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- PDB-2uxb: Crystal structure of an extended tRNA anticodon stem loop in comp... -

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Basic information

Entry
Database: PDB / ID: 2uxb
TitleCrystal structure of an extended tRNA anticodon stem loop in complex with its cognate mRNA GGGU in the context of the Thermus thermophilus 30S subunit.
Components
  • (RIBOSOMAL PROTEIN ...) x 20
  • 16S RIBOSOMAL RNA
  • A-SITE MESSENGER RNA FRAGMENT GGGU
  • ANTICODON STEM-LOOP OF TRANSFER RNA WITH ANTICODON ACCC
KeywordsRIBOSOME / RIBONUCLEOPROTEIN / 30S RIBOSOMAL SUBUNIT / FRAMESHIFT SUPPRESSOR TRNA / TRNA / MRNA / CODON / A SITE / DECODING / METAL-BINDING / MESSENGER RNA / RIBOSOMAL PROTEIN / RNA-BINDING / PAROMOMYCIN / ANTICODON / STEM-LOOP / FRAMESHIFT / ZINC-FINGER / RRNA-BINDING / TRNA-BINDING / TRANSFER RNA
Function / homology
Function and homology information


ribosomal small subunit assembly / small ribosomal subunit / cytosolic small ribosomal subunit / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / mRNA binding ...ribosomal small subunit assembly / small ribosomal subunit / cytosolic small ribosomal subunit / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / mRNA binding / zinc ion binding / metal ion binding / cytosol / cytoplasm
Similarity search - Function
Ribosomal protein S4/S9, N-terminal domain / Ribosomal Protein S4 Delta 41; Chain A, domain 1 / S16 Ribosomal Protein; Chain: A; / Ribosomal protein S16 / Ribosomal protein S18 / 30s Ribosomal Protein S18 / 30s ribosomal protein s13; domain 2 / Ribosomal protein S13/S18, C-terminal domain / Ribosomal protein S20 / 30s Ribosomal Protein S19; Chain A ...Ribosomal protein S4/S9, N-terminal domain / Ribosomal Protein S4 Delta 41; Chain A, domain 1 / S16 Ribosomal Protein; Chain: A; / Ribosomal protein S16 / Ribosomal protein S18 / 30s Ribosomal Protein S18 / 30s ribosomal protein s13; domain 2 / Ribosomal protein S13/S18, C-terminal domain / Ribosomal protein S20 / 30s Ribosomal Protein S19; Chain A / Ribosomal protein S19/S15 / Ribosomal protein S3, C-terminal domain / Ribosomal Protein S14/S29 / 30s Ribosomal Protein S14; Chain N / Ribosomal Protein S8; Chain: A, domain 1 - #30 / RNA-binding S4 domain / Ribosomal Protein S7 / Ribosomal protein S7/S5 / Ribosomal protein S6/Translation elongation factor EF1B / Ribosomal protein S3 C-terminal domain / Helix hairpin bin / Dna Ligase; domain 1 - #10 / Ribosomal protein S11/S14 / Ribosomal protein S10 / Structural Genomics Hypothetical 15.5 Kd Protein In mrcA-pckA Intergenic Region; Chain A / S15/NS1, RNA-binding / K homology (KH) domain / Double Stranded RNA Binding Domain - #20 / Helicase, Ruva Protein; domain 3 - #50 / Glucose-6-phosphate isomerase like protein; domain 1 / Ribosomal Protein S8; Chain: A, domain 1 / Ribosomal Protein S5; domain 2 - #10 / 30S ribosomal protein Thx / 30S ribosomal protein Thx / 30S ribosomal protein / GMP Synthetase; Chain A, domain 3 / Ribosomal Protein S5; domain 2 / Double Stranded RNA Binding Domain / Ribosomal protein S14, type Z / Helicase, Ruva Protein; domain 3 / Nucleic acid-binding proteins / Dna Ligase; domain 1 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Ribosomal protein S14/S29 / Ribosomal protein S3, bacterial-type / Ribosomal protein S6, conserved site / Ribosomal protein S6 signature. / Ribosomal protein S19, bacterial-type / Ribosomal protein S13, bacterial-type / Ribosomal protein S7, bacterial/organellar-type / Ribosomal protein S11, bacterial-type / Ribosomal protein S20 / Ribosomal protein S20 superfamily / Ribosomal protein S20 / Ribosomal protein S9, bacterial/plastid / Ribosomal protein S4, bacterial-type / 30S ribosomal protein S17 / Ribosomal protein S5, bacterial-type / Ribosomal protein S6, plastid/chloroplast / Ribosomal protein S2, bacteria/mitochondria/plastid / Ribosomal protein S18, conserved site / Ribosomal protein S18 signature. / Ribosomal protein S16 / Ribosomal protein S16 domain superfamily / Ribosomal protein S16 / Ribosomal protein S15, bacterial-type / Ribosomal protein S6 / Ribosomal protein S6 / Ribosomal protein S6 superfamily / Ribosomal protein S12, bacterial-type / Translation elongation factor EF1B/ribosomal protein S6 / Ribosomal protein S18 / Ribosomal protein S18 / Ribosomal protein S18 superfamily / K Homology domain / K homology RNA-binding domain / Few Secondary Structures / Irregular / Ribosomal protein S10, conserved site / Ribosomal protein S10 signature. / Ribosomal protein S3, conserved site / Ribosomal protein S3 signature. / Ribosomal protein S14, conserved site / Ribosomal protein S14 signature. / Ribosomal protein S2 signature 1. / KH domain / Type-2 KH domain profile. / K Homology domain, type 2 / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Ribosomal protein S3, C-terminal / Ribosomal protein S3, C-terminal domain / Ribosomal protein S3, C-terminal domain superfamily / Ribosomal protein S15/S19, conserved site / Ribosomal protein S19 signature. / Ribosomal protein S10 / : / Ribosomal protein S19/S15 / Ribosomal protein S19/S15, superfamily / Ribosomal protein S19 / Ribosomal protein S5, N-terminal, conserved site
Similarity search - Domain/homology
: / PAROMOMYCIN / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein uS14 / Small ribosomal subunit protein uS17 / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein uS7 ...: / PAROMOMYCIN / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein uS14 / Small ribosomal subunit protein uS17 / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein uS7 / Small ribosomal subunit protein uS2 / Small ribosomal subunit protein uS3 / Small ribosomal subunit protein uS4 / Small ribosomal subunit protein uS9 / Small ribosomal subunit protein uS11 / Small ribosomal subunit protein uS13 / Small ribosomal subunit protein bS20 / Small ribosomal subunit protein uS12 / Small ribosomal subunit protein uS10 / Small ribosomal subunit protein uS19 / 30S ribosomal protein S17 / 30S ribosomal protein S14 type Z / 30S ribosomal protein S8 / Small ribosomal subunit protein uS5 / Small ribosomal subunit protein bTHX / Small ribosomal subunit protein uS15 / Small ribosomal subunit protein bS16 / Small ribosomal subunit protein bS6 / Small ribosomal subunit protein bS18
Similarity search - Component
Biological speciesTHERMUS THERMOPHILUS (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 3.1 Å
AuthorsDunham, C.M. / Selmer, M. / Phelps, S.S. / Kelley, A.C. / Suzuki, T. / Joseph, S. / Ramakrishnan, V.
CitationJournal: RNA / Year: 2007
Title: Structures of tRNAs with an expanded anticodon loop in the decoding center of the 30S ribosomal subunit.
Authors: Dunham, C.M. / Selmer, M. / Phelps, S.S. / Kelley, A.C. / Suzuki, T. / Joseph, S. / Ramakrishnan, V.
History
DepositionMar 28, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 31, 2007Provider: repository / Type: Initial release
Revision 1.1Sep 19, 2012Group: Atomic model / Derived calculations ...Atomic model / Derived calculations / Non-polymer description / Other / Version format compliance
Revision 1.2Oct 10, 2012Group: Derived calculations
Revision 1.3Dec 25, 2013Group: Derived calculations / Other
Revision 2.0Mar 14, 2018Group: Advisory / Atomic model ...Advisory / Atomic model / Database references / Source and taxonomy
Category: atom_site / citation ...atom_site / citation / database_PDB_caveat / pdbx_entity_src_syn
Item: _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title
Revision 2.1Jan 30, 2019Group: Data collection / Database references / Experimental preparation
Category: exptl_crystal_grow / struct_ref_seq
Item: _exptl_crystal_grow.method / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end
Revision 2.2Mar 6, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 2.3May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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_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.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "QA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "QA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 5-STRANDED BARREL THIS IS REPRESENTED BY A 6-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 16S RIBOSOMAL RNA
B: RIBOSOMAL PROTEIN S2
C: RIBOSOMAL PROTEIN S3
D: RIBOSOMAL PROTEIN S4
E: RIBOSOMAL PROTEIN S5
F: RIBOSOMAL PROTEIN S6
G: RIBOSOMAL PROTEIN S7
H: RIBOSOMAL PROTEIN S8
I: RIBOSOMAL PROTEIN S9
J: RIBOSOMAL PROTEIN S10
K: RIBOSOMAL PROTEIN S11
L: RIBOSOMAL PROTEIN S12
M: RIBOSOMAL PROTEIN S13
N: RIBOSOMAL PROTEIN S14
O: RIBOSOMAL PROTEIN S15
P: RIBOSOMAL PROTEIN S16
Q: RIBOSOMAL PROTEIN S17
R: RIBOSOMAL PROTEIN S18
S: RIBOSOMAL PROTEIN S19
T: RIBOSOMAL PROTEIN S20
U: RIBOSOMAL PROTEIN THX
X: A-SITE MESSENGER RNA FRAGMENT GGGU
Y: ANTICODON STEM-LOOP OF TRANSFER RNA WITH ANTICODON ACCC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)795,008167
Polymers790,68623
Non-polymers4,321144
Water00
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area59690 Å2
ΔGint108 kcal/mol
Surface area336530 Å2
MethodPQS
Unit cell
Length a, b, c (Å)401.950, 401.950, 174.086
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

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RNA chain , 3 types, 3 molecules AXY

#1: RNA chain 16S RIBOSOMAL RNA


Mass: 493958.281 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: CHAIN A (16S RNA) HAS E. COLI NUMBERING / Source: (natural) THERMUS THERMOPHILUS (bacteria) / Strain: HB8
#22: RNA chain A-SITE MESSENGER RNA FRAGMENT GGGU


Mass: 1296.826 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#23: RNA chain ANTICODON STEM-LOOP OF TRANSFER RNA WITH ANTICODON ACCC


Mass: 5707.458 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: SEQUENCE BASED ON E.COLI TRNAPHE WITH EXTENDED ANTICODON
Source: (synth.) synthetic construct (others)

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RIBOSOMAL PROTEIN ... , 20 types, 20 molecules BCDEFGHIJKLMNOPQRSTU

#2: Protein RIBOSOMAL PROTEIN S2


Mass: 29317.703 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS (bacteria) / Strain: HB8 / References: UniProt: P80371
#3: Protein RIBOSOMAL PROTEIN S3


Mass: 26751.076 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS (bacteria) / Strain: HB8 / References: UniProt: P80372
#4: Protein RIBOSOMAL PROTEIN S4


Mass: 24373.447 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS (bacteria) / Strain: HB8 / References: UniProt: P80373
#5: Protein RIBOSOMAL PROTEIN S5


Mass: 17583.416 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS (bacteria) / Strain: HB8 / References: UniProt: Q5SHQ5
#6: Protein RIBOSOMAL PROTEIN S6


Mass: 11988.753 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS (bacteria) / Strain: HB8 / References: UniProt: Q5SLP8
#7: Protein RIBOSOMAL PROTEIN S7


Mass: 18050.973 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS (bacteria) / Strain: HB8 / References: UniProt: P17291
#8: Protein RIBOSOMAL PROTEIN S8


Mass: 15868.570 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS (bacteria) / Strain: HB8 / References: UniProt: Q5SHQ2, UniProt: P0DOY9*PLUS
#9: Protein RIBOSOMAL PROTEIN S9


Mass: 14429.661 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS (bacteria) / Strain: HB8 / References: UniProt: P80374
#10: Protein RIBOSOMAL PROTEIN S10


Mass: 11954.968 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS (bacteria) / Strain: HB8 / References: UniProt: Q5SHN7
#11: Protein RIBOSOMAL PROTEIN S11


Mass: 13737.868 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS (bacteria) / Strain: HB8 / References: UniProt: P80376
#12: Protein RIBOSOMAL PROTEIN S12


Mass: 14920.754 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS (bacteria) / Strain: HB8 / References: UniProt: Q5SHN3
#13: Protein RIBOSOMAL PROTEIN S13


Mass: 14338.861 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS (bacteria) / Strain: HB8 / References: UniProt: P80377
#14: Protein RIBOSOMAL PROTEIN S14


Mass: 7158.725 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS (bacteria) / Strain: HB8 / References: UniProt: Q5SHQ1, UniProt: P0DOY6*PLUS
#15: Protein RIBOSOMAL PROTEIN S15


Mass: 10578.407 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS (bacteria) / Strain: HB8 / References: UniProt: Q5SJ76
#16: Protein RIBOSOMAL PROTEIN S16


Mass: 10409.983 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS (bacteria) / Strain: HB8 / References: UniProt: Q5SJH3
#17: Protein RIBOSOMAL PROTEIN S17


Mass: 12324.670 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS (bacteria) / Strain: HB8 / References: UniProt: Q5SHP7, UniProt: P0DOY7*PLUS
#18: Protein RIBOSOMAL PROTEIN S18


Mass: 10258.299 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS (bacteria) / Strain: HB8 / References: UniProt: Q5SLQ0
#19: Protein RIBOSOMAL PROTEIN S19


Mass: 10605.464 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS (bacteria) / Strain: HB8 / References: UniProt: Q5SHP2
#20: Protein RIBOSOMAL PROTEIN S20


Mass: 11722.116 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS (bacteria) / Strain: HB8 / References: UniProt: P80380
#21: Protein/peptide RIBOSOMAL PROTEIN THX


Mass: 3350.030 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS (bacteria) / Strain: HB8 / References: UniProt: Q5SIH3

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Non-polymers , 4 types, 144 molecules

#24: Chemical ChemComp-PAR / PAROMOMYCIN / PAROMOMYCIN I / AMMINOSIDIN / CATENULIN / CRESTOMYCIN / MONOMYCIN A / NEOMYCIN E


Mass: 615.628 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H45N5O14 / Comment: Antimicrobial, medication*YM
#25: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 131 / Source method: obtained synthetically / Formula: Mg
#26: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: K
#27: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn

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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: 4.17 Å3/Da / Density % sol: 70.5 % / Description: NONE
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: MPD, AMMONIUM CHLORIDE, POTASSIUM CHLORIDE, MAGNESIUM ACETATE, SODIUM CACODYLATE, PH 6.5, VAPOR DIFFUSION, HANGING DROP AT 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9393
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 17, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9393 Å / Relative weight: 1
ReflectionResolution: 3.1→50 Å / Num. obs: 250188 / % possible obs: 96.7 % / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 8.3
Reflection shellResolution: 3.1→3.2 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.61 / Mean I/σ(I) obs: 2.1 / % possible all: 94

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Processing

Software
NameVersionClassification
CNS1.1refinement
XDSdata reduction
XDSdata scaling
CNSphasing
RefinementMethod to determine structure: OTHER / Resolution: 3.1→29.88 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 14368624.66 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUN LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.328 12509 5 %RANDOM
Rwork0.295 ---
obs0.295 250137 98.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 300 Å2 / ksol: 0.766748 e/Å3
Displacement parametersBiso mean: 75.3 Å2
Baniso -1Baniso -2Baniso -3
1--3.29 Å20 Å20 Å2
2---3.29 Å20 Å2
3---6.57 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.53 Å0.46 Å
Luzzati d res low-5 Å
Luzzati sigma a0.89 Å0.81 Å
Refinement stepCycle: LAST / Resolution: 3.1→29.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19237 32744 185 0 52166
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d28.5
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.51
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 3.1→3.29 Å / Rfactor Rfree error: 0.008 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.379 2151 5.2 %
Rwork0.369 39042 -
obs--97.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2NEW_DNA-RNA-MULTNEW_DNA-RNA-MULT
X-RAY DIFFRACTION3ION.PARAMION.TOP
X-RAY DIFFRACTION4PAR.PARPAR.TOP

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