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- PDB-5jjk: Rho transcription termination factor bound to rA7 and 6 ADP-BeF3 ... -

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Basic information

Entry
Database: PDB / ID: 5jjk
TitleRho transcription termination factor bound to rA7 and 6 ADP-BeF3 molecules
Components
  • Transcription termination factor Rho
  • rA12: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*A)-3')
KeywordsTRANSCRIPTION/RNA / protein-RNA complex / TRANSCRIPTION-RNA complex
Function / homology
Function and homology information


ATP-dependent activity, acting on RNA / helicase activity / DNA-templated transcription termination / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / hydrolase activity / RNA binding / ATP binding / membrane / identical protein binding / cytosol
Similarity search - Function
Transcription termination factor Rho / Rho termination factor, N-terminal / Rho termination factor, RNA-binding domain / Transcription termination factor Rho, ATP binding domain / Rho termination factor, RNA-binding domain / Rho termination factor, N-terminal domain / Rho RNA-binding domain profile. / Rho termination factor, N-terminal domain / Rho termination factor, N-terminal domain superfamily / Cold shock domain ...Transcription termination factor Rho / Rho termination factor, N-terminal / Rho termination factor, RNA-binding domain / Transcription termination factor Rho, ATP binding domain / Rho termination factor, RNA-binding domain / Rho termination factor, N-terminal domain / Rho RNA-binding domain profile. / Rho termination factor, N-terminal domain / Rho termination factor, N-terminal domain superfamily / Cold shock domain / Cold shock protein domain / ATPase, F1/V1/A1 complex, alpha/beta subunit, nucleotide-binding domain / ATP synthase alpha/beta family, nucleotide-binding domain / Nucleic acid-binding proteins / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / P-loop containing nucleotide triphosphate hydrolases / Nucleic acid-binding, OB-fold / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Beta Barrel / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / BERYLLIUM TRIFLUORIDE ION / RNA / RNA (> 10) / Transcription termination factor Rho / Transcription termination factor Rho
Similarity search - Component
Biological speciesEscherichia coli O157:H7 (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.15 Å
AuthorsThomsen, N.D. / Lawson, M.R. / Witkowsky, L.B. / Qu, S. / Berger, J.M.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM071747 United States
G. Harold and Leila Y. Mathers Foundation United States
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2016
Title: Molecular mechanisms of substrate-controlled ring dynamics and substepping in a nucleic acid-dependent hexameric motor.
Authors: Thomsen, N.D. / Lawson, M.R. / Witkowsky, L.B. / Qu, S. / Berger, J.M.
History
DepositionApr 24, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 16, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 21, 2016Group: Structure summary
Revision 1.2Dec 28, 2016Group: Database references
Revision 1.3Sep 13, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Revision 1.6Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.7Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Transcription termination factor Rho
B: Transcription termination factor Rho
C: Transcription termination factor Rho
D: Transcription termination factor Rho
E: Transcription termination factor Rho
F: Transcription termination factor Rho
G: rA12: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)294,70825
Polymers291,6037
Non-polymers3,10518
Water34219
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)68.760, 199.210, 112.200
Angle α, β, γ (deg.)90.000, 104.830, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein / RNA chain , 2 types, 7 molecules ABCDEFG

#1: Protein
Transcription termination factor Rho / ATP-dependent helicase Rho


Mass: 47949.500 Da / Num. of mol.: 6 / Mutation: N-terminal MGH insertion
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli O157:H7 (bacteria) / Gene: rho, Z5293, ECs4716 / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) pLysS
References: UniProt: P0AG32, UniProt: P0AG30*PLUS, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement
#2: RNA chain rA12: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*A)-3')


Mass: 3905.512 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 4 types, 37 molecules

#3: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#5: Chemical
ChemComp-BEF / BERYLLIUM TRIFLUORIDE ION


Mass: 66.007 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: BeF3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 19 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 2.58 Å3/Da / Density % sol: 52.36 %
Crystal growTemperature: 291 K / Method: microbatch / pH: 7.5 / Details: 200 mM KOAc, 40% MPD, 0.5% ethyl acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.116 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 11, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.116 Å / Relative weight: 1
ReflectionResolution: 3.15→49.803 Å / Num. obs: 49848 / % possible obs: 99 % / Observed criterion σ(I): -3 / Redundancy: 2.9 % / Biso Wilson estimate: 65.04 Å2 / Rmerge(I) obs: 0.121 / Net I/σ(I): 9.4
Reflection shellResolution: 3.15→3.26 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.6 / Mean I/σ(I) obs: 2 / % possible all: 99.5

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.2data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5JJI

5jji


Resolution: 3.15→49.803 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 27.7
RfactorNum. reflection% reflectionSelection details
Rfree0.2649 2514 5.04 %Random
Rwork0.2334 ---
obs0.235 49847 98.96 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 205.92 Å2 / Biso mean: 80.4692 Å2 / Biso min: 21.17 Å2
Refinement stepCycle: final / Resolution: 3.15→49.803 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18696 155 192 19 19062
Biso mean--69.91 64.5 -
Num. residues----2385
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00919380
X-RAY DIFFRACTIONf_angle_d0.5626134
X-RAY DIFFRACTIONf_chiral_restr0.042984
X-RAY DIFFRACTIONf_plane_restr0.0033334
X-RAY DIFFRACTIONf_dihedral_angle_d18.52211900
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 18

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.15-3.21060.32991460.323326572803100
3.2106-3.27610.32121390.31012625276499
3.2761-3.34730.38731410.315926132754100
3.3473-3.42520.34011360.28582667280399
3.4252-3.51080.29491440.2682625276999
3.5108-3.60570.31961450.26992630277599
3.6057-3.71180.29081330.28382600273399
3.7118-3.83150.28411410.26172671281299
3.8315-3.96840.25941420.23272581272399
3.9684-4.12730.2671350.22192647278299
4.1273-4.3150.24151420.2132645278799
4.315-4.54230.23281320.21152609274199
4.5423-4.82670.26881480.19262627277599
4.8267-5.1990.22951390.19932615275499
5.199-5.72150.28091360.22812662279899
5.7215-6.54790.26111380.23292619275799
6.5479-8.24360.22671380.21662611274998
8.2436-49.80870.21321390.19482629276897
Refinement TLS params.

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

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.0223-0.01430.01570.0096-0.01010.0119-0.15270.7532-0.3255-0.8527-0.335-0.0010.04650.2071-01.4103-0.033-0.08891.50460.16131.314644.299517.6948-21.5411
20.6750.3033-0.44360.1518-0.19450.2912-0.5996-0.1826-0.9847-0.6150.0225-0.32320.9836-0.2112-0.06181.33320.12830.00451.7078-0.61531.116244.3422-44.9421-19.1947
30.85850.14850.4230.08610.12560.25770.234-0.8096-0.47530.1464-0.7359-0.08111.14390.5254-0.04431.07030.08120.00250.91480.42211.615141.8798-71.261135.3174
40.1406-0.1038-0.08160.24720.02930.0927-0.3666-0.1954-0.32030.62620.38470.27410.8152-0.01050.00011.2180.2999-0.07131.3818-0.04290.492842.2587-39.713682.7717
50.04880.0301-0.00730.0674-0.06090.06960.33660.65860.0019-0.3509-0.08280.3336-0.1255-0.07490.00091.5865-0.4609-0.72851.90150.13841.566244.456844.707428.2353
60.25660.1907-0.01740.3994-0.34320.52320.03110.20180.5535-0.6157-0.0143-0.6301-0.11630.22260.00430.6466-0.1257-0.00610.32090.22421.086646.334820.6555-2.4178
70.84190.3422-0.54510.81890.43560.98170.07520.86980.1208-0.4049-0.1764-0.28490.35430.3752-0.04730.48840.20020.18061.17820.00640.362845.2691-25.3554-14.7598
80.45030.2794-0.68360.5015-0.18651.2470.14070.1157-0.9399-0.2061-0.2704-0.44140.52930.5606-0.03060.54410.1769-0.05390.3167-0.06861.131943.9285-58.539419.5093
90.9576-0.3596-0.18860.5196-0.08881.0060.0635-0.1749-0.65490.32990.1454-0.21470.16940.51180.00330.69860.1322-0.02731.16250.09040.506642.4024-45.574263.364
100.03670.045-0.03360.0521-0.04250.02890.6055-0.80070.0189-0.2326-0.6009-0.36330.0677-0.1982-01.40780.0402-0.32931.7122-0.11771.174340.6052-2.696975.3689
110.28630.3189-0.07640.5394-0.27360.2040.0867-0.7136-0.27560.3011-0.3223-0.05930.37590.2498-01.2003-0.0629-0.2471.1191-0.24791.125443.615332.291545.0167
121.61290.2276-0.33952.62260.45070.9131-0.13570.07240.62510.1118-0.10320.1278-0.3001-0.1223-0.00910.56140.0662-0.10950.29980.0420.785217.386610.80439.834
132.8018-0.09320.0661.1792-0.60321.84830.0580.54770.0796-0.0971-0.04380.225-0.034-0.0948-0.00210.38840.0276-0.00610.3651-0.01610.283316.1337-19.0895-0.2905
142.4857-0.12590.75271.30320.32582.5370.2605-0.2198-0.7058-0.03330.05540.28130.1482-0.43330.03960.3833-0.0508-0.01570.20890.11310.454514.6677-43.005320.4068
152.12320.19620.03551.5641-0.64762.82120.2576-0.9809-0.38220.4150.53610.41790.018-0.8740.3560.41780.01740.25241.09170.4690.251413.201-37.140951.4917
160.90220.30930.0273.845-0.32811.3959-0.0705-1.05230.3913-0.0375-0.02420.6082-0.3112-0.721-0.00430.94940.390.01391.58-0.26640.644812.2045-7.173662.6796
171.50031.1632-0.14141.0677-0.55653.8515-0.1124-0.21720.15550.2631-0.08070.021-0.3658-0.2211-0.00020.95010.1552-0.11150.5604-0.28251.072214.718.319141.1008
180.06650.3168-0.0952.0249-1.65672.9228-0.11130.32961.07120.38090.87170.4904-1.9689-0.81310.21971.07050.09440.20860.5770.02710.567325.2893-12.366430.6584
191.23710.1442-0.15520.2152-0.13380.0891-0.2753-0.53090.61970.29530.42190.0935-0.2556-0.2250.34640.5360.2739-0.0720.8413-0.00530.492317.4681-12.891830.9691
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 1:47 )A1 - 47
2X-RAY DIFFRACTION2( CHAIN B AND RESID 1:47 )B1 - 47
3X-RAY DIFFRACTION3( CHAIN C AND RESID 1:47 )C1 - 47
4X-RAY DIFFRACTION4( CHAIN D AND RESID 1:47 )D1 - 47
5X-RAY DIFFRACTION5( CHAIN F AND RESID 1:46 )F1 - 46
6X-RAY DIFFRACTION6( CHAIN A AND RESID 48:124 )A48 - 124
7X-RAY DIFFRACTION7( CHAIN B AND RESID 48:128 )B48 - 128
8X-RAY DIFFRACTION8( CHAIN C AND RESID 48:128 )C48 - 128
9X-RAY DIFFRACTION9( CHAIN D AND RESID 48:128 )D48 - 128
10X-RAY DIFFRACTION10( CHAIN E AND RESID 49:128 )E49 - 128
11X-RAY DIFFRACTION11( CHAIN F AND RESID 49:128 )F49 - 128
12X-RAY DIFFRACTION12( CHAIN A AND ( RESID 129:414 OR RESID 415:416 ) )A129 - 414
13X-RAY DIFFRACTION12( CHAIN A AND ( RESID 129:414 OR RESID 415:416 ) )A415 - 416
14X-RAY DIFFRACTION13( CHAIN B AND ( RESID 129:417 OR RESID 1000:1002 ) )B129 - 417
15X-RAY DIFFRACTION13( CHAIN B AND ( RESID 129:417 OR RESID 1000:1002 ) )B1000 - 1002
16X-RAY DIFFRACTION14( CHAIN C AND ( RESID 129:417 OR RESID 1000:1002 ) )C129 - 417
17X-RAY DIFFRACTION14( CHAIN C AND ( RESID 129:417 OR RESID 1000:1002 ) )C1000 - 1002
18X-RAY DIFFRACTION15( CHAIN D AND ( RESID 129:414 OR RESID 415:416 ) )D129 - 414
19X-RAY DIFFRACTION15( CHAIN D AND ( RESID 129:414 OR RESID 415:416 ) )D415 - 416
20X-RAY DIFFRACTION16( CHAIN E AND ( RESID 129:414 OR RESID 415:416 ) )E129 - 414
21X-RAY DIFFRACTION16( CHAIN E AND ( RESID 129:414 OR RESID 415:416 ) )E415 - 416
22X-RAY DIFFRACTION17( CHAIN F AND ( RESID 129:414 OR RESID 415:416 ) )F129 - 414
23X-RAY DIFFRACTION17( CHAIN F AND ( RESID 129:414 OR RESID 415:416 ) )F415 - 416
24X-RAY DIFFRACTION18( CHAIN G AND RESID 1:7 )G1 - 7
25X-RAY DIFFRACTION19( CHAIN A AND RESID 1101:1103 ) OR ( CHAIN C AND RESID 1101:1103 ) OR ( CHAIN B AND RESID 1101:1103 ) OR ( CHAIN E AND RESID 1101:1103 ) OR ( CHAIN D AND RESID 1101:1103 ) OR ( CHAIN G AND RESID 101:101 ) OR ( CHAIN F AND RESID 1101:1103 )A1101 - 1103
26X-RAY DIFFRACTION19( CHAIN A AND RESID 1101:1103 ) OR ( CHAIN C AND RESID 1101:1103 ) OR ( CHAIN B AND RESID 1101:1103 ) OR ( CHAIN E AND RESID 1101:1103 ) OR ( CHAIN D AND RESID 1101:1103 ) OR ( CHAIN G AND RESID 101:101 ) OR ( CHAIN F AND RESID 1101:1103 )C1101 - 1103
27X-RAY DIFFRACTION19( CHAIN A AND RESID 1101:1103 ) OR ( CHAIN C AND RESID 1101:1103 ) OR ( CHAIN B AND RESID 1101:1103 ) OR ( CHAIN E AND RESID 1101:1103 ) OR ( CHAIN D AND RESID 1101:1103 ) OR ( CHAIN G AND RESID 101:101 ) OR ( CHAIN F AND RESID 1101:1103 )B1101 - 1103
28X-RAY DIFFRACTION19( CHAIN A AND RESID 1101:1103 ) OR ( CHAIN C AND RESID 1101:1103 ) OR ( CHAIN B AND RESID 1101:1103 ) OR ( CHAIN E AND RESID 1101:1103 ) OR ( CHAIN D AND RESID 1101:1103 ) OR ( CHAIN G AND RESID 101:101 ) OR ( CHAIN F AND RESID 1101:1103 )E1101 - 1103
29X-RAY DIFFRACTION19( CHAIN A AND RESID 1101:1103 ) OR ( CHAIN C AND RESID 1101:1103 ) OR ( CHAIN B AND RESID 1101:1103 ) OR ( CHAIN E AND RESID 1101:1103 ) OR ( CHAIN D AND RESID 1101:1103 ) OR ( CHAIN G AND RESID 101:101 ) OR ( CHAIN F AND RESID 1101:1103 )D1101 - 1103
30X-RAY DIFFRACTION19( CHAIN A AND RESID 1101:1103 ) OR ( CHAIN C AND RESID 1101:1103 ) OR ( CHAIN B AND RESID 1101:1103 ) OR ( CHAIN E AND RESID 1101:1103 ) OR ( CHAIN D AND RESID 1101:1103 ) OR ( CHAIN G AND RESID 101:101 ) OR ( CHAIN F AND RESID 1101:1103 )G101
31X-RAY DIFFRACTION19( CHAIN A AND RESID 1101:1103 ) OR ( CHAIN C AND RESID 1101:1103 ) OR ( CHAIN B AND RESID 1101:1103 ) OR ( CHAIN E AND RESID 1101:1103 ) OR ( CHAIN D AND RESID 1101:1103 ) OR ( CHAIN G AND RESID 101:101 ) OR ( CHAIN F AND RESID 1101:1103 )F1101 - 1103

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  • 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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