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- PDB-1yit: Crystal Structure Of Virginiamycin M and S Bound To The 50S Ribos... -

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Entry
Database: PDB / ID: 1yit
TitleCrystal Structure Of Virginiamycin M and S Bound To The 50S Ribosomal Subunit Of Haloarcula Marismortui
Components
  • (50S RIBOSOMAL PROTEIN ...) x 28
  • 23S RIBOSOMAL RNA
  • 5S RIBOSOMAL RNA
  • ACIDIC RIBOSOMAL PROTEIN P0 HOMOLOG
  • VIRGINIAMYCIN ...
KeywordsRIBOSOME/ANTIBIOTIC / VIRGINIAMYCIN M / VIRGINIAMYCIN S / PEPTIDYL TRANSFERASE / RIBOSOME / STREPTOGRAMIN / RIBOSOME-ANTIBIOTIC COMPLEX / ANTIBIOTIC / CYCLOHEXADEPSIPEPTIDE
Function / homology
Function and homology information


ribonuclease P activity / tRNA 5'-leader removal / cytosolic ribosome / large ribosomal subunit rRNA binding / large ribosomal subunit / ribosome biogenesis / 5S rRNA binding / cytosolic large ribosomal subunit / tRNA binding / rRNA binding ...ribonuclease P activity / tRNA 5'-leader removal / cytosolic ribosome / large ribosomal subunit rRNA binding / large ribosomal subunit / ribosome biogenesis / 5S rRNA binding / cytosolic large ribosomal subunit / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / nucleotide binding / DNA repair / DNA binding / zinc ion binding / cytoplasm
Similarity search - Function
Single Heli x bin / Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A - #60 / Ribosomal protein L30/L7, central domain / Ribosomal protein L39 / 50s Ribosomal Protein L19e, Chain O, domain 1 - #10 / N-terminal domain of TfIIb - #30 / Ribosomal protein L21 / Ribosomal Protein L31e; Chain: W; / Ribosomal protein L31 / Nuclear Transport Factor 2; Chain: A, - #80 ...Single Heli x bin / Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A - #60 / Ribosomal protein L30/L7, central domain / Ribosomal protein L39 / 50s Ribosomal Protein L19e, Chain O, domain 1 - #10 / N-terminal domain of TfIIb - #30 / Ribosomal protein L21 / Ribosomal Protein L31e; Chain: W; / Ribosomal protein L31 / Nuclear Transport Factor 2; Chain: A, - #80 / Molecule: Ribosomal Protein L15; Chain: K; domain 1 / Molecule: Ribosomal Protein L15; Chain: K; domain 1 - #10 / 3-methyladenine DNA Glycosylase II; Chain A, domain 3 / Ribosomal protein L24 / Ribosomal protein L3; domain 3 / Ribosomal protein L3, domain 3 / Ribosomal protein L15e / Ribosomal protein L15 / Ribosomal Protein L15; Chain: K; domain 2 - #10 / Ribosomal Protein L3; Chain: B; domain 2, / Ribosomal Protein L3; Chain: B; domain 2, - #10 / Ribosomal protein L19e, domain 2 / Ribosomal protein L19e, domain 3 / 50s Ribosomal Protein L19e, Chain O, domain 1 / Ribosomal Protein L4; Chain: A; / Ribosomal protein L4/L1 / Helix Hairpins - #310 / 50S ribosomal protein L10, archaea / Ribosomal Protein L13p; Chain: A; / Ribosomal protein L13 / Atp Synthase Epsilon Chain; Chain: I; / Ribosomal Protein L24e; Chain: T; / Ribosomal Protein L15; Chain: K; domain 2 / Ribosomal Protein L15; Chain: K; domain 2 / Ribosomal protein L19e, archaeal / Ribosomal protein L2; domain 3 / Ribosomal protein L2, domain 3 / Ribosomal protein L11/L12, C-terminal domain / Ribosomal protein L15e, archaeal / Ribosomal protein L30, archaeal / Ribosomal protein L6P, archaea / Ribosomal protein L14P, archaeal / Ribosomal protein L21e, archaeal / Ribosomal protein L18e, archaea / Ribosomal protein L10e, archaea / Ribosomal protein L32e, archaeal / Ribosomal protein L3, archaeal / Ribosomal protein L4, archaea / Ribosomal protein L5, archaeal / Ribosomal protein L6 / 50s Ribosomal Protein L5; Chain: A, / Ribosomal protein L5 / Ribosomal protein L30/L7 / Nucleotidyltransferase; domain 5 - #100 / Ribosomal protein L16/L10 / Ribosomal protein L22/L17 / Ribosomal Protein L14 / Ribosomal protein L14/L23 / Outer Surface Protein A; domain 3 / Ribosomal protein L7Ae, archaea / Ribosomal Protein L22; Chain A / Ribosomal Protein L30; Chain: A, / Ribosomal protein L24e / SH3 type barrels. - #30 / Ribosomal protein L30/S12 / Aldehyde Oxidoreductase; domain 3 / DNA repair Rad51/transcription factor NusA, alpha-helical / Ribosomal protein L2, archaeal-type / Ribosomal L15/L27a, N-terminal / Ribosomal protein L23 / Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A / N-terminal domain of TfIIb / Helix-hairpin-helix domain / 50S ribosomal protein L10, insertion domain superfamily / Translation factors / 60S ribosomal protein L10P, insertion domain / Insertion domain in 60S ribosomal protein L10P / metallochaperone-like domain / TRASH domain / Ribosomal protein L10e, conserved site / Ribosomal protein L10e / Ribosomal protein L24e, conserved site / Ribosomal protein L44e / Ribosomal protein L44 / Ribosomal protein L31e, conserved site / Ribosomal protein L37ae / Ribosomal protein L44e signature. / Ribosomal protein L10e signature. / Ribosomal protein L32e, conserved site / RRM (RNA recognition motif) domain / Ribosomal protein L6, conserved site-2 / 60s Ribosomal Protein L30; Chain: A; / Ribosomal protein L19/L19e conserved site / Ribosomal L37ae protein family / Helix-hairpin-helix DNA-binding motif, class 1 / Helix-hairpin-helix DNA-binding motif class 1 / Ribosomal protein L39e, conserved site / Ribosomal protein L19e signature. / Ribosomal protein L24e signature. / Ribosomal protein L31e
Similarity search - Domain/homology
VIRGINIAMYCIN S1 / : / : / VIRGINIAMYCIN M1 / : / : / : / : / : / : ...VIRGINIAMYCIN S1 / : / : / VIRGINIAMYCIN M1 / : / : / : / : / : / : / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein uL22 / Large ribosomal subunit protein uL29 / Large ribosomal subunit protein uL24 / Large ribosomal subunit protein uL23 / Large ribosomal subunit protein eL18 / Large ribosomal subunit protein eL21 / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein eL32 / Large ribosomal subunit protein uL15 / Large ribosomal subunit protein eL8 / Large ribosomal subunit protein eL24 / Large ribosomal subunit protein eL19 / Large ribosomal subunit protein uL30 / Large ribosomal subunit protein uL11 / Large ribosomal subunit protein uL18 / Large ribosomal subunit protein uL5 / Large ribosomal subunit protein uL6 / Large ribosomal subunit protein uL10 / Large ribosomal subunit protein eL31 / Large ribosomal subunit protein uL2 / Large ribosomal subunit protein uL3 / Large ribosomal subunit protein uL14 / Large ribosomal subunit protein eL39 / Large ribosomal subunit protein uL13 / Large ribosomal subunit protein eL37 / Large ribosomal subunit protein eL42 / Large ribosomal subunit protein uL16 / Large ribosomal subunit protein eL15 / Large ribosomal subunit protein eL43
Similarity search - Component
Biological speciesHALOARCULA MARISMORTUI (Halophile)
STREPTOMYCES VIRGINIAE (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsTu, D. / Blaha, G. / Moore, P.B. / Steitz, T.A.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2005
Title: Structures of Mlsbk Antibiotics Bound to Mutated Large Ribosomal Subunits Provide a Structural Explanation for Resistance.
Authors: TU, D. / Blaha, G. / Moore, P.B. / Steitz, T.A.
History
DepositionJan 13, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 26, 2005Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 27, 2011Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Structure summary
Revision 1.4Dec 12, 2012Group: Other
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "BD" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "BD" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "KC" 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.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
0: 23S RIBOSOMAL RNA
1: 50S RIBOSOMAL PROTEIN L37E
2: 50S RIBOSOMAL PROTEIN L39E
3: 50S RIBOSOMAL PROTEIN L44E
8: VIRGINIAMYCIN S1
9: 5S RIBOSOMAL RNA
A: 50S RIBOSOMAL PROTEIN L2P
B: 50S RIBOSOMAL PROTEIN L3P
C: 50S RIBOSOMAL PROTEIN L4E
D: 50S RIBOSOMAL PROTEIN L5P
E: 50S RIBOSOMAL PROTEIN L6P
F: 50S RIBOSOMAL PROTEIN L7AE
G: ACIDIC RIBOSOMAL PROTEIN P0 HOMOLOG
H: 50S RIBOSOMAL PROTEIN L10E
I: 50S RIBOSOMAL PROTEIN L11P
J: 50S RIBOSOMAL PROTEIN L13P
K: 50S RIBOSOMAL PROTEIN L14P
L: 50S RIBOSOMAL PROTEIN L15P
M: 50S RIBOSOMAL PROTEIN L15E
N: 50S RIBOSOMAL PROTEIN L18P
O: 50S RIBOSOMAL PROTEIN L18E
P: 50S RIBOSOMAL PROTEIN L19E
Q: 50S RIBOSOMAL PROTEIN L21E
R: 50S RIBOSOMAL PROTEIN L22P
S: 50S RIBOSOMAL PROTEIN L23P
T: 50S RIBOSOMAL PROTEIN L24P
U: 50S RIBOSOMAL PROTEIN L24E
V: 50S RIBOSOMAL PROTEIN L29P
W: 50S RIBOSOMAL PROTEIN L30P
X: 50S RIBOSOMAL PROTEIN L31E
Y: 50S RIBOSOMAL PROTEIN L32E
Z: 50S RIBOSOMAL PROTEIN L37AE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,481,914264
Polymers1,475,18532
Non-polymers6,729232
Water0
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area105830 Å2
ΔGint-1086.4 kcal/mol
Surface area381780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)212.583, 299.758, 573.560
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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RNA chain , 2 types, 2 molecules 09

#1: RNA chain 23S RIBOSOMAL RNA /


Mass: 946157.375 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: ENCODED BY RRNA OPERON / Source: (natural) HALOARCULA MARISMORTUI (Halophile) / References: GenBank: 55229667
#6: RNA chain 5S RIBOSOMAL RNA /


Mass: 39303.402 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (natural) HALOARCULA MARISMORTUI (Halophile) / References: GenBank: 3377778

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50S RIBOSOMAL PROTEIN ... , 28 types, 28 molecules 123ABCDEFHIJKLMNOPQRSTUVWXYZ

#2: Protein 50S RIBOSOMAL PROTEIN L37E / Ribosome


Mass: 6330.203 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) HALOARCULA MARISMORTUI (Halophile) / References: UniProt: P32410
#3: Protein/peptide 50S RIBOSOMAL PROTEIN L39E / Ribosome


Mass: 6133.090 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) HALOARCULA MARISMORTUI (Halophile) / References: UniProt: P22452
#4: Protein 50S RIBOSOMAL PROTEIN L44E / Ribosome


Mass: 10815.245 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) HALOARCULA MARISMORTUI (Halophile) / References: UniProt: P32411
#7: Protein 50S RIBOSOMAL PROTEIN L2P / Ribosome


Mass: 25354.688 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) HALOARCULA MARISMORTUI (Halophile) / References: UniProt: P20276
#8: Protein 50S RIBOSOMAL PROTEIN L3P / Ribosome


Mass: 37396.395 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) HALOARCULA MARISMORTUI (Halophile) / References: GenBank: 55378384, UniProt: P20279*PLUS
#9: Protein 50S RIBOSOMAL PROTEIN L4E / Ribosome


Mass: 26442.098 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) HALOARCULA MARISMORTUI (Halophile) / References: UniProt: P12735
#10: Protein 50S RIBOSOMAL PROTEIN L5P / Ribosome


Mass: 19551.693 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) HALOARCULA MARISMORTUI (Halophile) / References: UniProt: P14124
#11: Protein 50S RIBOSOMAL PROTEIN L6P / Ribosome


Mass: 19961.719 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) HALOARCULA MARISMORTUI (Halophile) / References: UniProt: P14135
#12: Protein 50S RIBOSOMAL PROTEIN L7AE / Ribosome


Mass: 12791.941 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) HALOARCULA MARISMORTUI (Halophile) / References: UniProt: P12743
#14: Protein 50S RIBOSOMAL PROTEIN L10E / Ribosome


Mass: 19942.734 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) HALOARCULA MARISMORTUI (Halophile) / References: GenBank: 55231756, UniProt: P60617*PLUS
#15: Protein 50S RIBOSOMAL PROTEIN L11P / Ribosome


Mass: 17097.547 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) HALOARCULA MARISMORTUI (Halophile) / References: GenBank: 132647, UniProt: P14122*PLUS
#16: Protein 50S RIBOSOMAL PROTEIN L13P / Ribosome


Mass: 16249.214 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) HALOARCULA MARISMORTUI (Halophile) / References: UniProt: P29198
#17: Protein 50S RIBOSOMAL PROTEIN L14P / Ribosome


Mass: 14191.243 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) HALOARCULA MARISMORTUI (Halophile) / References: UniProt: P22450
#18: Protein 50S RIBOSOMAL PROTEIN L15P / Ribosome


Mass: 18005.367 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) HALOARCULA MARISMORTUI (Halophile) / References: UniProt: P12737
#19: Protein 50S RIBOSOMAL PROTEIN L15E / Ribosome


Mass: 22275.055 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) HALOARCULA MARISMORTUI (Halophile) / References: GenBank: 55231501, UniProt: P60618*PLUS
#20: Protein 50S RIBOSOMAL PROTEIN L18P / Ribosome


Mass: 20640.939 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) HALOARCULA MARISMORTUI (Halophile) / References: UniProt: P14123
#21: Protein 50S RIBOSOMAL PROTEIN L18E / Ribosome


Mass: 12438.915 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) HALOARCULA MARISMORTUI (Halophile) / References: UniProt: P12733
#22: Protein 50S RIBOSOMAL PROTEIN L19E / Ribosome


Mass: 16796.514 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) HALOARCULA MARISMORTUI (Halophile) / References: UniProt: P14119
#23: Protein 50S RIBOSOMAL PROTEIN L21E / Ribosome


Mass: 10567.801 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) HALOARCULA MARISMORTUI (Halophile) / References: UniProt: P12734
#24: Protein 50S RIBOSOMAL PROTEIN L22P / Ribosome


Mass: 16966.945 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) HALOARCULA MARISMORTUI (Halophile) / References: UniProt: P10970
#25: Protein 50S RIBOSOMAL PROTEIN L23P / Ribosome


Mass: 9612.537 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) HALOARCULA MARISMORTUI (Halophile) / References: UniProt: P12732
#26: Protein 50S RIBOSOMAL PROTEIN L24P / Ribosome


Mass: 13670.955 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) HALOARCULA MARISMORTUI (Halophile) / References: UniProt: P10972
#27: Protein 50S RIBOSOMAL PROTEIN L24E / Ribosome


Mass: 7233.720 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) HALOARCULA MARISMORTUI (Halophile) / References: UniProt: P14116
#28: Protein 50S RIBOSOMAL PROTEIN L29P / Ribosome


Mass: 7889.863 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) HALOARCULA MARISMORTUI (Halophile) / References: UniProt: P10971
#29: Protein 50S RIBOSOMAL PROTEIN L30P / Ribosome


Mass: 17062.885 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) HALOARCULA MARISMORTUI (Halophile) / References: UniProt: P14121
#30: Protein 50S RIBOSOMAL PROTEIN L31E / Ribosome


Mass: 10384.613 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) HALOARCULA MARISMORTUI (Halophile) / References: UniProt: P18138
#31: Protein 50S RIBOSOMAL PROTEIN L32E / Ribosome


Mass: 26455.727 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) HALOARCULA MARISMORTUI (Halophile) / References: UniProt: P12736
#32: Protein 50S RIBOSOMAL PROTEIN L37AE / Ribosome


Mass: 9409.338 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) HALOARCULA MARISMORTUI (Halophile) / References: GenBank: 55231162, UniProt: P60619*PLUS

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VIRGINIAMYCIN ... / Protein , 2 types, 2 molecules 8G

#13: Protein ACIDIC RIBOSOMAL PROTEIN P0 HOMOLOG


Mass: 37213.805 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) HALOARCULA MARISMORTUI (Halophile) / References: UniProt: P15825
#5: Protein/peptide VIRGINIAMYCIN S1 / / VIRGINIAMYCIN FACTOR S1 / VIRGINIAMYCIN S /


Type: Cyclic peptide / Class: Antibiotic, Antimicrobial / Mass: 841.907 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: VIRGINIAMYCIN S1 IS A CYLIC HEPTAPEPTIDE. THE RING IS GENERATED BY LINKING RESIDUE 2 SIDE-CHAIN AND RESIDUE 7 MAIN-CHAIN.
Source: (natural) STREPTOMYCES VIRGINIAE (bacteria) / References: NOR: NOR00679, VIRGINIAMYCIN S1

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Non-polymers , 6 types, 232 molecules

#33: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 118 / Source method: obtained synthetically / Formula: Mg
#34: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#35: Chemical...
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 85 / Source method: obtained synthetically / Formula: Na
#36: Chemical...
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 22 / Source method: obtained synthetically / Formula: Cl
#37: Chemical ChemComp-VIR / VIRGINIAMYCIN M1 / Pristinamycin IIA


Mass: 525.593 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C28H35N3O7 / Comment: antibiotic*YM
#38: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cd

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Details

Sequence detailsSEQUENCE REFERENCE FOR THE RIBOSOME: BALIGA, N.S., ET AL, (2004). GENOME SEQUENCE OF HALOARCULA ...SEQUENCE REFERENCE FOR THE RIBOSOME: BALIGA, N.S., ET AL, (2004). GENOME SEQUENCE OF HALOARCULA MARISMORTUI: A HALOPHILIC ARCHAEON FROM THE DEAD SEA. GENOME RES. 14, 2221-2234. DOI 10.1101/GR.2700304

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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: 3.1 Å3/Da / Density % sol: 60 %
Crystal growpH: 5.8
Details: PEG 6000, KCL, NH4CL, MGCL2, KACETATE, PH 5.8, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 292K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 600011
2KCl11
3NH4Cl11
4MgCl211
5Kacetate11
6H2O11
7PEG 600012
8KCl12
9NH4Cl12
10MgCl212
11Kacetate12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 17, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.85→50 Å / Num. obs: 420273 / Redundancy: 3.5 % / Biso Wilson estimate: 72 Å2 / Rmerge(I) obs: 0.082 / Net I/σ(I): 15.5
Reflection shellResolution: 2.85→2.95 Å / Rmerge(I) obs: 0.59 / Mean I/σ(I) obs: 2.2 / % possible all: 99.9

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Processing

Software
NameClassification
CNSrefinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→29.99 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 252771.94 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.221 4113 1 %RANDOM
Rwork0.175 ---
obs0.175 417595 93.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 36.08 Å2 / ksol: 0.32 e/Å3
Displacement parametersBiso mean: 53.6 Å2
Baniso -1Baniso -2Baniso -3
1-11.58 Å20 Å20 Å2
2---5.35 Å20 Å2
3----6.23 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.36 Å0.29 Å
Luzzati d res low-5 Å
Luzzati sigma a0.53 Å0.48 Å
Refinement stepCycle: LAST / Resolution: 2.8→29.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms29437 61620 269 0 91326
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
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
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d15.4
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.32
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.121.5
X-RAY DIFFRACTIONc_mcangle_it1.952
X-RAY DIFFRACTIONc_scbond_it1.472
X-RAY DIFFRACTIONc_scangle_it2.252.5
LS refinement shellResolution: 2.8→2.98 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.347 609 1 %
Rwork0.319 60070 -
obs--82.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2RNA_RIBO_MODNTS.PARAMRNA_RIBO_MODNTS_DRUGS.T
X-RAY DIFFRACTION3ION.PARAMION.TOP
X-RAY DIFFRACTION4WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION5VIR.PARVIR.TOP
X-RAY DIFFRACTION6VRS.PARVRS.TOP

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Jul 12, 2017. Major update of PDB

Major update of PDB

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External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

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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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