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- PDB-8qtf: Crystal structure of a C-terminally truncated version of Arabidop... -

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Basic information

Entry
Database: PDB / ID: 8qtf
TitleCrystal structure of a C-terminally truncated version of Arabidopsis thaliana 14-3-3 omega in complex with a phosphopeptide from the transcription factor BZR1.
Components
  • 14-3-3-like protein GF14 omega
  • Protein BRASSINAZOLE-RESISTANT 1
KeywordsPROTEIN BINDING / 14-3-3 / brassinosteroid signaling / phosphopeptide / transcription factor / signal transduction
Function / homology
Function and homology information


brassinosteroid mediated signaling pathway / plant-type vacuole / Golgi apparatus / mitochondrion / nucleus / cytosol
Similarity search - Function
14-3-3 proteins signature 2. / 14-3-3 protein, conserved site / 14-3-3 proteins signature 1. / 14-3-3 protein / 14-3-3 homologues / 14-3-3 domain / 14-3-3 domain superfamily / 14-3-3 protein
Similarity search - Domain/homology
ACETATE ION / FORMIC ACID / 14-3-3-like protein GF14 omega
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsHothorn, M. / Obergfell, E.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Science Foundation310030_205201 Switzerland
CitationJournal: Plant Cell.Physiol. / Year: 2024
Title: Mechanistic insights into the function of 14-3-3 proteins as negative regulators of brassinosteroid signaling in Arabidopsis.
Authors: Obergfell, E. / Hohmann, U. / Moretti, A. / Chen, H. / Hothorn, M.
History
DepositionOct 12, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 22, 2023Provider: repository / Type: Initial release
Revision 1.1Jun 5, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 14-3-3-like protein GF14 omega
B: 14-3-3-like protein GF14 omega
C: 14-3-3-like protein GF14 omega
D: 14-3-3-like protein GF14 omega
E: 14-3-3-like protein GF14 omega
F: 14-3-3-like protein GF14 omega
G: 14-3-3-like protein GF14 omega
H: 14-3-3-like protein GF14 omega
I: 14-3-3-like protein GF14 omega
J: 14-3-3-like protein GF14 omega
K: Protein BRASSINAZOLE-RESISTANT 1
L: Protein BRASSINAZOLE-RESISTANT 1
M: Protein BRASSINAZOLE-RESISTANT 1
N: Protein BRASSINAZOLE-RESISTANT 1
O: Protein BRASSINAZOLE-RESISTANT 1
P: Protein BRASSINAZOLE-RESISTANT 1
Q: Protein BRASSINAZOLE-RESISTANT 1
R: Protein BRASSINAZOLE-RESISTANT 1
S: Protein BRASSINAZOLE-RESISTANT 1
T: Protein BRASSINAZOLE-RESISTANT 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)282,35046
Polymers281,24520
Non-polymers1,10526
Water15,781876
1
A: 14-3-3-like protein GF14 omega
B: 14-3-3-like protein GF14 omega
K: Protein BRASSINAZOLE-RESISTANT 1
L: Protein BRASSINAZOLE-RESISTANT 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,53411
Polymers56,2494
Non-polymers2857
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4950 Å2
ΔGint-52 kcal/mol
Surface area23000 Å2
MethodPISA
2
C: 14-3-3-like protein GF14 omega
D: 14-3-3-like protein GF14 omega
M: Protein BRASSINAZOLE-RESISTANT 1
N: Protein BRASSINAZOLE-RESISTANT 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,3186
Polymers56,2494
Non-polymers692
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4400 Å2
ΔGint-24 kcal/mol
Surface area22860 Å2
MethodPISA
3
E: 14-3-3-like protein GF14 omega
F: 14-3-3-like protein GF14 omega
O: Protein BRASSINAZOLE-RESISTANT 1
P: Protein BRASSINAZOLE-RESISTANT 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,4959
Polymers56,2494
Non-polymers2465
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4590 Å2
ΔGint-46 kcal/mol
Surface area23170 Å2
MethodPISA
4
G: 14-3-3-like protein GF14 omega
H: 14-3-3-like protein GF14 omega
Q: Protein BRASSINAZOLE-RESISTANT 1
R: Protein BRASSINAZOLE-RESISTANT 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,57712
Polymers56,2494
Non-polymers3288
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5530 Å2
ΔGint-57 kcal/mol
Surface area22860 Å2
MethodPISA
5
I: 14-3-3-like protein GF14 omega
J: 14-3-3-like protein GF14 omega
S: Protein BRASSINAZOLE-RESISTANT 1
T: Protein BRASSINAZOLE-RESISTANT 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,4268
Polymers56,2494
Non-polymers1774
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4900 Å2
ΔGint-31 kcal/mol
Surface area22430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.641, 71.917, 151.662
Angle α, β, γ (deg.)100.250, 94.840, 89.230
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

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Protein / Protein/peptide , 2 types, 20 molecules ABCDEFGHIJKLMNOPQRST

#1: Protein
14-3-3-like protein GF14 omega


Mass: 27299.682 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Strain: Col0 / Gene: GRF2 / Plasmid: pMH-HStrxT / Production host: Escherichia coli BL21 (bacteria) / Variant (production host): DE3 RIL / References: UniProt: Q01525
#2: Protein/peptide
Protein BRASSINAZOLE-RESISTANT 1


Mass: 824.797 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Strain: Col0 / Gene: BZR1 / Plasmid: pMH-HStrxT / Production host: Escherichia coli BL21 (bacteria) / Variant (production host): DE3 RIL

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Non-polymers , 7 types, 902 molecules

#3: Chemical
ChemComp-FMT / FORMIC ACID / Formic acid


Mass: 46.025 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: CH2O2
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Na
#6: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#7: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#8: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 876 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.56 Å3/Da / Density % sol: 51.9 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Morpheus (Molecular Dimensions) condition G8 with a final precipitant stock concentration of 50% v/v 12.5% w/v PEG 1000, 12.5% w/v PEG 3350, 12.5% v/v MPD ,0.02M of each carboxylic acid, 0.1M MOPS/HEPES-Na pH7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.999995 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Jun 10, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999995 Å / Relative weight: 1
ReflectionResolution: 1.9→59.91 Å / Num. obs: 227664 / % possible obs: 97.5 % / Observed criterion σ(I): -3 / Redundancy: 3.2 % / Biso Wilson estimate: 37.07 Å2 / CC1/2: 1 / Rrim(I) all: 0.095 / Net I/σ(I): 9.47
Reflection shellResolution: 1.9→2.02 Å / Redundancy: 3.4 % / Mean I/σ(I) obs: 0.75 / Num. unique obs: 36285 / CC1/2: 0.49 / Rrim(I) all: 2.11 / % possible all: 96.2

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→59.91 Å / SU ML: 0.3106 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 30.1693
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2303 11342 5 %
Rwork0.195 215319 -
obs0.1968 226661 97.08 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 55.81 Å2
Refinement stepCycle: LAST / Resolution: 1.9→59.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19146 0 66 876 20088
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005719572
X-RAY DIFFRACTIONf_angle_d0.642526392
X-RAY DIFFRACTIONf_chiral_restr0.03652914
X-RAY DIFFRACTIONf_plane_restr0.00593438
X-RAY DIFFRACTIONf_dihedral_angle_d12.70277376
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.920.46093590.44976706X-RAY DIFFRACTION90.69
1.92-1.950.45123670.42256974X-RAY DIFFRACTION94.38
1.95-1.970.39013710.39677069X-RAY DIFFRACTION95.49
1.97-1.990.37763730.37897127X-RAY DIFFRACTION96.03
1.99-2.020.39153720.3677038X-RAY DIFFRACTION96.02
2.02-2.050.38193790.34737201X-RAY DIFFRACTION96.5
2.05-2.080.33063710.32477038X-RAY DIFFRACTION96.63
2.08-2.110.33033800.30517240X-RAY DIFFRACTION96.52
2.11-2.140.3183720.29577057X-RAY DIFFRACTION96.81
2.14-2.180.30853800.29037224X-RAY DIFFRACTION96.5
2.18-2.210.30893710.27117071X-RAY DIFFRACTION96.78
2.21-2.250.28683800.25177189X-RAY DIFFRACTION97.01
2.25-2.30.27453790.23717169X-RAY DIFFRACTION96.88
2.3-2.340.26193780.22547178X-RAY DIFFRACTION96.87
2.34-2.40.27563810.2227211X-RAY DIFFRACTION97.16
2.4-2.450.24913780.21587175X-RAY DIFFRACTION97.53
2.45-2.510.26163790.20737199X-RAY DIFFRACTION97.74
2.51-2.580.23543820.19967255X-RAY DIFFRACTION97.67
2.58-2.660.2633850.20667292X-RAY DIFFRACTION97.91
2.66-2.740.2463780.20767193X-RAY DIFFRACTION97.84
2.74-2.840.25833820.21387239X-RAY DIFFRACTION97.97
2.84-2.950.2333810.19577235X-RAY DIFFRACTION98.25
2.95-3.090.23413840.19017284X-RAY DIFFRACTION98.22
3.09-3.250.23633840.19327299X-RAY DIFFRACTION98.27
3.25-3.450.22453820.18647251X-RAY DIFFRACTION98.58
3.45-3.720.21063840.16557288X-RAY DIFFRACTION98.7
3.72-4.10.18053830.14477293X-RAY DIFFRACTION98.59
4.1-4.690.16273840.13497281X-RAY DIFFRACTION98.5
4.69-5.910.19333830.16097288X-RAY DIFFRACTION98.21
5.91-59.910.1823800.15447255X-RAY DIFFRACTION98.28
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)
11.260770652130.3501852862360.058904390222.04817052769-0.3842144123920.983365677458-0.100679667322-0.06106231660310.1602417513650.1203480291070.1097224310750.3313120813590.18678464174-0.06338420850720.04062302278220.3091400443560.06096102847310.04437415408690.3496599300720.04162111210620.33878605292141.91304862350.129982242818.7745616727
22.18722241044-1.60063124292-0.1085199535113.13081815429-0.1599975668872.732184420370.0339061681224-0.720844261262-0.282711467132-0.0540122165392-0.00656720361256-0.2075177906560.187205664370.5727560407320.1740326291450.4186294908260.1010272460690.04533450950570.2778212134880.04268720963780.29935545283254.25762858938.30944459223.1966441368
31.90350528129-0.559782437572-0.8584585943762.3577172835-0.0787844951212.082478141770.1900759986920.248699210313-0.05002610017710.0446088617052-0.09373817015210.4286240530360.0931561182884-0.5349539682220.08065314314160.4211266655960.04778366443690.07889881832890.4379362052580.007555057527250.42169524335430.227834674434.115126423619.0841967699
42.55466302964-0.7029804666180.6646912685994.5704549323-0.2321002095250.9778297522920.2371543721440.03866070641050.194901507093-0.788659108131-0.0299314835020.229595552174-0.372543133437-0.470379963221-0.04481601326590.5732350253750.142458600628-0.006306735129560.6675373934540.04539802260440.38878029494629.862217416633.94919848494.27428825602
55.907562627221.63071507997-0.5208588501663.19287322012-0.9194707295433.79537206687-0.0665382637051-0.167293461401-0.1823864394310.135368132249-0.0421408948979-0.4582552058930.07043969019460.6320973531230.1667346332860.3531781588490.1857991747690.0508331122250.4364637611850.06500820587990.36895500362669.630194165446.362009335614.5551027025
60.9558741934170.89866925423-0.1350744082951.52295196354-0.4504855697441.8092440264-0.0897703125083-0.001270323803710.389270682037-0.2052300539870.0937047348668-0.06004779023450.1026679979960.07850747714550.1910037599720.283533989490.00573673753312-0.02410710184130.3826732183070.06236739158050.31470469478555.211139606760.13775622316.85869625928
71.893231605910.944736488723-0.3033438080581.81508653219-0.6097376574211.58140549503-0.0506145157046-0.1852831335750.285596784382-0.01074831321240.09869542690210.0625889163477-0.1066875983320.3030673060840.1745511457030.2423261493010.0161007763172-0.06249359493640.4076836528640.03030252994620.31611761049362.315313754864.8799299049.33904798003
83.187979417981.177228215890.2220184953631.44599519848-0.6086920925612.4844329462-0.1769674523650.442782110556-0.016068432632-0.4434474205620.195780169929-0.0117954059462-0.0160810121605-0.0576807654133-0.02741704160580.353793158221-0.0773595074953-0.009631837812590.472591839140.03353775477150.30756962384968.489138146464.7722757138-8.34282952832
92.577639069750.231624518041-0.1167648489381.63421473523-0.4466039773290.9998806255510.03525371718560.665369689314-1.0460567787-0.7071911937550.1010724030310.3849251666220.784919900381-0.15973031144-0.2982661221770.62309563294-0.175221323611-0.03015711331360.632861557576-0.08541125400250.47874081637859.968469376357.1997951241-13.980500902
102.018951954881.1077881957-0.6330559264534.41124249326-0.4349295220141.77291987918-0.05247546349350.123662282188-0.551367276066-0.00568573835170.0553730343192-0.4391652170630.2093445319840.3584091864730.2391572398570.282631279453-0.000846693205152-0.03254159552510.39255529686-0.0571378281740.40915049755230.640343311410.9621286758-4.36575827393
111.849455280630.826521103532-0.6930759263852.01516141877-0.489609025761.07011225891-0.1580632301290.5068131999260.147216603513-0.256273872560.3207333912170.301937858701-0.150787609724-0.276164629547-0.1722920143210.31198945676-0.0410571573111-0.04771213406720.4295551765390.02948843806380.31298943023611.757628140417.9167208979-14.7520604507
122.70515668696-1.000837843551.425353036973.19921072777-1.451581851712.51141049943-0.1024270344230.0715972425332-0.0492944310836-0.1693111194320.247177392216-0.03203846777430.228897238836-0.462874143373-0.35122763730.247457667965-0.00553255036692-0.04122243969490.327316685874-0.01024771852210.3599952502312.47688307046.98682888205-1.9780889512
131.812065348880.983512254775-0.09332197405713.03764442049-0.3847628100821.025196640090.0894428440457-0.04449938726310.205808907740.3092849346140.195116276240.328297736991-0.404985804041-0.80911239176-0.05541023156170.3405015352410.09317891975940.04482491466250.4084926393570.01734864888370.3563681946673.0759316209211.95572511145.52429145572
142.249901442520.329242164928-1.001633507942.16712340802-1.27236276331.072240328730.692087346654-0.129411149990.9425072411591.03902651839-0.424743971264-0.325822648252-0.8082948140650.156961780368-0.05319338882640.9815808122060.1057456787250.08799811094860.400238453792-0.07123739793520.5996166265128.3138144280223.595699442811.3003097363
150.9264312440340.559630684288-1.229579211551.22119483106-1.234917697771.78965844371-0.2622257389310.877335387660.309946803792-0.3984858682290.3949993896930.272579073945-0.216975470013-0.197505281917-0.05487690524180.503569628647-0.189330314233-0.09827463842370.7737522469180.1758765963390.41505574088217.919434512530.9705193384-30.1290912585
161.498377262530.403222602393-0.7977605873271.55758647768-0.1617907956281.89952468423-0.03601561195850.3401388293020.106339590191-0.1230859847050.0847640975817-0.0730912800352-0.08587897237150.227136656338-0.21030264930.337618727425-0.138549920357-0.009623541815880.477586789067-0.01202301781610.32350897736135.654947282827.5529136427-15.8082432887
171.42986410296-0.9592145307410.3621256142487.213569876570.8674095489260.41765292220.6351089580520.467680410802-0.2152336639950.597088883617-0.363431407018-0.4826885781120.0995488427034-0.761991629521-0.3613393990610.883177573342-0.268687206544-0.08962592320821.046754704260.3249167009240.46433987695929.165860530340.8070099467-38.4492060436
182.50230072961.29972003296-0.2222860079272.57864532299-0.3994831280812.232867573250.06305790169790.08360422765130.4900625945710.1141082393270.04121968853730.165743054487-0.46106641920.06408230715650.2282064205430.572604668224-0.1981267528690.03880107633470.6158950984440.1157230842080.46395775991236.817435350847.562014173-22.6535702263
195.167220063981.582802788730.6256556254718.37991225746-2.034922753556.231077651740.117933977825-0.3058304578420.7336186242550.591817575748-0.04940711574970.999018022737-0.575547053294-0.957706273260.1183919460610.87785114571-0.05566204568790.2348444547150.813009055318-0.0761891322330.71109701070528.00943859752.5537829913-12.4940361962
201.786014399910.819845567658-0.3946132765551.97688449273-0.07917982050291.220761092990.210319755844-0.2415546544180.08476522317720.355886754511-0.1890457492050.0528011093457-0.05048683748730.0163102156019-0.0650252153860.455276796927-0.05492774545360.006622462385270.314940973873-0.01999078882320.32651412853230.949234140213.360924418462.8840119124
212.590546819730.776316757968-1.006631557882.50277550693-0.8302493281062.462314183260.04306427899150.2073042920760.295040734727-0.05401549518320.05230908531540.497908168782-0.346860794851-0.284906767164-0.03773026640890.337502975890.00546991892217-0.01148837778590.2259327857740.0007323721176690.38596552027833.667552021624.783319362846.4934661328
227.01321196285-0.448978746294-0.5348395339194.96068303237-1.34906001820.4323245062150.450355891087-1.66680961157-0.04164107968311.24998416597-0.541728002012-0.1418706587450.202772172948-0.139534470893-0.09023415575270.642845306559-0.1704265451630.1900961002950.453830460712-0.1362349161090.34442552862816.071846287319.807229057382.7063842276
230.2193062424230.393808376737-0.4237471331370.3242855318770.181741375004-0.04616397027850.222122778292-0.08847232395780.03020631526880.251390528395-0.0566782427390.1383521010530.00337256976457-0.007372315911150.07404607506290.520019266629-0.09397881377820.09035974928340.371906308102-0.03885401344380.3408591623315.45020112224.2543782129772.6104023862
240.5799201817490.1221734719250.1342867311880.215368274365-0.1777416150820.1427917024-0.0919940255995-0.43984195641-0.436479392190.292340691709-0.09342628934630.003476740502880.4503408532230.35086530760.0009658934545550.55066823331-0.09945735133240.002031060113420.3823788011640.03431151835530.37222815604422.3725000519-7.1024833217369.4776805703
250.9990747858090.673400764275-0.2755161891370.700606885042-0.1860867655450.1281967115340.156275598419-0.165301993547-0.08098307945270.1192576348820.0151889772860.09655116049750.0973067759086-0.09400704711140.06712646835330.553385844239-0.1666421546980.1309698956880.5212481575810.02796597380470.3865352694292.17908971714-4.4153794231877.4085252423
260.1359286234430.026654785303-0.01972398018340.0151298310569-0.09739511902060.2526817957990.07888260332970.00366012333171-0.535596485560.0217067437413-0.1448195432720.6592199317260.579732495075-0.4082961614650.009519661678610.568307532619-0.2163085662080.03314898816370.7622137809530.01049745817090.60333245444-8.31292237981-7.6212401089567.022011808
270.005940839867660.00138147627489-0.004957329235120.03628614558670.000870195621630.001816037731180.08395460423070.0364065095084-0.174924308261-0.00769872336377-0.01604572635550.0800874538677-0.3757989361550.314037214008-3.29833655347E-51.073555435020.066043955329-0.07406157814611.08525331417-0.1686716626111.61543236978-17.70292237569.7730265139472.0495413576
280.07213071115920.0534676841561-0.06503373324230.0585388780523-0.05038781861340.03710913350350.01755486809650.1631374955270.414321648329-0.0814918029233-0.2562432879330.0333780523691-0.576380021017-0.109283324876-5.77432148945E-50.785979541468-0.0448156358044-0.06349097983140.7784884836480.2006039000310.61787580564-6.140182448773.8031616285863.6268271787
290.3960100304320.251089288024-0.2072169642680.2127352304490.03223185193410.3552317145530.06103364158430.3318687249090.259582700130.1417664265180.1955739593110.116082309367-0.076562883424-0.140437795599-0.2016540825610.2768256645130.0773202818590.04638328451360.3455261275090.1036236058690.54985627309-13.1407271709-6.9709194351231.8087133562
300.960460346880.0134989574459-0.7269830657660.512553475235-0.4606986301210.7160641629280.06571075894360.06408083085340.2022700656850.179817003269-0.09570690700060.120262072526-0.05469475734730.312351394365-0.01345902805360.325962458490.04862140029680.007714683934090.3595385196820.03879880350080.3753385899633.33941752481-11.532483485934.4850251021
310.5799728145730.304628626688-0.5640979731221.036528860280.0470243971080.874184623394-0.06769669909740.128728283748-0.171477284973-0.495386781042-0.002006258764480.0761503419250.3031107139560.1249537875810.01373940196060.3177395275550.07239940526610.006988963930470.310491408019-0.0001049736433790.3875560715316.17234586668-16.445171882227.276806624
320.862229127069-0.06797062317870.06233043269520.269913358535-0.2692420150640.696802580277-0.09935730847610.1609783823330.1757329693090.0143721885574-0.000188598295657-0.0370258154777-0.3030892330810.2711079530793.42962457374E-60.368928561798-0.0549936760656-0.02936225357080.3614896113340.008463821344790.39607058537612.4829091246-0.42847757950831.3818495135
330.9730169368610.028327113854-0.6325498840460.747618627312-0.134745739871.47727416739-0.367247135824-0.1255159500480.1334224422370.754675134016-0.08602122428660.075187372568-0.7693264310280.315114494709-0.3877893670040.692521290462-0.069162800575-0.06773991905190.399826863629-0.1242249674890.41750939847214.05772428015.8200501232246.5286760418
340.7157340723660.2285240539090.4866455518440.09983708180930.1884687631380.451900228069-0.420473697328-0.109049294908-0.318739104935-0.2862345642920.0246649346762-0.4019740626370.5148374159360.161518777856-0.4045606074560.5982008011710.1302558558880.2232687820230.3155811009960.08567938825530.5628352940610.59599945745-34.56002239237.2037098997
350.7685346571960.27540453588-0.6681102133390.779517802937-0.5882655405820.0808494566097-0.156167152532-0.411227022777-0.2000717313260.04314300569910.06037119945640.1762050001230.2517629715380.0674499800394-0.00161952353240.432474358860.04740711429940.07978423341760.2363515469220.005630429304490.4062908123-12.2019134698-27.33628794544.022695735
360.8860547715650.521906795453-0.01202177196740.528339611094-0.008843227853240.5951318619520.1316098781290.09192463726370.0772547898729-0.289535662628-0.2099300665290.5166711419420.197380478281-0.1672050607410.006150681578490.3974090190280.03116851496340.03634973166260.265179693304-0.03586486887480.40171656905-20.9612407837-21.249044666237.4359512595
371.301593831360.9110581930480.1782197715691.92872444463-0.8282672895761.00594471970.226336719105-0.394258669867-0.108417014310.124007926317-0.2230662388440.01699421669130.245246874309-0.236276349941-0.01162422992090.498600943629-0.09983255266340.008311185268510.331111065386-0.002746948256370.31869200093-19.2450670063-36.887215052154.6743412315
380.0040496296186-0.007569420155710.0007458192190530.00578638463950.002391398589950.00966954318084-0.1379702336860.0163815651683-0.0976524143007-0.1189892502920.126083162973-0.217112441849-0.0405029693615-0.0437814103928-5.9552130652E-51.594660462140.040119887318-0.4141067191420.8498953411730.1695746233251.1257834032-4.55085699079-42.078046874171.4204891582
390.3333057577450.389127635358-0.3106272910940.572705493503-0.4870195686630.5297820175950.582012410677-0.791412739055-0.009472825743760.640871530263-0.372269902821-0.28655849603-0.7080827888270.7045832151590.2158865109410.633039267232-0.258399515819-0.195003114640.6789991760310.05504417692110.458085315919-9.32087893605-29.729123221265.1520206082
400.547521872489-0.140771601740.1742740565510.0495220138658-0.1275344673990.09723912264640.1422664502450.08730794501350.07765149872170.2188603702730.1462651411820.141056879973-0.445125176707-0.3183108809650.09256981033810.853558169895-0.2006235228510.1437594999450.6016472384860.01535416797610.347065684517-1.314001618976.00549920243-39.5710059361
41-0.1496029903880.6691530783360.1920178178360.202239970547-0.1688824550020.1012271675970.1352087950770.0231225563198-0.03430694859170.124577174188-0.01104578537830.00772376569793-0.118471372354-0.1212737658990.04805342984720.690268488843-0.2352853792750.05877803443020.6150284011990.03441759553620.3347126670590.340347861907-0.899136980154-55.9516901727
420.5102979153170.202550989102-0.06605526648010.2352894127060.2350118746290.3936244240150.03599456829690.2095847509830.297218351012-0.1317261061620.112092163050.165857147346-0.341762318318-0.2779459382590.02553346946120.738885649112-0.2021485651050.08445663226230.660890658090.1143776619150.414620055735-5.012358992094.00557182051-60.7619561756
430.6322326949640.0324384681469-0.229893106350.864071105576-0.6159167776840.2921465262250.06666480738730.185955030060.07440264646650.0549718766871-0.0161035049893-0.0424306508213-0.101796617202-0.0214111513103-4.57452674047E-60.633853893735-0.2337416725830.07923787425340.5155616270160.01860618216970.36129590183212.39165183256.60534624383-61.429804318
440.450274939444-0.1088512105240.01785610975240.4758763401030.2037154329390.103218455589-0.1634954297440.420502356515-0.3351766663180.2579168000370.0399262145657-0.466823709312-0.362540196450.4775734011130.0006012598316850.681448410514-0.1667120438770.0480674227470.5221998091650.02363725806020.60870776555923.6256864745-5.04119031687-57.7001341397
450.7705534360140.588202229229-0.4029763347320.7346326924830.27834900190.5378392577850.03833856086330.08760522344340.0007948002155970.07995565097020.1085497881290.106731642116-0.165296536332-0.277340005770.001969972497620.498961096898-0.1838706230030.005596358873240.6577818601190.1092727599650.336369089304-17.2046287158-13.1920062488-43.5019456499
460.8288696742090.403885271467-0.0425403882420.641546078496-0.1016613687430.7961127180780.06864012041060.0677454361499-0.1477786317940.23074567581-0.0541161169477-0.1545887114260.168375999512-0.02728574331726.62579439376E-60.485297611218-0.193311757298-0.01769336577170.7232320510230.1318562471110.462499332126-14.5278672278-32.5189706258-36.8063686509
470.7060743568991.907384467560.884184313125.752230113032.451519372021.099278514860.1226795362210.7516037690620.316662449957-1.032033128880.481240546561-0.2528945209850.010135010701-0.402785360863-0.1979983330820.5100009840020.02865162469560.00849788365420.4266772900530.007807101989660.41164281008338.937735411235.36865119859.86376379469
481.877911854841.91021794071-1.349211172232.1159174324-0.6842981679243.76863657888-0.382143756650.5599152930960.151995055525-0.670842317476-0.2047573126640.9765845915740.35710958446-0.385175299553-0.2352009112760.377837548951-0.0858076217716-0.06595712653570.609040671231-0.01489223319850.5076975181857.160105107760.1850991672-4.59123773431
491.14988090181-2.398668177451.515448542555.57865305949-3.397755416913.390728161420.564148760842-0.06491736943221.07951415620.0261281284626-0.377658470764-0.0565310832356-0.993949983367-0.157077859149-0.1656410207820.4592145302770.1620820802990.0339079837820.4353188669190.006147473926370.4782610108118.0153389762822.1014270522-0.885726753629
503.679678957325.276304572262.899617188838.175512942846.159274648748.840735352290.451088023127-0.716659646036-0.6354958103190.3056424900090.151952359285-0.2898842634070.2412360993690.143001425899-0.2619205544390.556874003273-0.1669511737070.0573168992050.7765832895790.2156638489740.58285972631532.619524256442.6027308915-12.486834579
510.893484572184-0.0872748668063-0.842640440280.1614553091510.1631194169621.14696683446-0.01111690284670.2001960677620.519855668524-0.218760719029-0.06675176293431.19737164526-0.151055697565-0.6690647778650.1803762259130.566124062374-0.0464302240250.01634045747860.469773253835-0.04457033348520.59257547038524.431521905223.650318498852.072085893
520.79318645124-0.1735730640350.7718663691160.4713480599890.07603321355230.8889963083340.5934519924890.2306670222670.410902668317-0.548401519380.482637155960.317727497752-0.0004726319454750.03640869886540.1294119468540.63113259579-0.1234279073480.1355478711920.5043294518540.07947240576880.477426480473.79249401237-0.41100716647564.079671656
530.02223554756770.01575912200090.01666520054470.036966756660.003646082084910.01777440551870.346359327261-0.514110266823-0.08846643276610.50758103957-0.3445111535080.1404307394190.07034327994090.637962534037-6.53304780483E-50.392813747633-0.0474774024834-0.02462523532210.452657882976-0.04765591009050.43344143496511.0447158555-6.7502806071242.7532188534
540.541210856239-0.309372418626-0.4962176261071.71333845353-1.06161756391.60000362248-0.0870854424178-0.2868954184460.197380393341-0.115539163258-0.786105419439-0.194207252069-0.552677395255-0.0806100144298-0.3073132385840.398043065633-0.101707060832-0.08148870952340.322412422869-0.07593417966770.415949136644-13.8846379474-25.266003019255.9391696367
550.0834916476018-0.03896165509050.06391028594770.0190200803033-0.002603816909730.0686512251706-0.300697058393-0.579826191402-0.50880494574-0.0742010872239-0.098508005484-0.262618931850.2685458977020.22733549541-0.002239584829370.663706972945-0.180000503120.171305523040.4720466829160.01639403144050.55794377024110.418418751-5.82622431096-59.0730263379
560.9851817047610.07900234608870.5560573385840.1834498385110.1885452086170.433082778255-0.3764425450720.136787497582-0.101672263022-0.343994682040.0619169271795-0.3563489416990.1450151928360.181304940555-0.06360110522370.496494721278-0.293232592124-0.06426901112110.6902620516010.1213495787840.568667742234-7.6980008515-23.7588779823-38.1350487095
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 4 through 75 )AA4 - 751 - 72
22chain 'A' and (resid 76 through 109 )AA76 - 10973 - 106
33chain 'A' and (resid 110 through 237 )AA110 - 237107 - 241
44chain 'B' and (resid -1 through 41 )BG-1 - 411 - 43
55chain 'B' and (resid 42 through 76 )BG42 - 7644 - 78
66chain 'B' and (resid 77 through 109 )BG77 - 10979 - 111
77chain 'B' and (resid 110 through 140 )BG110 - 140112 - 142
88chain 'B' and (resid 141 through 190 )BG141 - 190143 - 192
99chain 'B' and (resid 191 through 208 )BG191 - 208193 - 210
1010chain 'B' and (resid 209 through 235 )BG209 - 235211 - 237
1111chain 'B' and (resid 236 through 236 )BG236238 - 245
1212chain 'C' and (resid 3 through 76 )CL3 - 761 - 74
1313chain 'C' and (resid 77 through 117 )CL77 - 11775 - 115
1414chain 'C' and (resid 118 through 165 )CL118 - 165116 - 163
1515chain 'C' and (resid 166 through 236 )CL166 - 236164 - 241
1616chain 'D' and (resid 4 through 117 )DP4 - 1171 - 114
1717chain 'D' and (resid 118 through 165 )DP118 - 165115 - 162
1818chain 'D' and (resid 166 through 190 )DP166 - 190163 - 187
1919chain 'D' and (resid 191 through 236 )DP191 - 236188 - 240
2020chain 'E' and (resid 4 through 41 )ER4 - 411 - 38
2121chain 'E' and (resid 42 through 76 )ER42 - 7639 - 73
2222chain 'E' and (resid 77 through 117 )ER77 - 11774 - 114
2323chain 'E' and (resid 118 through 165 )ER118 - 165115 - 162
2424chain 'E' and (resid 166 through 236 )ER166 - 236163 - 240
2525chain 'F' and (resid 1 through 18 )FX1 - 181 - 18
2626chain 'F' and (resid 19 through 76 )FX19 - 7619 - 76
2727chain 'F' and (resid 77 through 117 )FX77 - 11777 - 117
2828chain 'F' and (resid 118 through 206 )FX118 - 206118 - 206
2929chain 'F' and (resid 207 through 236 )FX207 - 236207 - 243
3030chain 'G' and (resid 1 through 17 )GM1 - 171 - 17
3131chain 'G' and (resid 18 through 34 )GM18 - 3418 - 34
3232chain 'G' and (resid 35 through 76 )GM35 - 7635 - 76
3333chain 'G' and (resid 77 through 117 )GM77 - 11777 - 117
3434chain 'G' and (resid 118 through 140 )GM118 - 140118 - 140
3535chain 'G' and (resid 141 through 165 )GM141 - 165141 - 165
3636chain 'G' and (resid 166 through 190 )GM166 - 190166 - 190
3737chain 'G' and (resid 191 through 214 )GM191 - 214191 - 214
3838chain 'G' and (resid 215 through 237 )GM215 - 237215 - 244
3939chain 'H' and (resid 4 through 75 )HO4 - 751 - 72
4040chain 'H' and (resid 76 through 109 )HO76 - 10973 - 106
4141chain 'H' and (resid 110 through 190 )HO110 - 190107 - 187
4242chain 'H' and (resid 191 through 236 )HO191 - 236188 - 240
4343chain 'I' and (resid 3 through 140 )IQ3 - 1401 - 138
4444chain 'I' and (resid 141 through 237 )IQ141 - 237139 - 242
4545chain 'J' and (resid 4 through 41 )JS4 - 411 - 38
4646chain 'J' and (resid 42 through 76 )JS42 - 7639 - 73
4747chain 'J' and (resid 77 through 109 )JS77 - 10974 - 106
4848chain 'J' and (resid 110 through 117 )JS110 - 117107 - 114
4949chain 'J' and (resid 118 through 190 )JS118 - 190115 - 187
5050chain 'J' and (resid 191 through 207 )JS191 - 207188 - 204
5151chain 'J' and (resid 208 through 214 )JS208 - 214205 - 211
5252chain 'J' and (resid 215 through 236 )JS215 - 236212 - 240

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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

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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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