00980.03290.11060.32750.1125-0.03840.05350.04420.01880.09240.03080.107924.103143.514962.4798
500.6064-1.17850.33892.60390.62956.1489-0.1373-0.00560.2968-0.02560.1514-0.5264-1.2250.6585-0.01410.2827-0.1861-0.07860.38460.01680.367134.725457.396866.0747
5112.12470.1009-0.89010.5240.95141.82810.24010.31080.26390.04290.0226-0.12970.05270.0745-0.26270.13210.01740.03130.49960.00370.159139.970650.060972.4472
521.1173-0.9296-1.04710.98920.12264.55890.03060.02570.1193-0.1385-0.1093-0.1268-0.12210.54470.07870.2328-0.0884-0.01840.19750.04690.177529.19549.704949.0216
531.5432-0.1338-0.65490.82890.29482.90390.0490.2220.3117-0.2328-0.0764-0.1164-0.60070.49610.02740.3088-0.0945-0.00240.26040.05810.234329.977557.876847.069
541.45524.74841.347816.25494.4021.2542-0.2342-0.07830.283-0.5758-0.070.4628-0.3123-0.04430.30430.7149-0.0596-0.11970.30550.01220.475825.416366.668449.5987
551.3994-1.4819-0.11092.5581-1.13826.81380.05720.38620.0559-0.351-0.07970.168-0.5964-0.38960.02240.295-0.0776-0.07740.2510.07010.209118.490554.474541.3311
562.2176-2.20710.78692.90940.47232.4984-0.512-0.29610.09560.1941-0.0290.2117-0.7629-0.70890.5410.42790.1928-0.04950.3114-0.04650.343911.619158.682756.1988
572.9685-0.5932.74060.4496-1.85238.5310.03780.02330.0127-0.0290.16930.1273-0.3233-0.7495-0.20710.2770.0617-0.08950.11960.01420.24214.261855.695154.3187
583.0217-0.17090.82783.89621.7257.9348-0.31730.04820.1253-0.23230.12180.2568-0.3046-0.48110.19550.09050.07060.03650.24240.07330.228311.931350.530958.439
590.92311.19880.78422.06470.39649.3010.1039-0.1135-0.16760.22890.2293-0.0315-0.0011-0.5298-0.33320.12240.0920.05020.35640.06440.262111.024950.411166.785
6015.758916.5641-7.429117.4884-7.86143.5403-0.2040.08960.2199-0.24040.19730.01780.1107-0.15880.00670.72450.0335-0.00920.631-0.16870.705426.518158.408677.4836
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A176 - 184
2X-RAY DIFFRACTION2A185 - 206
3X-RAY DIFFRACTION3A207 - 231
4X-RAY DIFFRACTION4A232 - 237
5X-RAY DIFFRACTION5A238 - 263
6X-RAY DIFFRACTION6A264 - 306
7X-RAY DIFFRACTION7A307 - 334
8X-RAY DIFFRACTION8A335 - 358
9X-RAY DIFFRACTION9A359 - 369
10X-RAY DIFFRACTION10A370 - 396
11X-RAY DIFFRACTION11A397 - 414
12X-RAY DIFFRACTION12A415 - 437
13X-RAY DIFFRACTION13A438 - 450
14X-RAY DIFFRACTION14A451 - 481
15X-RAY DIFFRACTION15A482 - 487
16X-RAY DIFFRACTION16B175 - 183
17X-RAY DIFFRACTION17B184 - 214
18X-RAY DIFFRACTION18B215 - 234
19X-RAY DIFFRACTION19B235 - 252
20X-RAY DIFFRACTION20B253 - 275
21X-RAY DIFFRACTION21B276 - 304
22X-RAY DIFFRACTION22B305 - 327
23X-RAY DIFFRACTION23B328 - 345
24X-RAY DIFFRACTION24B346 - 361
25X-RAY DIFFRACTION25B362 - 393
26X-RAY DIFFRACTION26B394 - 414
27X-RAY DIFFRACTION27B415 - 435
28X-RAY DIFFRACTION28B436 - 449
29X-RAY DIFFRACTION29B450 - 467
30X-RAY DIFFRACTION30B468 - 490
31X-RAY DIFFRACTION31C179 - 184
32X-RAY DIFFRACTION32C185 - 212
33X-RAY DIFFRACTION33C213 - 232
34X-RAY DIFFRACTION34C233 - 252
35X-RAY DIFFRACTION35C253 - 274
36X-RAY DIFFRACTION36C275 - 316
37X-RAY DIFFRACTION37C317 - 329
38X-RAY DIFFRACTION38C330 - 355
39X-RAY DIFFRACTION39C356 - 370
40X-RAY DIFFRACTION40C371 - 387
41X-RAY DIFFRACTION41C388 - 414
42X-RAY DIFFRACTION42C415 - 435
43X-RAY DIFFRACTION43C436 - 450
44X-RAY DIFFRACTION44C451 - 470
45X-RAY DIFFRACTION45C471 - 491
46X-RAY DIFFRACTION46D178 - 186
47X-RAY DIFFRACTION47D187 - 233
48X-RAY DIFFRACTION48D234 - 254
49X-RAY DIFFRACTION49D255 - 304
50X-RAY DIFFRACTION50D305 - 319
51X-RAY DIFFRACTION51D320 - 328
52X-RAY DIFFRACTION52D329 - 365
53X-RAY DIFFRACTION53D366 - 396
54X-RAY DIFFRACTION54D397 - 406
55X-RAY DIFFRACTION55D407 - 427
56X-RAY DIFFRACTION56D428 - 437
57X-RAY DIFFRACTION57D438 - 450
58X-RAY DIFFRACTION58D451 - 471
59X-RAY DIFFRACTION59D472 - 482
60X-RAY DIFFRACTION60D483 - 489

+
About Yorodumi

-
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

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242):Coronavirus Proteases

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

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • 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

-
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

Read more