[English] 日本語
Yorodumi
- PDB-2ymd: Crystal structure of a mutant binding protein (5HTBP-AChBP) in co... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2ymd
TitleCrystal structure of a mutant binding protein (5HTBP-AChBP) in complex with serotonin (5-hydroxytryptamine)
ComponentsSOLUBLE ACETYLCHOLINE RECEPTOR
KeywordsRECEPTOR / PENTAMERIC LIGAND-GATED ION CHANNEL
Function / homology
Function and homology information


extracellular ligand-gated monoatomic ion channel activity / transmembrane signaling receptor activity / membrane / identical protein binding / metal ion binding
Similarity search - Function
Acetylcholine Binding Protein; Chain: A, / Neurotransmitter-gated ion-channel ligand-binding domain / Neurotransmitter-gated ion-channel / Neurotransmitter-gated ion-channel ligand-binding domain / Neurotransmitter-gated ion-channel ligand-binding domain superfamily / Neurotransmitter-gated ion-channel ligand binding domain / Distorted Sandwich / Mainly Beta
Similarity search - Domain/homology
PHOSPHATE ION / SEROTONIN / Soluble acetylcholine receptor
Similarity search - Component
Biological speciesAPLYSIA CALIFORNICA (California sea hare)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.96 Å
AuthorsKesters, D. / Thompson, A.J. / Brams, M. / Elk, R.v. / Spurny, R. / Geitmann, M. / Villalgordo, J.M. / Guskov, A. / Danielson, U.H. / Lummis, S.C.R. ...Kesters, D. / Thompson, A.J. / Brams, M. / Elk, R.v. / Spurny, R. / Geitmann, M. / Villalgordo, J.M. / Guskov, A. / Danielson, U.H. / Lummis, S.C.R. / Smit, A.B. / Ulens, C.
CitationJournal: Embo Rep. / Year: 2013
Title: Structural Basis of Ligand Recognition in 5-Ht(3) Receptors.
Authors: Kesters, D. / Thompson, A.J. / Brams, M. / Van Elk, R. / Spurny, R. / Geitmann, M. / Villalgordo, J.M. / Guskov, A. / Helena Danielson, U. / Lummis, S.C. / Smit, A.B. / Ulens, C.
History
DepositionOct 9, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 12, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 30, 2013Group: Database references
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: SOLUBLE ACETYLCHOLINE RECEPTOR
B: SOLUBLE ACETYLCHOLINE RECEPTOR
C: SOLUBLE ACETYLCHOLINE RECEPTOR
D: SOLUBLE ACETYLCHOLINE RECEPTOR
E: SOLUBLE ACETYLCHOLINE RECEPTOR
F: SOLUBLE ACETYLCHOLINE RECEPTOR
G: SOLUBLE ACETYLCHOLINE RECEPTOR
H: SOLUBLE ACETYLCHOLINE RECEPTOR
I: SOLUBLE ACETYLCHOLINE RECEPTOR
J: SOLUBLE ACETYLCHOLINE RECEPTOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)244,93044
Polymers240,92910
Non-polymers4,00134
Water48,0102665
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area46760 Å2
ΔGint-254.7 kcal/mol
Surface area76430 Å2
MethodPISA
2
A: SOLUBLE ACETYLCHOLINE RECEPTOR
B: SOLUBLE ACETYLCHOLINE RECEPTOR
C: SOLUBLE ACETYLCHOLINE RECEPTOR
D: SOLUBLE ACETYLCHOLINE RECEPTOR
E: SOLUBLE ACETYLCHOLINE RECEPTOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,64924
Polymers120,4645
Non-polymers2,18519
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20760 Å2
ΔGint-116.5 kcal/mol
Surface area41320 Å2
MethodPISA
3
F: SOLUBLE ACETYLCHOLINE RECEPTOR
G: SOLUBLE ACETYLCHOLINE RECEPTOR
H: SOLUBLE ACETYLCHOLINE RECEPTOR
I: SOLUBLE ACETYLCHOLINE RECEPTOR
J: SOLUBLE ACETYLCHOLINE RECEPTOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,28120
Polymers120,4645
Non-polymers1,81615
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20020 Å2
ΔGint-112.4 kcal/mol
Surface area41090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)203.565, 140.064, 126.528
Angle α, β, γ (deg.)90.00, 99.08, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-1, -0.029, -0.004), (-0.024, 0.725, 0.689), (-0.017, 0.689, -0.725)
Vector: 52.963, 0.539, 0.403)

-
Components

#1: Protein
SOLUBLE ACETYLCHOLINE RECEPTOR / ACHBP


Mass: 24092.885 Da / Num. of mol.: 10 / Fragment: ACETYLCHOLINE BINDING DOMAIN, RESIDUES 20-231 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) APLYSIA CALIFORNICA (California sea hare)
Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / Strain (production host): SF21 / References: UniProt: Q8WSF8
#2: Chemical
ChemComp-SRO / SEROTONIN / 3-(2-AMINOETHYL)-1H-INDOL-5-OL / Serotonin


Mass: 176.215 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C10H12N2O / Comment: neurotransmitter*YM
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 2665 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsSEROTONIN (SRO): SYNONYM 5-HYDROXYTRYPTAMINE
Sequence detailsTHE CONFLICTS BETWEEN THE UNIPROT AND PROTEIN SEQUENCE ARE DUE TO DIFFERENCES IN THE CLONING METHOD ...THE CONFLICTS BETWEEN THE UNIPROT AND PROTEIN SEQUENCE ARE DUE TO DIFFERENCES IN THE CLONING METHOD USED TO OBTAIN THE GENE.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.21 Å3/Da / Density % sol: 61.41 % / Description: NONE
Crystal growDetails: 400 MM (NH4)H2PO4

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 2, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.96→46.9 Å / Num. obs: 249028 / % possible obs: 99.6 % / Observed criterion σ(I): 1 / Redundancy: 3.8 % / Biso Wilson estimate: 22.28 Å2 / Rmerge(I) obs: 0.01 / Net I/σ(I): 6.4
Reflection shellResolution: 1.96→2.19 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.08 / Mean I/σ(I) obs: 1 / % possible all: 99.6

-
Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2XYS
Resolution: 1.96→46.903 Å / SU ML: 0.18 / σ(F): 1.42 / Phase error: 19.56 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2011 2294 1 %
Rwork0.1591 --
obs0.1595 239406 95.78 %
Solvent computationShrinkage radii: 1 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 2 Å2 / ksol: 2 e/Å3
Displacement parametersBiso mean: 29.2 Å2
Refinement stepCycle: LAST / Resolution: 1.96→46.903 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16864 0 264 2665 19793
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00717569
X-RAY DIFFRACTIONf_angle_d1.06123927
X-RAY DIFFRACTIONf_dihedral_angle_d14.0866321
X-RAY DIFFRACTIONf_chiral_restr0.0732624
X-RAY DIFFRACTIONf_plane_restr0.0053067
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9609-2.00360.28621200.259312058X-RAY DIFFRACTION78
2.0036-2.05020.31241380.235613761X-RAY DIFFRACTION89
2.0502-2.10140.22431360.212114212X-RAY DIFFRACTION92
2.1014-2.15830.23711380.199514470X-RAY DIFFRACTION94
2.1583-2.22180.23271440.196814718X-RAY DIFFRACTION95
2.2218-2.29350.2381440.188814802X-RAY DIFFRACTION96
2.2935-2.37540.23791430.176414981X-RAY DIFFRACTION97
2.3754-2.47060.23231470.173915090X-RAY DIFFRACTION98
2.4706-2.5830.2381460.17315098X-RAY DIFFRACTION98
2.583-2.71910.21931470.166115157X-RAY DIFFRACTION98
2.7191-2.88950.22281460.158215304X-RAY DIFFRACTION99
2.8895-3.11250.19321460.148315367X-RAY DIFFRACTION99
3.1125-3.42570.17621500.136415463X-RAY DIFFRACTION100
3.4257-3.92120.17671480.130115427X-RAY DIFFRACTION100
3.9212-4.93940.13651490.116115559X-RAY DIFFRACTION100
4.9394-46.91620.19171520.164115645X-RAY DIFFRACTION100
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)
12.713-3.62670.58896.35521.83216.73840.2181-0.69450.26150.3426-0.0861-0.1764-0.19310.3744-0.11530.1678-0.0873-0.02270.3047-0.07590.276744.9986-2.020520.4183
23.13090.80481.17768.3432-4.59963.3929-2.12180.16092.4123-0.28420.4002-2.0308-0.2932-0.06671.73110.6874-0.0692-0.18270.702-0.04030.877139.03818.386416.4779
38.05211.58272.93312.33712.59413.08510.12580.7620.4757-0.68690.1559-0.412-0.78480.6758-0.07170.3123-0.04960.07880.29130.10890.372128.46628.90973.6555
40.64170.64470.48312.0715-0.52380.62450.0176-0.0496-0.17580.0166-0.0198-0.05120.0530.0688-0.01430.1623-0.018-0.01840.1784-0.0310.117710.8648-11.94813.6799
54.93084.69-5.17174.513-4.93615.4235-0.27390.2416-0.3546-0.3950.0916-0.26120.60840.15890.31320.2219-0.03080.02950.202-0.0240.236525.635-8.6699.9132
66.16250.31320.86927.0264-3.96737.29090.14020.3306-0.1572-0.27940.1215-0.45830.1720.4654-0.24180.141-0.03520.02760.1866-0.0920.198544.3832-4.543511.3326
73.7572-0.3592-0.21090.0606-0.10430.5822-0.08-0.0792-0.01910.03050.0614-0.0393-0.00730.09580.01010.1747-0.0305-0.01120.1532-0.030.180823.7747-4.36915.8365
88.39196.6931-7.40717.359-6.28599.76840.1941-0.3209-0.59210.1768-0.3719-0.3916-0.08990.49160.16110.1407-0.0476-0.00910.1947-0.02750.188127.1871-8.970613.7463
90.235-0.8454-0.06882.9303-0.27542.4614-0.1421-0.0644-0.2096-0.19460.080.3172-0.0522-0.21830.04970.108-0.02860.01910.13040.02160.16763.1867-13.835614.3364
102.2562.4723-3.58473.5302-4.81056.7137-0.29890.366-0.14-0.76910.18870.54740.1736-0.14030.06240.1807-0.0178-0.01510.2838-0.06630.27630.4864-20.22286.1431
113.62690.1502-1.16898.0434-0.04952.4657-0.11230.64760.3289-0.52230.1042-0.1544-0.00810.22630.00330.1675-0.0415-0.04510.23510.04330.093417.85791.01434.0525
122.18871.0923-1.90314.6443-2.10517.9796-0.02420.1534-0.2598-0.1294-0.0236-0.05680.33560.12390.05810.14220.0031-0.01780.1237-0.06140.152713.2593-20.90279.0219
133.8163-0.2394.65333.4066-1.30426.01420.1440.7953-0.32820.3415-0.35110.46030.5525-0.25090.0410.252-0.03680.01880.24220.00890.140811.9646-1.6584-2.1032
146.1899-6.0488-0.55396.00840.89322.0361-0.45-1.05190.44950.32940.6922-0.1435-0.3951-0.3164-0.20420.28360.0013-0.04760.30850.01110.213711.63476.91110.4859
158.59066.8027-5.16115.8066-5.06526.1560.0814-0.1470.14040.1265-0.12610.46150.25040.07810.12590.1894-0.0381-0.00340.2279-0.05710.18276.6951-17.98048.0986
162.62571.2071-4.21638.8144-0.91957.4360.1543-0.3989-0.18670.3819-0.3647-0.87690.08470.41160.17530.1635-0.0931-0.03690.30880.06220.248431.264717.603710.0411
173.06651.90051.52562.0876-1.57757.8331.0653-2.6850.5376-0.3278-0.93520.4813-0.12332.2197-0.36130.5818-0.08990.14480.7959-0.090.512127.695524.484919.8763
185.5176-3.5163-0.36662.8324-1.6556.6985-0.0460.47841.0671-0.54920.1846-0.1879-0.48860.7472-0.15090.4338-0.19990.01050.1780.00750.35412.636331.336321.5469
192.55822.333-0.28574.0014-0.61181.2814-0.07190.13830.0643-0.17250.14630.0737-0.0366-0.0044-0.05570.11710.0042-0.01220.1348-0.00890.10161.08419.404916.5395
207.7563-0.1318-2.49056.16450.9824.14270.11970.44210.232-0.3486-0.2195-0.1487-0.38910.1990.07130.1837-0.0746-0.02820.28780.03320.134125.181622.19675.1127
212.57520.9986-1.59161.0578-0.61340.9429-0.05890.01340.0385-0.01210.0535-0.0478-0.01260.03130.00030.1791-0.0525-0.01650.2096-0.00880.128911.157413.244618.4259
229.5617.2201-7.39135.649-6.15397.30430.0439-0.26680.07580.2732-0.27220.0674-0.2494-0.1280.2220.1772-0.0611-0.02250.1716-0.01030.155211.521813.331911.7884
231.5106-2.0674-0.5243.2681.14953.73530.0715-0.1951-0.1267-0.01630.01820.23290.0645-0.3541-0.11830.1365-0.0440.00060.14430.01060.1368-5.91493.884622.5059
245.8731-2.30324.52635.6478-3.1624.31230.5998-0.0753-0.56380.0884-0.03561.68520.1807-1.182-0.50270.2205-0.1126-0.00150.5038-0.04660.3647-20.0382-1.042714.5945
254.07391.20081.80040.74771.49312.7940.078-0.13560.2447-0.0118-0.14470.1023-0.2427-0.09330.04280.16280.01290.0020.10160.01520.1461-0.527920.347421.7557
265.26752.31664.86333.44592.06834.5804-1.14111.39910.3921-1.76830.80030.358-0.95540.22760.2690.4322-0.0756-0.02150.35420.01730.27-2.481318.58526.9682
272.3750.30171.05366.8650.37791.43880.10530.09280.0819-0.1603-0.08190.06680.1246-0.0596-0.01570.1293-0.04290.00090.15390.00950.1037-6.29725.981710.5511
288.4527-3.62572.35167.0424-6.08848.49750.70270.9775-0.9661-0.652-1.13141.11511.94021.04170.4170.84180.32740.05530.8209-0.1320.7052-4.953725.779829.7472
295.4741.0391.93152.9842-1.60332.14170.2365-0.67130.65640.8155-0.38030.2945-0.1032-0.30730.14950.2206-0.00710.06140.2084-0.01990.1987-4.4520.509220.2078
304.9117-2.567-1.61387.53734.8933.21110.23340.2154-0.4732-0.0464-0.45040.72340.6508-0.37430.2510.2331-0.0546-0.04660.2703-0.00840.2621-13.4164-1.170212.5618
315.02831.4776-0.82743.5563-3.08763.46840.04020.4398-0.5023-0.4290.3181-1.12830.10780.52070.00090.242-0.08660.08090.1909-0.01760.337721.409231.83929.1625
328.53420.7735-4.41192.87861.33283.37720.4972-2.5219-0.21170.3918-1.5709-1.8673-1.22160.74991.18520.6341-0.0695-0.24610.85450.05030.835326.391726.497839.3554
333.8306-1.1348-2.89735.55760.49814.3916-0.1234-0.57950.34710.4068-0.0962-0.4126-0.29510.0340.09330.392-0.1454-0.16480.23140.00230.401418.193123.167453.1831
341.37940.09240.58492.28170.35272.6569-0.03260.00380.0194-0.13990.08070.0667-0.0312-0.1189-0.06530.1031-0.02980.03450.14120.00290.0878-2.39939.891241.2526
354.6134.4715-2.87124.4235-2.39276.53160.2459-0.32240.33150.2015-0.319-0.0853-0.4017-0.06870.11220.2365-0.0109-0.01780.1288-0.01850.226810.75427.672942.8004
365.52534.81013.97054.59644.85547.43350.04810.19671.094-0.0656-0.12880.195-0.64810.02910.08490.2357-0.00610.06370.1544-0.00910.331217.502140.298833.1127
371.06042.3327-0.68884.5856-1.42870.84590.0332-0.00850.0420.06940.0164-0.0519-0.02070.0217-0.04690.1189-0.016-0.0040.12990.01240.16979.426118.658938.0099
387.97577.17017.64416.58867.2458.2857-0.1780.29730.2876-0.14080.04230.75120.0311-0.0740.14510.1562-0.04140.00240.2169-0.01650.17475.81321.69737.1016
390.6125-0.81560.73111.362-0.68440.9405-0.1059-0.1748-0.1475-0.0230.07670.09870.2598-0.36930.05070.2085-0.1059-0.01020.22630.02570.1348-4.99192.641942.4247
405.022-5.425-3.37846.24833.56993.18540.3081-0.6362-0.82350.858-0.47740.93220.2064-1.46860.30150.308-0.1415-0.00350.56150.01530.2878-21.61641.770143.6205
416.1218-0.02410.5960.4319-0.91981.67760.1059-0.42220.03260.2395-0.1585-0.0284-0.0925-0.06860.05790.2456-0.06120.0090.1586-0.01340.12914.180213.658952.1154
426.01874.71785.73.78734.54735.43560.0499-0.89761.55330.395-0.62641.0715-0.3812-0.33710.4970.34980.01990.03260.3379-0.06830.3618-5.818723.553247.6515
432.53371.51761.4282.63412.25795.71670.1817-0.2680.16450.2292-0.11160.21130.0238-0.2955-0.03150.13790.00030.03460.1746-0.01760.1451-11.044513.080540.7366
443.2424-4.48092.39828.1959-2.09092.55710.947-0.0385-0.23870.6226-0.87430.4331-0.052-0.4565-0.03710.9408-0.08350.06340.72950.0040.38517.02338.820761.4123
453.59082.16522.80712.99071.45382.92880.3348-0.1266-0.0510.4477-0.23110.04030.0760.01470.34220.2746-0.0920.01450.31780.02030.1813-6.740810.494848.3629
464.04842.3035-0.26326.35230.48023.1832-0.55070.84620.384-0.64070.4342-0.2594-0.96560.6906-0.01770.4447-0.3205-0.03260.20880.07070.235529.009621.032251.6613
474.60222.15110.82973.50694.3668.5886-1.39430.0636-1.5827-0.81990.294-2.5267-0.36210.16760.95990.6814-0.26810.17840.849-0.01470.949536.538611.819347.8504
482.7674-4.1143.11399.0851-5.35844.104-0.0505-0.91140.30920.5249-0.0203-0.814-0.18870.54450.18430.2281-0.0686-0.06840.5544-0.08570.403336.8487-3.225554.6027
491.6955-0.9149-0.14090.6569-0.34960.921-0.0534-0.07960.0463-0.0491-0.0310.09030.0607-0.11370.08730.1851-0.058-0.00850.1160.03120.07898.6088-8.179350.5931
504.72986.27753.05388.76743.028.1390.2-0.5291-0.24130.3998-0.2794-0.36790.05180.07940.01320.2046-0.0037-0.03630.1691-0.00480.178825.57974.071457.8002
512.0192-0.77261.24446.7689-3.20311.9165-0.2152-0.42490.61091.0134-0.0651-0.0093-0.45020.3470.18190.3684-0.155-0.02370.2748-0.0250.229530.565321.063561.6785
520.44850.53490.39781.39180.42640.5163-0.00180.0270.0742-0.0310.019-0.0267-0.08180.0967-0.0220.2303-0.08460.01980.21640.00530.161120.13763.262350.4401
536.40824.56356.30946.24741.85969.0756-0.0286-0.50410.62130.1497-0.15330.1467-0.1513-0.06460.210.1619-0.0659-0.00570.1923-0.01240.129417.81764.439454.4711
540.4769-1.1513-0.24764.7715-0.65091.0670.0297-0.0621-0.13440.3537-0.00980.19770.3557-0.3081-0.03820.2244-0.0846-0.0130.1974-0.01720.14956.2126-13.392647.0911
551.8385-1.6264-1.26262.33981.07210.8818-0.3546-0.107-0.75040.63190.07620.56371.9643-2.17380.16890.447-0.18440.0590.4503-0.02210.3432-6.5506-20.269955.7502
565.53112.633-3.56232.7308-0.74492.8408-0.0872-0.0917-0.15740.03370.1253-0.16390.15710.1447-0.04410.1794-0.0101-0.03980.12420.00690.110722.1648-12.059753.7888
575.9094-6.0386-6.74597.05226.3988.13070.1113-1.1722-0.1020.3685-0.04140.07780.36610.2018-0.07490.248-0.0023-0.02670.28530.04740.138514.9343-6.490865.4457
586.5161-1.26520.95690.9821-0.61221.18610.035-0.0118-0.35350.07190.07180.17740.0583-0.1212-0.11660.1805-0.0681-0.00310.13520.00770.10783.9063-8.341857.9589
594.6333-5.2655-4.74856.02125.42244.89330.24860.26390.122-0.11430.1657-0.18540.1199-0.1286-0.42760.44440.0620.01770.38390.03360.471528.6215-20.502851.8812
608.4304-0.888-0.34131.1365-0.56962.50540.1158-0.0003-0.40140.01460.04630.21790.1912-0.1281-0.13030.2016-0.05850.00310.10330.00220.14318.8682-13.994356.1749
613.19851.13473.4847.6433-0.20856.8846-0.003-0.071.27590.4023-0.1786-0.1097-0.3030.06520.24150.2463-0.1048-0.06180.23480.00110.377743.58910.079646.0333
625.41645.68365.68055.98935.99066.011-1.67480.97280.0647-0.90961.65210.0847-0.57542.82480.00240.6238-0.20580.02311.01130.09550.587644.54250.456833.6654
636.3519-6.3072-6.17136.39876.0046.2262-0.1766-0.151-0.1946-0.20710.2459-0.81860.00481.3201-0.20650.2253-0.01780.01250.54560.03470.338243.3927-12.69823.7859
642.69160.071-0.38471.0154-0.38271.54260.0788-0.0949-0.06130.0537-0.04710.0060.1106-0.0547-0.04010.2037-0.0291-0.01320.093-0.01230.132118.095-21.222534.0625
654.00125.77721.02058.52121.61032.1489-0.04720.3004-0.4554-0.0480.1605-0.36690.230.36940.01940.22160.0011-0.05440.22440.00440.206940.1137-14.621536.7234
668.40151.4992-5.89374.54622.796610.0010.1325-0.9993-0.53860.5936-0.2049-1.08480.61570.55290.13340.3169-0.0539-0.17130.22080.05870.364950.2897-7.122648.4642
673.78881.41841.60970.55071.03081.4370.0803-0.03940.00530.042-0.0312-0.102-0.00980.0104-0.04430.2165-0.0434-0.02240.15730.03310.175430.2869-11.350436.584
684.9512-0.23411.23373.34731.69391.28390.0437-0.2372-0.23020.1855-0.03140.00540.35120.17120.01430.124-0.0597-0.00890.17850.06060.158631.021-14.586740.0735
690.4473-0.7596-0.36631.868-0.82483.64140.02790.0911-0.117-0.04160.07970.42780.4152-0.3939-0.10090.1803-0.0669-0.00520.22710.00480.178110.5812-24.408930.8873
707.76841.9444-2.99820.4982-0.72921.1742-0.2898-0.1061-0.5626-0.2771-0.0639-0.16470.9546-0.65050.3060.4015-0.14840.01960.2630.01190.44739.5308-35.963432.648
715.71223.1966-2.32376.2095-4.40495.62850.0024-0.0073-0.39670.0752-0.1892-0.29660.1590.30010.20850.18170.0221-0.01360.1624-0.06610.144231.3865-22.646627.2648
726.8602-1.1156-3.69543.0211.11473.6869-0.1895-0.3135-0.46180.39130.1230.02710.28950.14990.06950.2479-0.0347-0.02640.15270.02570.193117.5181-28.690939.3832
735.9239-6.26984.44699.3022-6.25224.2102-2.0867-0.49460.4191.4286-0.18110.40110.1294-2.95811.96941.3961-0.1536-0.00061.2464-0.29590.610628.2712-23.937715.6417
741.98210.54860.35072.0702-0.85060.5606-0.24812.14650.1362-2.09830.63231.30561.0338-1.4885-0.40060.9322-0.3217-0.2221.2411-0.01030.676733.3486-21.694414.7417
754.51493.3724-5.35014.0929-3.54117.6431-0.16060.3356-0.05770.09520.21960.13640.4484-0.2561-0.02030.2389-0.0345-0.02060.169-0.02270.223516.5503-29.95833.4142
762.92963.01383.37723.54413.51433.8991-0.06740.12240.4777-0.2627-0.02621.1161-0.249-0.04730.13180.2194-0.038-0.02520.227-0.04150.4041-47.0328-62.788517.2466
773.16955.50833.84699.74166.88154.90320.9456-1.912-0.3701-0.0041-1.2138-0.23291.0148-0.81260.22740.5516-0.10720.10870.710.05640.5767-47.841-63.233129.7672
784.3774-4.83934.23035.3674-4.68594.1806-0.27650.208-1.0756-0.28060.13320.36481.0462-0.5050.03740.5229-0.12970.10490.3399-0.00410.4519-35.2575-66.693639.7876
791.8282-0.2893-0.5360.6333-0.9392.46070.00330.08990.0226-0.190.0317-0.1678-0.06440.167-0.02490.0986-0.0165-0.02440.1180.00130.1698-17.9959-46.001129.3487
809.12286.1897-0.91754.2897-0.89483.43930.0047-0.1122-0.3689-0.1502-0.1927-0.02450.3869-0.12130.21930.2508-0.04890.00110.154-0.03280.2762-31.3921-63.481426.907
818.44752.3675-0.00659.2248-6.21324.5239-0.30830.6826-1.0549-0.68590.1475-0.36170.87650.11370.1530.2206-0.0203-0.00570.1993-0.1040.3589-42.7281-71.66715.1685
821.68932.74812.12973.51882.18032.0426-0.02840.1201-0.1664-0.01150.1368-0.03450.05440.0645-0.08410.1271-0.02910.02250.1716-0.03150.2304-31.7388-54.269226.703
839.61634.0682-2.54355.4538-3.18594.7727-0.09420.5899-0.4563-0.01370.131-0.09620.00840.0159-0.04510.1431-0.0452-0.00540.1775-0.03610.2379-28.9183-56.185223.3548
840.6423-0.7562-0.38681.49830.36915.6804-0.021-0.22870.18680.04750.0275-0.3013-0.0360.3432-0.02090.2042-0.0597-0.03740.1328-0.01140.2611-14.5576-40.86732.9092
854.65215.4684-5.29646.4688-6.27396.11680.3359-0.4586-0.27810.3547-0.5499-1.5534-0.04681.3930.25990.2964-0.0882-0.00690.6388-0.00430.48261.18-40.340229.2673
868.91940.064-1.40230.17360.5121.78270.0087-0.13090.14220.0496-0.00050.19460.15960.09110.00540.2419-0.0253-0.0420.11910.02230.2007-22.5997-56.763439.2355
874.79372.9201-3.50919.0525-7.31448.6386-0.08230.2036-0.4158-0.462-0.092-0.45680.51630.15740.15120.15980.00250.00010.2065-0.0720.2359-13.0996-51.226621.9415
885.00173.2525-1.41947.2944-2.36133.53040.00730.0302-0.64070.0203-0.1434-0.83830.09180.52220.15570.14740.0168-0.04210.2241-0.04170.2757-10.1239-52.266630.0348
892.4547-3.52172.64647.4718-0.82396.5822-0.4585-0.14731.41180.2604-0.6234-0.2991-1.0852-0.87831.03140.97750.1607-0.36470.8051-0.11120.7272-21.4109-57.157749.658
904.86383.2642-2.37364.6669-2.95926.75090.2601-0.3119-0.11740.197-0.2824-0.2308-0.06780.56620.01290.1450.0039-0.03040.1626-0.02140.3002-11.2158-49.235331.6582
916.47444.3701-0.79947.52022.0846.0698-0.11960.6723-0.1527-0.38850.34820.78710.6534-0.8683-0.13790.2963-0.141-0.09280.24440.06250.2809-45.891-64.389243.3144
924.83124.6475-0.03844.70351.36599.197-0.6765-1.70351.3609-0.2083-0.61952.25360.98480.43391.14310.5072-0.07120.02910.85480.08290.8963-53.4483-55.191546.8848
933.35594.62520.67246.46650.79371.85390.1757-0.8441-0.42010.6502-0.44570.56340.4698-0.50490.25990.3379-0.03470.14210.47060.16630.5038-50.329-45.04259.4098
941.4631-0.8036-0.38910.5310.44951.07180.0244-0.1684-0.15470.0473-0.0193-0.19040.06270.0626-0.01850.1729-0.0623-0.04180.16520.00440.1348-24.818-36.816649.4081
954.80536.6859-2.85089.65-2.48028.27220.393-0.7361-0.11220.6345-0.32020.44870.38970.0256-0.08650.2776-0.04780.00240.22880.05870.2649-40.2212-52.988555.4643
969.1346-0.0201-4.27897.63770.93722.14780.0047-0.491-0.5780.62140.0326-0.45220.28640.1379-0.03810.3388-0.0839-0.16030.26950.11550.3163-42.6777-68.402751.3451
971.45562.7122-0.4566.9519-0.69810.77720.0518-0.113-0.0779-0.0297-0.06960.04320.1024-0.05080.0140.1525-0.0448-0.05110.1630.02540.1988-36.367-45.984347.3918
985.46645.3614-5.26126.7953-3.20577.52490.0398-0.0758-0.36490.08850.1088-0.29520.18380.2494-0.17340.1724-0.0502-0.0220.17430.03520.2897-33.0594-50.210849.5871
991.9139-2.3288-0.23613.02720.61281.57570.0015-0.21560.19620.1201-0.1061-0.1137-0.24330.24450.14090.1753-0.08750.00950.20470.00940.1442-23.0174-30.089748.0721
1005.579-3.93951.02133.4715-0.75056.8989-0.0077-0.57610.45981.0225-0.0931-1.3659-1.05771.6291-0.07670.3539-0.1741-0.15240.3838-0.07940.6277-7.447-27.2154.5543
1015.9111-0.50273.16140.7850.45112.3740.07360.09930.03120.19140.0380.0687-0.00840.02-0.10330.2392-0.08010.00810.1802-0.00820.1667-33.3675-33.718856.1683
1022.2453-2.2461-2.43093.99261.17865.3987-0.3787-1.0034-0.32510.58490.3240.4380.1818-0.2819-0.01850.3802-0.07570.07210.34290.01220.2073-40.6203-41.525263.0601
1038.63530.5249-3.4991.3709-0.11035.45370.1364-0.7681-0.09650.3612-0.147-0.11010.18860.24780.02670.2393-0.0619-0.06730.22210.02930.1839-18.9377-40.480555.5658
1047.7574-3.39354.014.3249-4.42854.60850.24080.681-0.41050.34870.3922-0.55962.32261.2784-0.60950.90630.1009-0.03720.6779-0.21040.5967-41.9934-27.845562.449
1058.40931.8508-4.25022.8046-0.76794.83330.3506-0.41460.30750.2733-0.2654-0.0671-0.15020.2047-0.06140.2277-0.0619-0.0510.187-0.00210.1424-22.5129-34.035956.7925
1066.1693.0571-0.64116.5322-1.67686.266-0.27640.4548-1.0244-0.40920.0265-0.3570.7534-0.12580.2090.3321-0.19260.07480.2845-0.04140.3809-59.7178-44.595652.9413
1077.59634.9079-3.38874.8137-0.27193.7412-1.5672-0.16310.4253-1.46971.88491.86231.6557-0.9525-0.46430.6535-0.22790.01450.94930.08460.6908-64.6649-39.273542.822
1086.5319-2.7358-1.04232.14791.60789.2512-0.3694-1.06650.2851-0.08110.55850.84470.0836-0.668-0.13190.2272-0.1336-0.01320.5920.03140.3156-65.3762-22.965940.1464
1095.1832-2.64825.47094.4377-2.18487.03460.3069-1.0722-0.08650.0031-0.24660.31040.3341-1.4643-0.08990.17-0.05310.02650.3983-0.02110.1981-60.5076-19.717646.8315
1101.9821-0.52480.36571.3197-0.67313.5976-0.0878-0.0808-0.0795-0.0793-0.0178-0.02870.10310.1710.1070.1553-0.05020.01210.1062-0.0320.1212-33.9901-17.943644.1898
1118.49965.7581-2.82217.6771-1.9767.534-0.1217-0.29610.16860.11240.07540.44110.0198-0.43830.05620.1701-0.01550.02820.2477-0.010.1555-58.2828-27.046750.8581
1127.3578-1.44882.38939.316-4.5066.8399-0.1019-0.5893-0.53591.0892-0.08110.4254-0.1325-0.44930.16770.3732-0.12440.08170.291-0.02450.2224-64.6268-39.813360.3622
1131.2570.4778-0.43860.9171-0.35611.30940.0145-0.02110.01040.0364-0.02180.03690.0699-0.03180.00490.1786-0.07840.00840.1855-0.02540.1335-45.9311-25.972145.3137
1144.253.29563.70073.43612.53153.3511-0.2497-0.48761.4462-0.35250.0482-0.8125-1.3230.833-0.05890.3974-0.1555-0.0580.2358-0.01540.4342-24.1038-3.508748.3702
1156.35984.09583.76553.46692.40253.8698-0.09630.2590.1660.0030.10390.1208-0.1375-0.2159-0.00880.1413-00.00490.16470.02260.1079-50.864-14.318440.4391
1167.2296-2.12651.23711.9001-0.31422.95440.007-0.3186-0.02970.15420.1137-0.0197-0.0548-0.1282-0.12320.1962-0.0488-0.01110.1262-0.01870.1331-36.4481-15.969654.1785
1173.45330.60344.18512.95220.9855.3083-0.2234-0.10370.6709-0.0198-0.01870.1215-0.1527-0.18210.28020.1744-0.02870.02110.11170.03470.1559-41.7717-9.15750.0333
1185.27666.50865.73659.99947.50796.41290.27331.1999-0.48971.56791.9269-0.81290.52792.6097-2.17470.78630.22380.11190.8726-0.07450.7079-53.7298-8.593232.3205
1190.1541-0.55370.32834.72860.44042.427-0.23381.32570.0753-0.42740.42080.3942-0.1662-0.4705-0.10520.2153-0.0653-0.03490.51260.09250.164-50.5432-10.31541.045
1208.48972.00324.40457.52330.9924.1048-0.13950.13540.12160.55110.0258-0.53760.22790.8701-0.02640.2567-0.0962-0.01190.31250.0180.1581-26.1155-9.604850.1564
1213.196-1.4407-3.57488.1288-2.2076.14410.2539-0.8091-0.94080.0627-0.41260.11720.5287-0.23530.1760.1925-0.1096-0.00510.31830.05170.4093-69.3364-31.892431.9021
1226.06033.1645-3.89654.6684-4.13674.37770.0555-0.45080.09720.525-0.17890.81060.4134-1.12180.24010.373-0.1568-0.01420.4366-0.14630.3758-60.7669-33.706515.1896
1237.5878-3.0408-2.1146.11255.78565.60280.43830.785-1.1935-0.2346-1.13331.320.5326-1.24170.64490.3696-0.0517-0.11430.5158-0.07320.345-60.5964-27.85576.1695
1240.30350.26790.66820.84680.4981.16290.0182-0.14990.14680.0305-0.0271-0.0143-0.0331-0.047-0.00580.2026-0.04480.00820.20340.02230.1422-37.8694-15.461522.5226
1254.17974.3583-2.73084.6168-3.33186.0679-0.16750.45230.2256-0.20590.1710.4163-0.0128-0.3514-0.00210.14070.0053-0.00120.2206-0.04060.2264-61.3607-22.521219.4216
1269.08794.5932.34593.076-1.19689.39650.16890.07330.87120.10020.05770.8155-0.2967-0.9135-0.23670.18890.02280.04190.23610.02430.3476-75.6705-24.033228.9372
1276.59420.8115-1.9098-0.1786-0.14290.77850.1203-0.14590.08530.0222-0.03490.05070.0247-0.0444-0.08210.1871-0.04690.01510.1316-0.00230.1861-52.4636-24.420724.3569
1284.62613.44685.66075.22743.68867.04650.1424-0.22560.03220.0656-0.01790.0042-0.1513-0.2339-0.11730.1506-0.05590.02480.17010.00240.1749-54.0441-20.020325.1825
1290.3393-0.8572-0.22862.03440.50311.7480.20630.1530.3448-0.1152-0.0458-0.1956-0.39250.1615-0.0870.1739-0.0650.02850.20430.00790.1565-32.3696-16.609420.1816
1305.4197-3.25433.25413.0814-0.77543.2164-0.34221.07591.0686-0.6339-0.1969-1.6095-1.20441.03170.52750.4222-0.14220.06680.36010.00810.3772-25.6856-0.965718.7382
1310.74290.4444-0.88074.5008-0.11191.1278-0.02680.2536-0.0927-0.219-0.02460.1003-0.0548-0.19110.05840.1718-0.027-0.02640.23160.00210.1108-45.754-21.491210.3109
1324.22155.10734.90366.21725.94055.7045-0.15320.70630.9945-0.2447-0.08911.2186-0.6991-0.32810.18240.34140.03880.00010.35680.02440.4164-51.624-8.617514.5522
1334.55981.11932.92841.5909-0.4945.1374-0.04350.0850.20340.00160.07770.0378-0.24570.0193-0.03520.1606-0.01620.02210.08290.01110.1494-39.8896-6.877822.3542
1348.1878-4.74210.46814.00711.66186.4817-0.39160.2187-0.34991.16450.9731-0.5184-1.36340.9218-0.46450.7531-0.05710.08380.79360.05820.482-42.4618-25.07991.3396
1358.86546.94414.60119.03925.40895.4286-0.04780.4273-0.2892-0.30770.298-0.3053-0.2549-0.0965-0.25930.2067-0.06130.02270.27980.04310.1783-39.0673-12.285614.0703
1362.0532-0.94113.50066.36-3.26396.7420.3112-1.0896-0.08670.3179-0.15480.3030.2031-0.8108-0.140.2001-0.14330.00610.345-0.00730.2351-61.4867-41.926110.9999
1372.6905-3.4523.60854.4276-4.44865.9367-0.59760.1966-2.5347-0.4891-0.29520.1249-1.1801-0.49370.79710.6151-0.1451-0.05310.8137-0.02440.8916-55.5292-52.180815.1278
1385.2607-5.0221-4.27344.85634.12544.3348-0.26771.0819-1.0547-0.3614-0.31110.35850.4142-1.03730.58490.467-0.1735-0.08040.3024-0.08110.4483-41.2604-57.97968.4094
1390.5199-0.1825-0.45752.0185-0.68210.8069-0.08490.092-0.0084-0.08310.0545-0.0034-0.07220.05170.05480.1322-0.04590.0460.1416-0.02240.1219-26.8223-33.263312.2492
1402.64582.76144.34023.15284.83837.4136-0.21420.6956-0.3411-0.48780.1325-0.1594-0.2843-0.00280.00040.2334-0.0441-0.03440.2488-0.00870.2725-40.8032-42.49885.3501
1414.6644-5.13432.11816.4221-1.38166.75650.43720.4221-0.4817-0.252-0.26320.20710.2905-0.5216-0.17610.2192-0.1031-0.02360.2847-0.00250.192-58.4668-46.37482.4446
1428.4794-4.86373.86663.9998-3.45823.03250.08450.70580.3617-0.6047-0.10170.2805-0.06190.58880.02870.2385-0.1121-0.01980.28910.02970.171-57.2418-38.59392.7993
1432.30880.28291.5740.41980.4151.08750.0494-0.1168-0.18870.00110.00230.00760.1213-0.185-0.05550.1912-0.08440.00210.22070.02060.1837-39.8496-40.210913.4377
1445.46535.5315.48635.59695.49236.9337-0.16130.38650.2343-0.14420.22180.5499-0.23-0.0752-0.02970.1917-0.07030.00310.2297-0.00750.1915-41.8323-37.51998.3175
1451.87891.21750.35883.694-0.08290.5742-0.04210.1431-0.1857-0.2238-0.0113-0.36310.01680.14080.06270.1622-0.03650.01780.1836-0.01920.1637-22.938-38.960211.0685
1464.40875.344-4.8016.4741-5.8265.2513-0.54151.4028-0.365-1.04790.99890.10740.5522-0.3621-0.3740.4086-0.0583-0.0080.3992-0.0440.2694-30.4896-39.0007-2.6008
1472.25311.6862-0.3728.86662.95563.1955-0.01480.1633-0.111-0.11620.08-0.2243-0.12790.0166-0.07570.1522-0.0370.01320.17470.0080.0758-24.8301-29.07824.837
1489.4819-5.82690.4824.0216-1.30362.40630.4070.23930.23980.38590.5787-0.5318-1.4187-0.2689-0.91450.75050.1368-0.03690.6134-0.20340.8836-21.5259-55.654611.9187
1495.77273.2109-1.90261.7878-1.01544.40430.3207-0.4851-0.90870.252-0.6242-0.72360.41350.15670.26760.2108-0.0116-0.04870.2053-0.02570.327-24.682-46.47916.6622
1505.90982.36843.8677.9958-3.40869.7355-0.0345-0.30250.44350.6101-0.181-0.2246-0.5137-0.06990.18950.1878-0.05410.05390.2453-0.03250.2157-16.7951-22.85287.3545
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 1:12)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 13:17)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 18:25)
4X-RAY DIFFRACTION4(CHAIN A AND RESID 26:52)
5X-RAY DIFFRACTION5(CHAIN A AND RESID 53:59)
6X-RAY DIFFRACTION6(CHAIN A AND RESID 60:76)
7X-RAY DIFFRACTION7(CHAIN A AND RESID 77:112)
8X-RAY DIFFRACTION8(CHAIN A AND RESID 113:117)
9X-RAY DIFFRACTION9(CHAIN A AND RESID 118:132)
10X-RAY DIFFRACTION10(CHAIN A AND RESID 133:139)
11X-RAY DIFFRACTION11(CHAIN A AND RESID 140:155)
12X-RAY DIFFRACTION12(CHAIN A AND RESID 156:180)
13X-RAY DIFFRACTION13(CHAIN A AND RESID 181:185)
14X-RAY DIFFRACTION14(CHAIN A AND RESID 186:194)
15X-RAY DIFFRACTION15(CHAIN A AND RESID 195:205)
16X-RAY DIFFRACTION16(CHAIN B AND RESID 1:12)
17X-RAY DIFFRACTION17(CHAIN B AND RESID 13:17)
18X-RAY DIFFRACTION18(CHAIN B AND RESID 18:25)
19X-RAY DIFFRACTION19(CHAIN B AND RESID 26:60)
20X-RAY DIFFRACTION20(CHAIN B AND RESID 61:77)
21X-RAY DIFFRACTION21(CHAIN B AND RESID 78:112)
22X-RAY DIFFRACTION22(CHAIN B AND RESID 113:117)
23X-RAY DIFFRACTION23(CHAIN B AND RESID 118:129)
24X-RAY DIFFRACTION24(CHAIN B AND RESID 130:135)
25X-RAY DIFFRACTION25(CHAIN B AND RESID 136:154)
26X-RAY DIFFRACTION26(CHAIN B AND RESID 155:160)
27X-RAY DIFFRACTION27(CHAIN B AND RESID 161:183)
28X-RAY DIFFRACTION28(CHAIN B AND RESID 184:190)
29X-RAY DIFFRACTION29(CHAIN B AND RESID 191:200)
30X-RAY DIFFRACTION30(CHAIN B AND RESID 201:205)
31X-RAY DIFFRACTION31(CHAIN C AND RESID 1:12)
32X-RAY DIFFRACTION32(CHAIN C AND RESID 13:17)
33X-RAY DIFFRACTION33(CHAIN C AND RESID 18:24)
34X-RAY DIFFRACTION34(CHAIN C AND RESID 25:54)
35X-RAY DIFFRACTION35(CHAIN C AND RESID 55:64)
36X-RAY DIFFRACTION36(CHAIN C AND RESID 65:72)
37X-RAY DIFFRACTION37(CHAIN C AND RESID 73:112)
38X-RAY DIFFRACTION38(CHAIN C AND RESID 113:117)
39X-RAY DIFFRACTION39(CHAIN C AND RESID 118:129)
40X-RAY DIFFRACTION40(CHAIN C AND RESID 130:135)
41X-RAY DIFFRACTION41(CHAIN C AND RESID 136:154)
42X-RAY DIFFRACTION42(CHAIN C AND RESID 155:160)
43X-RAY DIFFRACTION43(CHAIN C AND RESID 161:183)
44X-RAY DIFFRACTION44(CHAIN C AND RESID 184:190)
45X-RAY DIFFRACTION45(CHAIN C AND RESID 191:205)
46X-RAY DIFFRACTION46(CHAIN D AND RESID 1:12)
47X-RAY DIFFRACTION47(CHAIN D AND RESID 13:17)
48X-RAY DIFFRACTION48(CHAIN D AND RESID 18:25)
49X-RAY DIFFRACTION49(CHAIN D AND RESID 26:53)
50X-RAY DIFFRACTION50(CHAIN D AND RESID 54:64)
51X-RAY DIFFRACTION51(CHAIN D AND RESID 65:72)
52X-RAY DIFFRACTION52(CHAIN D AND RESID 73:112)
53X-RAY DIFFRACTION53(CHAIN D AND RESID 113:117)
54X-RAY DIFFRACTION54(CHAIN D AND RESID 118:129)
55X-RAY DIFFRACTION55(CHAIN D AND RESID 130:135)
56X-RAY DIFFRACTION56(CHAIN D AND RESID 136:154)
57X-RAY DIFFRACTION57(CHAIN D AND RESID 155:160)
58X-RAY DIFFRACTION58(CHAIN D AND RESID 161:183)
59X-RAY DIFFRACTION59(CHAIN D AND RESID 184:191)
60X-RAY DIFFRACTION60(CHAIN D AND RESID 192:205)
61X-RAY DIFFRACTION61(CHAIN E AND RESID 1:12)
62X-RAY DIFFRACTION62(CHAIN E AND RESID 13:17)
63X-RAY DIFFRACTION63(CHAIN E AND RESID 18:25)
64X-RAY DIFFRACTION64(CHAIN E AND RESID 26:54)
65X-RAY DIFFRACTION65(CHAIN E AND RESID 55:64)
66X-RAY DIFFRACTION66(CHAIN E AND RESID 65:72)
67X-RAY DIFFRACTION67(CHAIN E AND RESID 73:112)
68X-RAY DIFFRACTION68(CHAIN E AND RESID 113:117)
69X-RAY DIFFRACTION69(CHAIN E AND RESID 118:132)
70X-RAY DIFFRACTION70(CHAIN E AND RESID 133:138)
71X-RAY DIFFRACTION71(CHAIN E AND RESID 139:160)
72X-RAY DIFFRACTION72(CHAIN E AND RESID 161:182)
73X-RAY DIFFRACTION73(CHAIN E AND RESID 183:188)
74X-RAY DIFFRACTION74(CHAIN E AND RESID 189:193)
75X-RAY DIFFRACTION75(CHAIN E AND RESID 194:205)
76X-RAY DIFFRACTION76(CHAIN F AND RESID 1:12)
77X-RAY DIFFRACTION77(CHAIN F AND RESID 13:17)
78X-RAY DIFFRACTION78(CHAIN F AND RESID 18:25)
79X-RAY DIFFRACTION79(CHAIN F AND RESID 26:53)
80X-RAY DIFFRACTION80(CHAIN F AND RESID 54:64)
81X-RAY DIFFRACTION81(CHAIN F AND RESID 65:72)
82X-RAY DIFFRACTION82(CHAIN F AND RESID 73:112)
83X-RAY DIFFRACTION83(CHAIN F AND RESID 113:117)
84X-RAY DIFFRACTION84(CHAIN F AND RESID 118:130)
85X-RAY DIFFRACTION85(CHAIN F AND RESID 131:136)
86X-RAY DIFFRACTION86(CHAIN F AND RESID 137:154)
87X-RAY DIFFRACTION87(CHAIN F AND RESID 155:171)
88X-RAY DIFFRACTION88(CHAIN F AND RESID 172:183)
89X-RAY DIFFRACTION89(CHAIN F AND RESID 184:191)
90X-RAY DIFFRACTION90(CHAIN F AND RESID 192:205)
91X-RAY DIFFRACTION91(CHAIN G AND RESID 1:12)
92X-RAY DIFFRACTION92(CHAIN G AND RESID 13:17)
93X-RAY DIFFRACTION93(CHAIN G AND RESID 18:25)
94X-RAY DIFFRACTION94(CHAIN G AND RESID 26:54)
95X-RAY DIFFRACTION95(CHAIN G AND RESID 55:64)
96X-RAY DIFFRACTION96(CHAIN G AND RESID 65:75)
97X-RAY DIFFRACTION97(CHAIN G AND RESID 76:112)
98X-RAY DIFFRACTION98(CHAIN G AND RESID 113:117)
99X-RAY DIFFRACTION99(CHAIN G AND RESID 118:129)
100X-RAY DIFFRACTION100(CHAIN G AND RESID 130:135)
101X-RAY DIFFRACTION101(CHAIN G AND RESID 136:149)
102X-RAY DIFFRACTION102(CHAIN G AND RESID 150:155)
103X-RAY DIFFRACTION103(CHAIN G AND RESID 156:183)
104X-RAY DIFFRACTION104(CHAIN G AND RESID 184:191)
105X-RAY DIFFRACTION105(CHAIN G AND RESID 192:205)
106X-RAY DIFFRACTION106(CHAIN H AND RESID 1:12)
107X-RAY DIFFRACTION107(CHAIN H AND RESID 13:17)
108X-RAY DIFFRACTION108(CHAIN H AND RESID 18:24)
109X-RAY DIFFRACTION109(CHAIN H AND RESID 25:30)
110X-RAY DIFFRACTION110(CHAIN H AND RESID 31:54)
111X-RAY DIFFRACTION111(CHAIN H AND RESID 55:64)
112X-RAY DIFFRACTION112(CHAIN H AND RESID 65:72)
113X-RAY DIFFRACTION113(CHAIN H AND RESID 73:129)
114X-RAY DIFFRACTION114(CHAIN H AND RESID 130:135)
115X-RAY DIFFRACTION115(CHAIN H AND RESID 136:154)
116X-RAY DIFFRACTION116(CHAIN H AND RESID 155:172)
117X-RAY DIFFRACTION117(CHAIN H AND RESID 173:183)
118X-RAY DIFFRACTION118(CHAIN H AND RESID 184:189)
119X-RAY DIFFRACTION119(CHAIN H AND RESID 190:200)
120X-RAY DIFFRACTION120(CHAIN H AND RESID 201:205)
121X-RAY DIFFRACTION121(CHAIN I AND RESID 1:14)
122X-RAY DIFFRACTION122(CHAIN I AND RESID 15:22)
123X-RAY DIFFRACTION123(CHAIN I AND RESID 23:27)
124X-RAY DIFFRACTION124(CHAIN I AND RESID 28:54)
125X-RAY DIFFRACTION125(CHAIN I AND RESID 55:64)
126X-RAY DIFFRACTION126(CHAIN I AND RESID 65:72)
127X-RAY DIFFRACTION127(CHAIN I AND RESID 73:112)
128X-RAY DIFFRACTION128(CHAIN I AND RESID 113:117)
129X-RAY DIFFRACTION129(CHAIN I AND RESID 118:129)
130X-RAY DIFFRACTION130(CHAIN I AND RESID 130:135)
131X-RAY DIFFRACTION131(CHAIN I AND RESID 136:154)
132X-RAY DIFFRACTION132(CHAIN I AND RESID 155:160)
133X-RAY DIFFRACTION133(CHAIN I AND RESID 161:182)
134X-RAY DIFFRACTION134(CHAIN I AND RESID 183:190)
135X-RAY DIFFRACTION135(CHAIN I AND RESID 191:205)
136X-RAY DIFFRACTION136(CHAIN J AND RESID 1:12)
137X-RAY DIFFRACTION137(CHAIN J AND RESID 13:17)
138X-RAY DIFFRACTION138(CHAIN J AND RESID 18:25)
139X-RAY DIFFRACTION139(CHAIN J AND RESID 26:53)
140X-RAY DIFFRACTION140(CHAIN J AND RESID 54:60)
141X-RAY DIFFRACTION141(CHAIN J AND RESID 61:71)
142X-RAY DIFFRACTION142(CHAIN J AND RESID 72:76)
143X-RAY DIFFRACTION143(CHAIN J AND RESID 77:112)
144X-RAY DIFFRACTION144(CHAIN J AND RESID 113:117)
145X-RAY DIFFRACTION145(CHAIN J AND RESID 118:154)
146X-RAY DIFFRACTION146(CHAIN J AND RESID 155:160)
147X-RAY DIFFRACTION147(CHAIN J AND RESID 161:183)
148X-RAY DIFFRACTION148(CHAIN J AND RESID 184:190)
149X-RAY DIFFRACTION149(CHAIN J AND RESID 191:200)
150X-RAY DIFFRACTION150(CHAIN J AND RESID 201:205)

+
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