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- PDB-7rgt: The crystal structure of RocC, containing FinO domain, 1-126 -

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Basic information

Entry
Database: PDB / ID: 7rgt
TitleThe crystal structure of RocC, containing FinO domain, 1-126
ComponentsRepressor of competence, RNA Chaperone
KeywordsRNA BINDING PROTEIN / RNA chaperone / FinO / ProQ
Function / homologyRNA chaperone ProQ / RNA strand-exchange activity / ProQ/FinO domain superfamily / ProQ/FINO family / ProQ/FinO domain / ProQ/FINO family / RNA strand annealing activity / post-transcriptional regulation of gene expression / ProP effector
Function and homology information
Biological speciesLegionella pneumophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.02 Å
AuthorsKim, H.J. / Edwards, R.A. / Glover, J.N.M.
Funding support Canada, 1items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada) Canada
CitationJournal: Nat Commun / Year: 2022
Title: Structural basis for recognition of transcriptional terminator structures by ProQ/FinO domain RNA chaperones.
Authors: Kim, H.J. / Black, M. / Edwards, R.A. / Peillard-Fiorente, F. / Panigrahi, R. / Klingler, D. / Eidelpes, R. / Zeindl, R. / Peng, S. / Su, J. / Omar, A.R. / MacMillan, A.M. / Kreutz, C. / ...Authors: Kim, H.J. / Black, M. / Edwards, R.A. / Peillard-Fiorente, F. / Panigrahi, R. / Klingler, D. / Eidelpes, R. / Zeindl, R. / Peng, S. / Su, J. / Omar, A.R. / MacMillan, A.M. / Kreutz, C. / Tollinger, M. / Charpentier, X. / Attaiech, L. / Glover, J.N.M.
History
DepositionJul 15, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 9, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 30, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Apr 3, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Repressor of competence, RNA Chaperone
B: Repressor of competence, RNA Chaperone
C: Repressor of competence, RNA Chaperone
D: Repressor of competence, RNA Chaperone
E: Repressor of competence, RNA Chaperone
F: Repressor of competence, RNA Chaperone
G: Repressor of competence, RNA Chaperone
H: Repressor of competence, RNA Chaperone
I: Repressor of competence, RNA Chaperone
hetero molecules


Theoretical massNumber of molelcules
Total (without water)133,91318
Polymers133,0499
Non-polymers8659
Water8,701483
1
A: Repressor of competence, RNA Chaperone
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,8792
Polymers14,7831
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Repressor of competence, RNA Chaperone
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,8792
Polymers14,7831
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Repressor of competence, RNA Chaperone
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,8792
Polymers14,7831
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Repressor of competence, RNA Chaperone
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,9753
Polymers14,7831
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Repressor of competence, RNA Chaperone
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,8792
Polymers14,7831
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Repressor of competence, RNA Chaperone
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,8792
Polymers14,7831
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
G: Repressor of competence, RNA Chaperone
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,8792
Polymers14,7831
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
H: Repressor of competence, RNA Chaperone


Theoretical massNumber of molelcules
Total (without water)14,7831
Polymers14,7831
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
9
I: Repressor of competence, RNA Chaperone
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,8792
Polymers14,7831
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)139.010, 100.303, 110.718
Angle α, β, γ (deg.)90.000, 107.571, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 28 through 71 or resid 73 through 114 or resid 116 or resid 118 through 122))
d_2ens_1(chain "B" and (resid 28 through 71 or resid 73 through 114 or resid 116 or resid 118 through 122))
d_3ens_1(chain "C" and (resid 28 through 71 or resid 73 through 114 or resid 116 or resid 118 through 122))
d_4ens_1(chain "D" and (resid 28 through 71 or resid 73 through 114 or resid 116 or resid 118 through 122))
d_5ens_1(chain "E" and (resid 28 through 71 or resid 73 through 114 or resid 116 or resid 118 through 122))
d_6ens_1(chain "F" and (resid 28 through 71 or resid 73 through 114 or resid 116 or resid 118 through 122))
d_7ens_1(chain "G" and (resid 28 through 71 or resid 73 through 114 or resid 116 or resid 118 through 122))
d_8ens_1(chain "H" and (resid 28 through 71 or resid 73 through 114 or resid 116 or resid 118 through 122))
d_9ens_1(chain "I" and (resid 28 through 71 or resid 73 through 114 or resid 116 or resid 118 through 122))

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1ALALYSA10 - 53
d_12ens_1LYSGLUA55 - 96
d_13ens_1ALAALAA98
d_14ens_1METLYSA100 - 104
d_21ens_1ALALYSB21 - 64
d_22ens_1LYSGLUB67 - 108
d_23ens_1ALAALAB111
d_24ens_1METLYSB113 - 117
d_31ens_1ALALYSC7 - 50
d_32ens_1LYSGLUC53 - 94
d_33ens_1ALAALAC96
d_34ens_1METLYSC98 - 102
d_41ens_1ALALYSD11 - 54
d_42ens_1LYSGLUD57 - 98
d_43ens_1ALAALAD100
d_44ens_1METLYSD102 - 106
d_51ens_1ALALYSE7 - 50
d_52ens_1LYSGLUE53 - 94
d_53ens_1ALAALAE96
d_54ens_1METLYSE98 - 102
d_61ens_1ALALYSF5 - 48
d_62ens_1LYSGLUF51 - 92
d_63ens_1ALAALAF94
d_64ens_1METLYSF96 - 100
d_71ens_1ALALYSG26 - 69
d_72ens_1LYSGLUG73 - 114
d_73ens_1ALAALAG116
d_74ens_1METLYSG118 - 122
d_81ens_1ALALYSH7 - 50
d_82ens_1LYSGLUH52 - 93
d_83ens_1ALAALAH95
d_84ens_1METLYSH98 - 102
d_91ens_1ALALYSI1 - 44
d_92ens_1LYSGLUI47 - 88
d_93ens_1ALAALAI90
d_94ens_1METLYSI92 - 96

NCS oper:
IDCodeMatrixVector
1given(0.55948425896, 0.616819570711, -0.55363433886), (0.712209648999, -0.016114216141, 0.701781837832), (0.423951388545, -0.786939609644, -0.448320500228)18.5674097639, -0.588157672659, 35.4002971137
2given(-0.475171235363, 0.696522186676, -0.537651504742), (-0.71269802424, 0.0536774158972, 0.699414227241), (0.516017270378, 0.715524687548, 0.47090402226)10.6070156707, 37.0548152496, 27.1444725543
3given(0.49101794146, -0.715110037319, -0.497512829673), (-0.720454152401, -0.0122828779322, -0.693393787972), (0.489741968237, 0.698903974402, -0.521235109248)17.9684425401, 74.4317752421, 36.68368628
4given(0.509396006244, 0.73360177018, 0.449826801792), (0.682289208203, -0.0257622009707, -0.730628322317), (-0.524401702125, 0.67909112186, -0.513651733199)-24.7760840762, 13.2338230526, 27.9419508606
5given(0.544733608578, 0.761622287806, 0.350993997673), (0.641341079318, -0.108680071182, -0.759519757549), (-0.540321122727, 0.638842807617, -0.54766134745)8.85954540085, 38.297556593, 27.5292349351
6given(-0.0652114797726, -0.118097898805, -0.990858390086), (-0.12614529462, -0.984030233449, 0.125586083243), (-0.989866065461, 0.133181777872, 0.0492725734253)54.4430617645, -1.29986104266, 51.1746409709
7given(-0.11926769294, -0.128492040602, -0.984512576315), (0.16284329228, -0.980693885297, 0.10826617893), (-0.979416805849, -0.147408611833, 0.137889164103)56.8163926248, 15.9592823408, 85.5488394714
8given(0.34406593401, 0.729877812635, -0.590675047447), (0.792069894405, 0.112207624864, 0.600028942052), (0.504226055883, -0.674305440839, -0.539507420731)-10.4196958027, -25.7076068328, 34.6440023093

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Components

#1: Protein
Repressor of competence, RNA Chaperone


Mass: 14783.208 Da / Num. of mol.: 9 / Fragment: ProQ/FinO-domain, UNP residues 1-126
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila (bacteria) / Gene: C3926_00530, DIZ73_10055 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A128QHZ1
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 483 / Source method: isolated from a natural source / Formula: H2O
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: 2.77 Å3/Da / Density % sol: 55.52 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, hanging drop / pH: 7.3
Details: 0.2M Ammonium Sulfate, 0.1M HEPES:NaOH, pH 7.3, 20% PEG 3350 with various additives

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 1.03319 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jan 29, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03319 Å / Relative weight: 1
ReflectionResolution: 2.02→50 Å / Num. obs: 94465 / % possible obs: 99.7 % / Redundancy: 6.2 % / Biso Wilson estimate: 44.09 Å2 / CC1/2: 0.989 / Net I/σ(I): 17.4
Reflection shellResolution: 2.02→2.05 Å / Redundancy: 4.7 % / Num. unique obs: 4477 / CC1/2: 0.672 / % possible all: 95.6

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Processing

Software
NameVersionClassification
MxDCdata collection
HKL-2000data scaling
Cootmodel building
HKL-2000data processing
PHASERphasing
PHENIX1.18.2_3874refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: RocC(24-126)

Resolution: 2.02→45.3 Å / SU ML: 0.2254 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 24.2696
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2126 4642 4.92 %
Rwork0.1928 89766 -
obs0.1938 94408 99.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 66.76 Å2
Refinement stepCycle: LAST / Resolution: 2.02→45.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7607 0 45 483 8135
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0057806
X-RAY DIFFRACTIONf_angle_d0.707510492
X-RAY DIFFRACTIONf_chiral_restr0.04741190
X-RAY DIFFRACTIONf_plane_restr0.00471350
X-RAY DIFFRACTIONf_dihedral_angle_d13.98063050
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS0.681712718795
ens_1d_3AX-RAY DIFFRACTIONTorsion NCS0.575110915192
ens_1d_4AX-RAY DIFFRACTIONTorsion NCS0.720679609991
ens_1d_5AX-RAY DIFFRACTIONTorsion NCS0.812835330516
ens_1d_6AX-RAY DIFFRACTIONTorsion NCS0.652418941187
ens_1d_7AX-RAY DIFFRACTIONTorsion NCS0.874465057229
ens_1d_8AX-RAY DIFFRACTIONTorsion NCS0.921404550833
ens_1d_9AX-RAY DIFFRACTIONTorsion NCS0.989480621714
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.02-2.040.29871580.29062727X-RAY DIFFRACTION90.58
2.04-2.070.31381620.28762862X-RAY DIFFRACTION97.05
2.07-2.090.31081470.26782969X-RAY DIFFRACTION98.58
2.09-2.120.27661580.25032902X-RAY DIFFRACTION99.42
2.12-2.150.25091530.24953047X-RAY DIFFRACTION99.84
2.15-2.180.30621430.24012977X-RAY DIFFRACTION99.84
2.18-2.210.27551410.22223016X-RAY DIFFRACTION100
2.21-2.240.24771590.22092997X-RAY DIFFRACTION99.97
2.24-2.270.29991790.21752977X-RAY DIFFRACTION99.94
2.28-2.310.26461330.21583029X-RAY DIFFRACTION99.97
2.31-2.350.24031610.22082963X-RAY DIFFRACTION99.9
2.35-2.390.25711620.21533018X-RAY DIFFRACTION100
2.39-2.440.23191460.21033009X-RAY DIFFRACTION99.97
2.44-2.490.25241590.20772985X-RAY DIFFRACTION100
2.49-2.540.23931640.21062978X-RAY DIFFRACTION99.97
2.54-2.60.23561410.20823019X-RAY DIFFRACTION99.97
2.6-2.670.24391570.21313015X-RAY DIFFRACTION100
2.67-2.740.27161520.22352957X-RAY DIFFRACTION99.97
2.74-2.820.28831610.22453018X-RAY DIFFRACTION99.97
2.82-2.910.26151740.23672992X-RAY DIFFRACTION100
2.91-3.020.2891370.23223030X-RAY DIFFRACTION99.97
3.02-3.140.24261420.22133036X-RAY DIFFRACTION100
3.14-3.280.2751330.21673023X-RAY DIFFRACTION100
3.28-3.450.2041370.19553040X-RAY DIFFRACTION99.97
3.45-3.670.1861510.18322995X-RAY DIFFRACTION100
3.67-3.950.17311800.16063010X-RAY DIFFRACTION100
3.95-4.350.18191610.16033016X-RAY DIFFRACTION100
4.35-4.980.15511570.15273055X-RAY DIFFRACTION100
4.98-6.270.18221700.17963010X-RAY DIFFRACTION100
6.27-45.30.18561640.16973094X-RAY DIFFRACTION99.66
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)
17.51986316165-0.0194132529103-2.767784275638.27009176812-0.5666592696052.740169154670.1605042079940.297760872345-0.692986081268-0.204463402632-0.2629462059710.7131402702041.17332180962-0.1722611837880.03029183721640.8371791962850.152166696637-0.04963990888540.652794287177-0.1398004234280.48426989918925.1065334623-4.554013775398.85706867662
23.20893811193-0.820126993878-0.8773948228795.335315503983.687638227246.049719789770.3927448651030.546783975468-0.13148239009-0.778243193151-0.199119925817-0.4089136812320.0419480997310.0726077611153-0.2180096983460.3950839220810.1163797969030.02453256099580.354696793869-0.03766431128870.34130758660827.06094039657.7799570376410.674028816
35.51087489558-1.05531289443-1.924259830576.732280073374.162212828462.916188921380.3832188505980.83706568714-0.372645008839-0.604756401134-0.4939332766110.4182563969450.6930379927590.1075211534810.1810005838130.3925529793870.118839288061-0.05582652163970.379383224374-0.1220008218930.34478104499319.66483267140.99373564490510.9685386009
48.365934857845.291717117610.3640868999596.90441590346-3.16972910864.96282188470.1811071789130.0763422650169-0.776209002810.0151992565919-0.321104856773-0.5570700465190.5534521427490.7154178101370.208799347560.4395759900610.0770141518776-0.02936867171770.36101108752-0.05779545923990.39987123162423.7666926543.8265587929225.2957894044
58.60101084067-1.24414088561-3.114375636082.929445668724.406034391688.013848341080.3933138079720.2470663990710.237576456475-0.432751094716-0.132301108626-0.46759484766-0.4862162081570.0368423870304-0.2812253302830.3701145484630.03115597361930.02882570598050.256875261179-0.002152049940780.30636040703926.189463478716.478219798121.5111238579
65.978243179820.299101712585-0.5712550833713.49086027161-2.953528490892.53901270089-0.188727010533-0.323673878118-0.6352768393181.01232904390.4670294061782.02279179081-0.0963610259984-0.871952285971-0.231034473290.477023206496-0.07668557738930.0813501700870.5734690641120.01209810873070.62667776052114.84862776946.5390457997130.4218252366
79.09500542622-3.233782999740.9248259308437.79490056423-4.364927801176.4612055068-1.22862018374-0.107733250798-0.5135116095371.266976737361.121984719240.616468793164-0.266749084233-1.757642208030.01408325278571.08521606341-0.0366253896210.1497341264591.09474866941-0.310327374381.01958728033-12.189807268816.391962864745.3286093652
87.03173424914-1.541492021252.614342047275.887803315250.414811218779.378768743610.0742686367481-1.02949836578-0.2982227026230.783537461311-0.1046147465040.8538089826570.140026763302-0.7812367838160.06026217438480.693080538383-0.04383241146740.08740823245740.3841664489810.01946597447370.43894069676824.346781690723.426654360445.8613308788
98.328787657111.041526229021.905609068946.42120385321-0.5803600264767.275931373210.134455969392-0.7268497361080.712641992310.415437169133-0.06976170405260.0289680719189-1.390001996070.164053246952-0.08776776942390.478045919017-0.08051020938930.07474435196070.344293817670.002223657475010.41294384541130.700483943533.027132160833.7965926118
108.46194267245-0.02275103058491.886712754464.0673975173-3.905544771674.766759947750.177772597601-0.0523814136382-0.5491831809570.267164897938-0.233618403534-0.563258550851.245878946931.071310512090.1104724628720.5486090829110.0664316815607-0.01275628031750.3614270650650.01701825152520.42011039867834.90100321418.113535422138.5162637353
113.14893742563-1.17406397471.667373583953.63071474144-0.4405100536214.218361878140.1585780132230.09163213627140.1729630165360.0281918336483-0.1340730978380.04973112205270.001952760712910.141661160764-0.02825871277430.296724045095-0.01514129493420.06435562317450.215534429576-0.008887594647510.28372795044526.637006847128.443260528130.6125998781
124.09963492285-2.2621598696-3.992318765752.430364751022.284435783174.350174429770.3499734387140.778839407769-0.29550556469-0.960731355052-0.3374328635481.262019467030.322478804347-1.15022804765-0.03165939884680.495115012265-0.0293322618179-0.1104112088180.4758349594610.0288235632790.62442865027215.269046675730.598658521622.1507994494
134.121845004721.17640323321-0.8332944233183.098128184310.5226915353557.49243704887-0.06489181658020.756572085629-0.205517121034-0.407641569061-0.336047960550.4269414613930.177441463165-1.498641150330.2855031707750.405343866072-0.1225640359820.03278928217540.703071475958-0.2028087666870.465395961402-8.2790349956124.015065131946.5027930734
147.761747870083.629593488460.2988243543948.03646574069-0.5945374380315.071444026510.2846163217810.00219082132814-0.4336027794020.473183641329-0.1255970687791.048814678380.171419215552-1.04386000161-0.1130675205610.404624543863-0.09510548457920.06161213120340.63476512386-0.08649453396520.567750510251-8.0276721896430.319396290657.6066635942
158.612483929265.965017077316.710905372726.077481268577.488690453449.36435360370.3983582893830.30906681362-1.080860039070.2420649373940.274865815841-1.711542717860.636135953903-0.260937142501-0.595413839750.460669044138-0.1005675660610.05156731525880.591723691168-0.1329153020440.5330004151113.0464560772822.538328924745.9927823596
165.24908606556-3.7217318433-4.294876060727.648534794196.906510921429.268891863760.1502416460060.622636148542-0.21413448366-0.68186898325-0.465342033790.240736977995-0.669213614479-0.653379409610.2918824817070.413627978085-0.08102667499170.006665513547080.646912494352-0.1109988261160.370527269693-3.8753231599630.726315279742.9203115078
179.119665371-5.665021181866.426431164129.64462570854-7.54745011418.16977255697-0.4892572079020.573833005508-0.964451233202-0.1724785652770.6742734796510.25099611490.368777778023-1.09277377132-0.1333872859710.419513622313-0.1440921264540.05036949368070.621458677039-0.08781276589330.350875765113-11.646734770638.192297703654.0964970003
183.67524847995-0.873207628631-0.008565906806657.125948509131.137645996155.814265320740.0113159586941-0.3163776212130.02520540086820.4353708483220.250397375582-0.1342509056770.199895253563-0.188978941347-0.2387032007040.353012791086-0.1091871698470.02459885368430.417700774756-0.07698203955640.351667624507-1.9181219414934.164982206762.5238385195
194.24578812776-4.007573821724.938415239997.7701211379-4.222163245085.696918525950.5561238078980.3828412708761.11256084408-0.0921351189978-0.37369229732-0.429104542223-0.8235572158240.4486603093440.1257235664530.720728796029-0.007903343134740.2477348084630.5971881814930.0127012384440.603892447083-6.9398121843847.832137375454.5570889818
207.18904040568-3.347688920531.520770247993.67445341741-3.241760804498.446962418390.4857736185710.2419054232751.11621759603-1.6684560874-0.493647211714-0.561080447115-0.9073101393282.17320332339-0.05961862392680.775954279979-0.2731212821370.1828078997890.721394923088-0.1668169470991.0187756521729.54789954750.414757490140.399371775
217.962749869450.9209531234420.1741409587914.38742005232-1.266617729747.579762820520.0991956457381-0.587095793388-0.610385141767-0.1042859129860.292071646879-0.9647455609290.09463525628130.772265266949-0.4488658980670.354346273525-0.03667704218310.03627575749240.369835473979-0.09811123318790.55421292534518.024041148840.528867454847.8920242841
226.769707403821.74068287827-0.3102797358351.33722558696-1.330045311621.778300377130.0729295429272-0.7396222749951.344585158660.7543780997870.497176584205-1.3632328977-1.149319162730.957288809813-0.3705412108350.603681733346-0.127027430751-0.02731243430970.62368813693-0.3421887234811.1071522913922.919182467155.286099098452.0344804484
237.803345955176.58076053391.367384811996.372154709170.4285324099760.6938918536310.06781301640810.5887719093381.00016214358-1.802593618760.500545006695-1.42277188989-1.286404675230.835581991396-0.2094542088140.592380051343-0.2143832446060.2337012077510.423936891725-0.1185464108790.94704909838921.661858164152.920220947741.2746255248
249.687718464950.453177935041-2.847523596695.361952798461.219709197528.22553656703-0.047294643866-0.06388855436030.251738090566-0.858607052737-0.0449121522473-0.9612685087930.5325948159780.5406853341230.1082701319640.379799272380.02140614143920.1293714778070.299013107655-0.01204899197640.44355396443714.360593771539.785635322237.7464746101
259.453979306512.471273911761.114081623866.34504707816-1.045837058673.176185567890.0367876947821-0.5677870254690.0836056858133-0.000460418824141-0.0415492206467-0.2951016560460.0819368626852-0.21716162560.009764171727840.335660853194-0.001228056700780.01433611656870.403669446472-0.1092890636050.3696872361118.4453176989740.505774565449.7880468859
264.09712238333-4.50422181755-0.4081737377147.935663154233.209009328834.959218069390.8605255722431.167835857180.612679731231-1.52101506525-0.877377196983-0.0365885692388-1.9502182832-1.614324331460.03551619911730.831352794830.128445618737-0.09192768237280.5976363575910.01720442106330.5053824673035.2676771445442.670962914432.7131845722
271.31116523029-2.3408718537-1.209101498187.07783623914-0.9190287234525.95489288093-0.571192667364-0.9675299845761.21930599514-0.501085318751-0.2955711761711.06907359668-1.00992490623-1.814401828460.8544438754170.8601110482720.515255123493-0.1795492910131.04716212439-0.003548570015950.859059137978-9.5033748085224.73257660127.53143374395
287.42994155568-1.646459910890.7278953249886.57333008134-2.210553506953.186753720650.0918060650820.4312040674440.758725918222-0.146036409993-0.1374615111220.729002019203-1.18677404822-1.18137578890.02487767322760.5870169744540.279204778665-0.118199244770.701288268904-0.04390915602770.511940639138-3.4048651579321.994740486913.2567701865
296.236995256280.1189171136380.9884392986123.360330977940.7629249976176.1046110405-0.1169416537410.4856496597140.339284024771-0.1311880902270.01597569148270.263576945023-0.334002137553-0.2882115977180.1007207093680.3726510365410.0738309297381-0.0615910056190.3231145025510.0003626706540250.2547149004967.7319059033513.817318536211.6922834641
305.235474124835.51778429175.524562932528.094668657465.010277100116.009149022450.244746896573-0.295364543784-0.819543659330.17569467146-0.006273008529780.5369476718471.44718153221-1.29316172068-0.3512570650120.634219829211-0.140734880428-0.0009980250346950.695474141305-0.04095955547440.6328568247311.295910436440.8806820795369.19614144339
314.214243363691.23538800865-1.609018650125.11585338542-1.337495341258.241963925560.02659729622140.01146228248150.4458754424580.2171285418130.1675050045530.689680874949-1.11284942901-0.0656431180997-0.1747867944580.7270834059570.006178627195530.09645649466140.4443478803880.1689193903360.53798769999231.45574931847.384578526810.7262618359
325.9676712213-1.26501108682-1.58541916488.816182867570.3440201854945.4806652815-0.02107022089940.7570354847460.0848119478844-0.7562071735630.04352934095220.6587442922890.12250482294-0.942192974014-0.1448784208250.692360199806-0.01022766620320.05887580947340.6001996211170.1953830489720.57336025951627.020833149239.76835251119.15676257375
337.238929111361.790743853730.4630909364387.02169462241-1.0320829536.74673682497-0.379538841640.120593277681-1.19752085486-0.110225562667-0.0951581346714-0.6232388389261.66839010551.06101565790.4220180786251.021343676480.09373447299050.2724613464480.6264605628960.184369984410.57281195080339.455021711631.612167717610.6593143439
345.53881733984-3.64422018545-5.291136611288.29753293343.640571806975.158249922290.559690023198-0.3929463149231.736493222251.14343581817-0.164068693418-0.15188239306-0.9103132852011.13590341837-0.4728242825980.985461822917-0.0711818677647-0.0882343685040.69964938371-0.06949864748480.85019598272632.255051749129.474632945850.7424019812
358.165417735492.911675798130.301169219675.557581444982.220820733142.52135901229-0.07394207622950.04446102681661.49659828973-0.778208260916-0.498641852227-0.461139288501-0.9438239165250.8481717061470.5783848458040.6836340367880.000832549307754-0.05277765914820.8062474667420.2387304936160.8339005516245.28802028913.1636347929526.5410046367
366.318185699830.830679345396-0.9575457789018.43602372879-0.7913964192685.21888065887-0.06056956768740.3149313154650.0976583131663-0.798976692871-0.28220511716-0.7951504039810.5143948035781.076317232510.29735292760.4946532926390.1397444091310.03264702190660.5934397349470.1254651306730.38715627978241.7231651344-8.3277560829728.2619654541
376.73473378036-3.37609112622-0.7245939188037.18681423073-1.394445790999.44603135260.1018078739730.0944754799233-1.24327416599-0.799903177559-0.03907798086840.8894910362851.26201438589-0.0944882058954-0.05550639789220.616605768784-0.0142795884195-0.1307653515110.3673048487090.039149657750.55285562452528.9410017152-14.343344522828.7917765663
383.61509679795-3.622430336631.801307200094.44189186587-4.012221269197.03835878305-0.687233083554-1.65465539179-0.5495131510571.716885334421.619968244911.01792735424-0.71589848783-1.15157643463-0.8871458859610.7306440505470.04569299678690.08604671754161.044393843690.1516509094570.64974476794222.4334621836-5.8647713974938.9619982011
395.832654512965.237408289995.950330279856.286240070564.548018666676.507066508081.05041292784-0.4007274656471.229756721670.4538052226950.758692624061-1.19923834863-1.410513323671.319454677-1.749499281131.01098285562-0.4421821884940.2224791870630.894639080986-0.1434443914751.0373783341445.063803951224.06666660161.2590036595
402.06291501967-0.3235502372910.9546081902856.85052099155-0.5471474163748.04975462494-0.205369796497-0.6812973324240.1197601214170.5021337755680.264750295783-1.12435814694-0.1365323362191.47399654442-0.01343020413770.653554888084-0.032887128837-0.1126200807570.775009175174-0.03498163016580.6329564959542.172366692513.878586843359.2696586188
417.231092899683.18753031071.771082061097.406027557611.088073937215.48560417419-0.415557063764-0.3865019772281.259972298530.5218141032140.559219864489-0.674699226855-0.5574707817281.3970093555-0.1277601494330.774391508019-0.0708710682627-0.04212545255480.958522376422-0.2430990286530.68399264012138.519874767119.075823559766.8975615188
427.685211131671.124081357870.2084705130397.239051261932.308199293717.16863269156-0.00464380200697-1.202583152230.4033543060251.00579493222-0.0745304029320.52694186211-0.286759399306-0.2530138222360.1232044851220.6405252764890.07000927275260.06285195171290.5143279310210.02931952871760.37500802740127.560492062710.31371831366.7672295742
436.111362978211.92288908338-0.2907715881314.2727735015-0.1016050220226.188342363750.47501985507-1.81493848178-1.290633065470.610807430794-0.5067012784570.4861146710821.73954151892-1.67696838027-0.5379006934221.1377144195-0.431415202671-0.08899887801980.8668123177530.1425012512390.735405571059-4.353413848453.1325734674743.8814974867
448.246325230731.633029702233.689411934062.69892264009-1.900145401977.054841513220.710475739374-0.499431089206-0.4334037887850.312101137602-0.461206395980.7393383384550.937748510543-0.679722614407-0.3028561484370.483012506181-0.2530065483960.06045003446520.53822042094-0.1457503548930.487404735261-4.555859564959.140719301434.6995897636
457.376382748760.4763145250713.187163533793.83867759715-1.60993416332.256643150171.12093065846-1.05797011417-2.68824415460.2598660324590.288754755741-0.5374749976193.21349191637-0.503563878795-0.7063065212811.59134925433-0.153894501575-0.3805914524680.7059331466730.1271477584421.347761963651.77301998406-4.2059112098240.4217130004
460.8468572336620.488503212875-0.06008654051331.112494027511.241690772871.971638836260.828241047651-0.528516196462-2.574772600110.8854502253210.2021374371871.582665377131.64178468389-0.758491450713-0.6088904978421.30601221252-1.36702675036-0.296246740080.9037577376860.1756197580281.34005703598-9.16759676665-3.8050879359537.9339277728
472.155152565521.63113693089-3.621287134755.77518042467-2.132924513556.360513984530.6886307177890.501107618782-0.07339882911340.446645030116-0.3175772617930.7654932718140.723533518551-1.65850592738-0.3302234962750.604172295702-0.268489000132-0.09696011517121.14260624271-0.1096739399080.748257041601-11.711356050210.091414895826.5437200492
486.811236387240.003024071912321.191993039976.28310697507-1.581799749415.112010630110.5074887677920.241333978947-0.427875918707-0.15220380593-0.2741766585910.09758376199431.10082467689-0.210183998762-0.2244527397360.509957231144-0.0491800657495-0.01091294912510.601466868778-0.1571217210880.5019384016340.274432305418.4838945864626.8371750358
492.7583939232.10840832222-3.278704299434.11947119354-0.9013459794135.54168800921-0.6034163857151.601500860870.563301984113-0.5834507286360.5226289222421.132415713581.40551691388-1.37736385653-0.04579672615790.953800553289-0.33462733024-0.3790194804491.49037883258-0.1869639716891.03624225746-17.14613747615.8208599690719.847317119
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 19 through 35 )AA19 - 351 - 17
22chain 'A' and (resid 36 through 67 )AA36 - 6718 - 49
33chain 'A' and (resid 68 through 83 )AA68 - 8350 - 65
44chain 'A' and (resid 84 through 90 )AA84 - 9066 - 72
55chain 'A' and (resid 91 through 109 )AA91 - 10973 - 91
66chain 'A' and (resid 110 through 125 )AA110 - 12592 - 107
77chain 'B' and (resid -2 through 17 )BB-2 - 171 - 10
88chain 'B' and (resid 18 through 35 )BB18 - 3511 - 28
99chain 'B' and (resid 36 through 52 )BB36 - 5229 - 45
1010chain 'B' and (resid 53 through 67 )BB53 - 6746 - 60
1111chain 'B' and (resid 68 through 109 )BB68 - 10961 - 103
1212chain 'B' and (resid 110 through 123 )BB110 - 123104 - 118
1313chain 'C' and (resid 22 through 40 )CC22 - 401 - 19
1414chain 'C' and (resid 41 through 52 )CC41 - 5220 - 31
1515chain 'C' and (resid 53 through 67 )CC53 - 6732 - 46
1616chain 'C' and (resid 68 through 83 )CC68 - 8347 - 63
1717chain 'C' and (resid 84 through 90 )CC84 - 9064 - 70
1818chain 'C' and (resid 91 through 109 )CC91 - 10971 - 89
1919chain 'C' and (resid 110 through 123 )CC110 - 12390 - 103
2020chain 'D' and (resid 18 through 35 )DD18 - 351 - 18
2121chain 'D' and (resid 36 through 52 )DD36 - 5219 - 35
2222chain 'D' and (resid 53 through 67 )DD53 - 6736 - 50
2323chain 'D' and (resid 68 through 83 )DD68 - 8351 - 67
2424chain 'D' and (resid 84 through 90 )DD84 - 9068 - 74
2525chain 'D' and (resid 91 through 109 )DD91 - 10975 - 93
2626chain 'D' and (resid 110 through 125 )DD110 - 12594 - 109
2727chain 'E' and (resid 22 through 35 )EE22 - 351 - 14
2828chain 'E' and (resid 36 through 83 )EE36 - 8315 - 63
2929chain 'E' and (resid 84 through 109 )EE84 - 10964 - 89
3030chain 'E' and (resid 110 through 125 )EE110 - 12590 - 105
3131chain 'F' and (resid 24 through 67 )FF24 - 671 - 44
3232chain 'F' and (resid 68 through 90 )FF68 - 9045 - 68
3333chain 'F' and (resid 91 through 122 )FF91 - 12269 - 100
3434chain 'G' and (resid -3 through 15 )GG-3 - 151 - 13
3535chain 'G' and (resid 16 through 35 )GG16 - 3514 - 33
3636chain 'G' and (resid 36 through 83 )GG36 - 8334 - 83
3737chain 'G' and (resid 84 through 109 )GG84 - 10984 - 109
3838chain 'G' and (resid 110 through 125 )GG110 - 125110 - 125
3939chain 'H' and (resid 22 through 35 )HH22 - 351 - 14
4040chain 'H' and (resid 36 through 67 )HH36 - 6715 - 46
4141chain 'H' and (resid 68 through 90 )HH68 - 9047 - 69
4242chain 'H' and (resid 91 through 124 )HH91 - 12470 - 104
4343chain 'I' and (resid 28 through 35 )II28 - 351 - 8
4444chain 'I' and (resid 36 through 52 )II36 - 529 - 25
4545chain 'I' and (resid 53 through 67 )II53 - 6726 - 40
4646chain 'I' and (resid 68 through 83 )II68 - 8341 - 57
4747chain 'I' and (resid 84 through 95 )II84 - 9558 - 69
4848chain 'I' and (resid 96 through 109 )II96 - 10970 - 83
4949chain 'I' and (resid 110 through 122 )II110 - 12284 - 96

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  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
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  • 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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