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- PDB-8cqw: Crystal structure of the Candida albicans 80S ribosome in complex... -

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Basic information

Entry
Database: PDB / ID: 8cqw
TitleCrystal structure of the Candida albicans 80S ribosome in complex with Hygromycin B
Components
  • (40S ribosomal protein ...) x 25
  • (60S ribosomal protein ...) x 38
  • (Ribosomal protein ...) x 10
  • 18S
  • 25S
  • 5.8S
  • 5S
  • 60S acidic ribosomal protein P0
  • Guanine nucleotide-binding protein subunit beta-like protein
  • Ribosomal protein
  • Ubiquitin-40S ribosomal protein S31 fusion protein
  • Uncharacterized protein CaJ7.0206
KeywordsRIBOSOME / Candida albicans / hygromycin B
Function / homology
Function and homology information


negative regulation of cell integrity MAPK cascade / positive regulation of conjugation with cellular fusion / yeast-form cell wall / regulation of cytoplasmic translation / GCN2-mediated signaling / hyphal cell wall / triplex DNA binding / ribosome hibernation / preribosome / negative regulation of p38MAPK cascade ...negative regulation of cell integrity MAPK cascade / positive regulation of conjugation with cellular fusion / yeast-form cell wall / regulation of cytoplasmic translation / GCN2-mediated signaling / hyphal cell wall / triplex DNA binding / ribosome hibernation / preribosome / negative regulation of p38MAPK cascade / translation elongation factor binding / regulation of translational initiation in response to stress / regulation of amino acid metabolic process / negative regulation of glucose mediated signaling pathway / positive regulation of translational fidelity / ribosome-associated ubiquitin-dependent protein catabolic process / GDP-dissociation inhibitor activity / pre-mRNA 5'-splice site binding / preribosome, small subunit precursor / nonfunctional rRNA decay / telomeric DNA binding / mRNA destabilization / signaling receptor activator activity / negative regulation of translational frameshifting / TOR signaling / negative regulation of mRNA splicing, via spliceosome / translational elongation / 90S preribosome / G-protein alpha-subunit binding / ribosomal subunit export from nucleus / protein-RNA complex assembly / ribosomal small subunit export from nucleus / translation regulator activity / positive regulation of autophagy / translation repressor activity / rescue of stalled ribosome / DNA-(apurinic or apyrimidinic site) endonuclease activity / telomere maintenance / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosomal large subunit biogenesis / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA / small-subunit processome / maintenance of translational fidelity / modification-dependent protein catabolic process / protein tag activity / rRNA processing / ribosome biogenesis / large ribosomal subunit / ribosome binding / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / 5S rRNA binding / ribosomal large subunit assembly / cytosolic small ribosomal subunit / large ribosomal subunit rRNA binding / small ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / cytoplasmic translation / negative regulation of translation / rRNA binding / protein ubiquitination / ribosome / structural constituent of ribosome / G protein-coupled receptor signaling pathway / translation / ribonucleoprotein complex / mRNA binding / ubiquitin protein ligase binding / negative regulation of apoptotic process / nucleolus / cell surface / RNA binding / extracellular region / zinc ion binding / metal ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
RNA binding protein HABP4/SERBP1 / Stm1-like, N-terminal / Stm1 / Hyaluronan/mRNA-binding protein / Hyaluronan / mRNA binding family / 60s Acidic ribosomal protein / 60S acidic ribosomal protein P0 / : / 50S ribosomal protein L10, insertion domain superfamily / 60S ribosomal protein L10P, insertion domain ...RNA binding protein HABP4/SERBP1 / Stm1-like, N-terminal / Stm1 / Hyaluronan/mRNA-binding protein / Hyaluronan / mRNA binding family / 60s Acidic ribosomal protein / 60S acidic ribosomal protein P0 / : / 50S ribosomal protein L10, insertion domain superfamily / 60S ribosomal protein L10P, insertion domain / Insertion domain in 60S ribosomal protein L10P / : / : / Ribosomal protein S26e signature. / Ribosomal protein L41 / Ribosomal protein L41 / Ribosomal protein S21e, conserved site / Ribosomal protein S21e signature. / Ribosomal protein L1, conserved site / Ribosomal protein S26e / Ribosomal protein S26e superfamily / Ribosomal protein S26e / Ribosomal protein L1 signature. / : / Ribosomal protein S12e signature. / Ribosomal protein L1 / Ribosomal protein S12e / Ribosomal protein L29e / Ribosomal L29e protein family / Small (40S) ribosomal subunit Asc1/RACK1 / Ribosomal protein S5, eukaryotic/archaeal / Ribosomal protein S21e / Ribosomal protein S21e superfamily / Ribosomal protein S21e / Ribosomal protein L13e, conserved site / Ribosomal protein L13e signature. / Ribosomal protein S2, eukaryotic / S27a-like superfamily / Ribosomal protein L22e / Ribosomal protein L22e superfamily / Ribosomal L22e protein family / Ribosomal protein L10e, conserved site / Ribosomal protein L10e signature. / Ribosomal protein L27e, conserved site / Ribosomal protein L27e signature. / Ribosomal protein L10e / 40S Ribosomal protein S10 / Ribosomal protein L38e / Ribosomal protein L38e superfamily / Ribosomal L38e protein family / : / Ribosomal protein S7e signature. / Ribosomal protein L44e signature. / : / Ribosomal protein L1, 3-layer alpha/beta-sandwich / Plectin/S10, N-terminal / Plectin/S10 domain / Ribosomal protein L24e, conserved site / Ribosomal protein L24e signature. / : / Ribosomal protein S10, eukaryotic/archaeal / Ribosomal protein L19, eukaryotic / Ribosomal protein S8e subdomain, eukaryotes / Ribosomal protein L19/L19e conserved site / Ribosomal protein L19e signature. / Ribosomal protein L6e signature. / Ribosomal protein L13e / Ribosomal protein L13e / 60S ribosomal protein L18a/ L20, eukaryotes / Ribosomal protein S25 / S25 ribosomal protein / Ribosomal protein S27a / Ribosomal protein S17e, conserved site / : / Ribosomal protein S27a / Ribosomal protein S17e signature. / Ribosomal protein S27a / Ribosomal protein S3Ae, conserved site / Ribosomal protein S3Ae signature. / Ribosomal protein L44e / Ribosomal protein S30 / Ribosomal protein L44 / Ribosomal protein S30 / Ribosomal protein S2, eukaryotic/archaeal / Ribosomal protein L34e, conserved site / Ribosomal protein L34e signature. / Ribosomal protein L5 eukaryotic, C-terminal / Ribosomal L18 C-terminal region / Ribosomal protein L30e signature 1. / 50S ribosomal protein L18Ae/60S ribosomal protein L20 and L18a / 40S ribosomal protein S29/30S ribosomal protein S14 type Z / 40S ribosomal protein S4, C-terminal domain / Ribosomal L40e family / 40S ribosomal protein S4 C-terminus / Ribosomal protein S27e signature. / Ribosomal protein S4e, N-terminal, conserved site / Ribosomal protein S4e signature. / Ribosomal protein 50S-L18Ae/60S-L20/60S-L18A / Ribosomal proteins 50S-L18Ae/60S-L20/60S-L18A / Ribosomal protein L23/L25, N-terminal
Similarity search - Domain/homology
Chem-3K5 / HYGROMYCIN B / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein eS4 / Large ribosomal subunit protein eL37 / Large ribosomal subunit protein eL38 / Small ribosomal subunit protein uS19 ...Chem-3K5 / HYGROMYCIN B / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein eS4 / Large ribosomal subunit protein eL37 / Large ribosomal subunit protein eL38 / Small ribosomal subunit protein uS19 / Large ribosomal subunit protein eL19 / Ribosome-associated protein STM1 / Large ribosomal subunit protein eL40 / Large ribosomal subunit protein eL22 / Large ribosomal subunit protein eL30 / Small ribosomal subunit protein uS17 / Large ribosomal subunit protein eL43 / Small ribosomal subunit protein eS30 / Small ribosomal subunit protein uS14 / 60S ribosomal protein L42-B / Ribosomal protein S7 / 40S ribosomal protein S17-B / 40S ribosomal protein S26 / Ribosomal protein L22 / 60S ribosomal protein L7-A / 60S ribosomal protein L28 / 60S ribosomal protein L33-A / 40S ribosomal protein S27 / 40S ribosomal protein S10-A / Ribosomal protein S10 / 40S ribosomal protein S3 / 40S ribosomal protein S6 / Ribosomal protein L13 / Small ribosomal subunit protein uS5 / 60S ribosomal protein L20 / 40S ribosomal protein S28-B / 60S ribosomal protein L8 / Small ribosomal subunit protein eS1 / Small ribosomal subunit protein uS2 / 40S ribosomal protein S12 / Guanine nucleotide-binding protein subunit beta-like protein / 40S ribosomal protein S24 / 60S ribosomal protein L9-B / 60S ribosomal protein L23-A / 60S ribosomal protein L24-A / 60S ribosomal protein L18-A / 40S ribosomal protein S19-A / 60S ribosomal protein L12-A / 40S ribosomal protein S7 / 40S ribosomal protein S25 / 60S ribosomal protein L29 / 40S ribosomal protein S22-A / 40S ribosomal protein S8 / Ribosomal protein S23 (S12) / 40S ribosomal protein S14-A / 60S ribosomal protein L34-B / 60S ribosomal protein L21-A / 60S ribosomal protein L31-B / 60S ribosomal protein L11-B / Ribosomal protein S4 / 60S ribosomal protein L2-B / 60S ribosomal protein L14-B / Ribosomal protein L24 / 40S ribosomal protein S18-B / Ribosomal protein / 40S ribosomal protein S13 / 60S ribosomal protein L4-B / 60S ribosomal protein L13 / 60S ribosomal protein L25 / Ribosomal protein L29 / 60S acidic ribosomal protein P0 / Uncharacterized protein CaJ7.0206 / Large ribosomal subunit protein eL32 / Small ribosomal subunit protein uS9 / Large ribosomal subunit protein eL36 / Small ribosomal subunit protein eS32 / Large ribosomal subunit protein uL3 / Ubiquitin-ribosomal protein eS31 fusion protein / Large ribosomal subunit protein eL15 / Large ribosomal subunit protein uL16 / Large ribosomal subunit protein eL39 / 60S ribosomal protein L6 / Large ribosomal subunit protein eL27 / Small ribosomal subunit protein eS21
Similarity search - Component
Biological speciesCandida albicans (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.05 Å
AuthorsKolosova, O. / Zgadzay, Y. / Yusupov, M.
Funding support France, Russian Federation, 4items
OrganizationGrant numberCountry
Foundation for Medical Research (France)DEQ20181039600 France
Foundation for Medical Research (France)DBF20160635745 France
Foundation for Medical Research (France)FDT202204014886 France
Russian Science Foundation20-65-47031 Russian Federation
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2025
Title: Mechanism of read-through enhancement by aminoglycosides and mefloquine
Authors: Kolosova, O. / Zgadzay, Y. / Yusupov, M.
History
DepositionMar 7, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 18, 2024Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2025Group: Database references / Structure summary / Category: citation / pdbx_entry_details
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
1: 25S
3: 5S
4: 5.8S
j: 60S ribosomal protein L2-B
k: 60S ribosomal protein L3
l: 60S ribosomal protein L4-B
m: Uncharacterized protein CaJ7.0206
n: 60S ribosomal protein L6
o: 60S ribosomal protein L7-A
p: 60S ribosomal protein L8
q: 60S ribosomal protein L9-B
r: 60S ribosomal protein L10
s: 60S ribosomal protein L11-B
t: 60S ribosomal protein L13
u: 60S ribosomal protein L14-B
v: 60S ribosomal protein L15-A
w: Ribosomal protein L13
x: Ribosomal protein L22
y: 60S ribosomal protein L18-A
z: 60S ribosomal protein L19-A
0: 60S ribosomal protein L20
2: 60S ribosomal protein L21-A
5: 60S ribosomal protein L22-B
6: 60S ribosomal protein L23-A
7: 60S ribosomal protein L24-A
8: 60S ribosomal protein L25
9: Ribosomal protein L24
AA: 60S ribosomal protein L27
AB: 60S ribosomal protein L28
AC: 60S ribosomal protein L29
AD: 60S ribosomal protein L30
AE: 60S ribosomal protein L31-B
AF: 60S ribosomal protein L32
AG: 60S ribosomal protein L33-A
AH: 60S ribosomal protein L34-B
AI: Ribosomal protein L29
AJ: 60S ribosomal protein L36
AK: 60S ribosomal protein L37-B
AL: 60S ribosomal protein L38
AM: 60S ribosomal protein L39
AN: 60S ribosomal protein L40-B
AO: 60S ribosomal protein L41
AP: 60S ribosomal protein L42-B
AQ: 60S ribosomal protein L43-A
i: 60S ribosomal protein CAALFM_C304810CA
B: 18S
C: 40S ribosomal protein S0
D: 40S ribosomal protein S1
E: Ribosomal protein S5
F: Ribosomal protein S3
G: 40S ribosomal protein S4
H: Ribosomal protein S7
I: 40S ribosomal protein S6
J: 40S ribosomal protein S7
K: 40S ribosomal protein S8
L: Ribosomal protein S4
M: 40S ribosomal protein S10-A
N: 40S ribosomal protein S11A
O: 40S ribosomal protein S12
P: 40S ribosomal protein S13
Q: 40S ribosomal protein S14-A
R: 40S ribosomal protein S15
S: 40S ribosomal protein S16
T: 40S ribosomal protein S17-B
U: 40S ribosomal protein S18-B
V: 40S ribosomal protein S19-A
W: Ribosomal protein S10
X: 40S ribosomal protein S21
Y: 40S ribosomal protein S22-A
Z: Ribosomal protein S23 (S12)
a: 40S ribosomal protein S24
b: 40S ribosomal protein S25
c: 40S ribosomal protein S26
d: 40S ribosomal protein S27
e: 40S ribosomal protein S28-B
f: 40S ribosomal protein S29A
g: 40S ribosomal protein S30
h: Ubiquitin-40S ribosomal protein S31 fusion protein
AR: Guanine nucleotide-binding protein subunit beta-like protein
AS: 25S
AT: 5S
AU: 5.8S
AW: 60S ribosomal protein L2-B
AX: 60S ribosomal protein L3
AY: 60S ribosomal protein L4-B
AZ: Uncharacterized protein CaJ7.0206
BA: 60S ribosomal protein L6
BB: 60S ribosomal protein L7-A
BC: 60S ribosomal protein L8
BD: 60S ribosomal protein L9-B
BE: 60S ribosomal protein L10
BF: 60S ribosomal protein L11-B
BG: 60S ribosomal protein L13
BH: 60S ribosomal protein L14-B
BI: 60S ribosomal protein L15-A
BJ: Ribosomal protein L13
BK: Ribosomal protein L22
BL: 60S ribosomal protein L18-A
BM: 60S ribosomal protein L19-A
BN: 60S ribosomal protein L20
BO: 60S ribosomal protein L21-A
BP: 60S ribosomal protein L22-B
BQ: 60S ribosomal protein L23-A
BR: 60S ribosomal protein L24-A
BS: 60S ribosomal protein L25
BT: Ribosomal protein L24
BU: 60S ribosomal protein L27
BV: 60S ribosomal protein L28
BW: 60S ribosomal protein L29
BX: 60S ribosomal protein L30
BY: 60S ribosomal protein L31-B
BZ: 60S ribosomal protein L32
CA: 60S ribosomal protein L33-A
CB: 60S ribosomal protein L34-B
CC: Ribosomal protein L29
CD: 60S ribosomal protein L36
CE: 60S ribosomal protein L37-B
CF: 60S ribosomal protein L38
CG: 60S ribosomal protein L39
CH: 60S ribosomal protein L40-B
CI: 60S ribosomal protein L41
CJ: 60S ribosomal protein L42-B
CK: 60S ribosomal protein L43-A
CL: 60S ribosomal protein CAALFM_C304810CA
CM: 18S
CN: 40S ribosomal protein S0
CO: 40S ribosomal protein S1
CP: Ribosomal protein S5
CQ: Ribosomal protein S3
CR: 40S ribosomal protein S4
CS: Ribosomal protein S7
CT: 40S ribosomal protein S6
CU: 40S ribosomal protein S7
CV: 40S ribosomal protein S8
CW: Ribosomal protein S4
CX: 40S ribosomal protein S10-A
CY: 40S ribosomal protein S11A
CZ: 40S ribosomal protein S12
DA: 40S ribosomal protein S13
DB: 40S ribosomal protein S14-A
DC: 40S ribosomal protein S15
DD: 40S ribosomal protein S16
DE: 40S ribosomal protein S17-B
DF: 40S ribosomal protein S18-B
DG: 40S ribosomal protein S19-A
DH: Ribosomal protein S10
DI: 40S ribosomal protein S21
DJ: 40S ribosomal protein S22-A
DK: Ribosomal protein S23 (S12)
DL: 40S ribosomal protein S24
DM: 40S ribosomal protein S25
DN: 40S ribosomal protein S26
DO: 40S ribosomal protein S27
DP: 40S ribosomal protein S28-B
DQ: 40S ribosomal protein S29A
DR: 40S ribosomal protein S30
DS: Ubiquitin-40S ribosomal protein S31 fusion protein
DT: Guanine nucleotide-binding protein subunit beta-like protein
P0: 60S acidic ribosomal protein P0
12: 60S ribosomal protein L12-A
L1: Ribosomal protein
l1: Ribosomal protein
p0: 60S acidic ribosomal protein P0
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,404,3841394
Polymers6,371,199163
Non-polymers33,1861231
Water54030
1
1: 25S
3: 5S
4: 5.8S
j: 60S ribosomal protein L2-B
k: 60S ribosomal protein L3
l: 60S ribosomal protein L4-B
m: Uncharacterized protein CaJ7.0206
n: 60S ribosomal protein L6
o: 60S ribosomal protein L7-A
p: 60S ribosomal protein L8
q: 60S ribosomal protein L9-B
r: 60S ribosomal protein L10
s: 60S ribosomal protein L11-B
t: 60S ribosomal protein L13
u: 60S ribosomal protein L14-B
v: 60S ribosomal protein L15-A
w: Ribosomal protein L13
x: Ribosomal protein L22
y: 60S ribosomal protein L18-A
z: 60S ribosomal protein L19-A
0: 60S ribosomal protein L20
2: 60S ribosomal protein L21-A
5: 60S ribosomal protein L22-B
6: 60S ribosomal protein L23-A
7: 60S ribosomal protein L24-A
8: 60S ribosomal protein L25
9: Ribosomal protein L24
AA: 60S ribosomal protein L27
AB: 60S ribosomal protein L28
AC: 60S ribosomal protein L29
AD: 60S ribosomal protein L30
AE: 60S ribosomal protein L31-B
AF: 60S ribosomal protein L32
AG: 60S ribosomal protein L33-A
AH: 60S ribosomal protein L34-B
AI: Ribosomal protein L29
AJ: 60S ribosomal protein L36
AK: 60S ribosomal protein L37-B
AL: 60S ribosomal protein L38
AM: 60S ribosomal protein L39
AN: 60S ribosomal protein L40-B
AO: 60S ribosomal protein L41
AP: 60S ribosomal protein L42-B
AQ: 60S ribosomal protein L43-A
i: 60S ribosomal protein CAALFM_C304810CA
B: 18S
C: 40S ribosomal protein S0
D: 40S ribosomal protein S1
E: Ribosomal protein S5
F: Ribosomal protein S3
G: 40S ribosomal protein S4
H: Ribosomal protein S7
I: 40S ribosomal protein S6
J: 40S ribosomal protein S7
K: 40S ribosomal protein S8
L: Ribosomal protein S4
M: 40S ribosomal protein S10-A
N: 40S ribosomal protein S11A
O: 40S ribosomal protein S12
P: 40S ribosomal protein S13
Q: 40S ribosomal protein S14-A
R: 40S ribosomal protein S15
S: 40S ribosomal protein S16
T: 40S ribosomal protein S17-B
U: 40S ribosomal protein S18-B
V: 40S ribosomal protein S19-A
W: Ribosomal protein S10
X: 40S ribosomal protein S21
Y: 40S ribosomal protein S22-A
Z: Ribosomal protein S23 (S12)
a: 40S ribosomal protein S24
b: 40S ribosomal protein S25
c: 40S ribosomal protein S26
d: 40S ribosomal protein S27
e: 40S ribosomal protein S28-B
f: 40S ribosomal protein S29A
g: 40S ribosomal protein S30
h: Ubiquitin-40S ribosomal protein S31 fusion protein
AR: Guanine nucleotide-binding protein subunit beta-like protein
P0: 60S acidic ribosomal protein P0
12: 60S ribosomal protein L12-A
l1: Ribosomal protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,215,471877
Polymers3,194,49582
Non-polymers20,976795
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
AS: 25S
AT: 5S
AU: 5.8S
AW: 60S ribosomal protein L2-B
AX: 60S ribosomal protein L3
AY: 60S ribosomal protein L4-B
AZ: Uncharacterized protein CaJ7.0206
BA: 60S ribosomal protein L6
BB: 60S ribosomal protein L7-A
BC: 60S ribosomal protein L8
BD: 60S ribosomal protein L9-B
BE: 60S ribosomal protein L10
BF: 60S ribosomal protein L11-B
BG: 60S ribosomal protein L13
BH: 60S ribosomal protein L14-B
BI: 60S ribosomal protein L15-A
BJ: Ribosomal protein L13
BK: Ribosomal protein L22
BL: 60S ribosomal protein L18-A
BM: 60S ribosomal protein L19-A
BN: 60S ribosomal protein L20
BO: 60S ribosomal protein L21-A
BP: 60S ribosomal protein L22-B
BQ: 60S ribosomal protein L23-A
BR: 60S ribosomal protein L24-A
BS: 60S ribosomal protein L25
BT: Ribosomal protein L24
BU: 60S ribosomal protein L27
BV: 60S ribosomal protein L28
BW: 60S ribosomal protein L29
BX: 60S ribosomal protein L30
BY: 60S ribosomal protein L31-B
BZ: 60S ribosomal protein L32
CA: 60S ribosomal protein L33-A
CB: 60S ribosomal protein L34-B
CC: Ribosomal protein L29
CD: 60S ribosomal protein L36
CE: 60S ribosomal protein L37-B
CF: 60S ribosomal protein L38
CG: 60S ribosomal protein L39
CH: 60S ribosomal protein L40-B
CI: 60S ribosomal protein L41
CJ: 60S ribosomal protein L42-B
CK: 60S ribosomal protein L43-A
CL: 60S ribosomal protein CAALFM_C304810CA
CM: 18S
CN: 40S ribosomal protein S0
CO: 40S ribosomal protein S1
CP: Ribosomal protein S5
CQ: Ribosomal protein S3
CR: 40S ribosomal protein S4
CS: Ribosomal protein S7
CT: 40S ribosomal protein S6
CU: 40S ribosomal protein S7
CV: 40S ribosomal protein S8
CW: Ribosomal protein S4
CX: 40S ribosomal protein S10-A
CY: 40S ribosomal protein S11A
CZ: 40S ribosomal protein S12
DA: 40S ribosomal protein S13
DB: 40S ribosomal protein S14-A
DC: 40S ribosomal protein S15
DD: 40S ribosomal protein S16
DE: 40S ribosomal protein S17-B
DF: 40S ribosomal protein S18-B
DG: 40S ribosomal protein S19-A
DH: Ribosomal protein S10
DI: 40S ribosomal protein S21
DJ: 40S ribosomal protein S22-A
DK: Ribosomal protein S23 (S12)
DL: 40S ribosomal protein S24
DM: 40S ribosomal protein S25
DN: 40S ribosomal protein S26
DO: 40S ribosomal protein S27
DP: 40S ribosomal protein S28-B
DQ: 40S ribosomal protein S29A
DR: 40S ribosomal protein S30
DS: Ubiquitin-40S ribosomal protein S31 fusion protein
DT: Guanine nucleotide-binding protein subunit beta-like protein
L1: Ribosomal protein
p0: 60S acidic ribosomal protein P0
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,188,913517
Polymers3,176,70381
Non-polymers12,210436
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)298.810, 292.840, 450.180
Angle α, β, γ (deg.)90.00, 100.11, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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RNA chain , 4 types, 8 molecules 1AS3AT4AUBCM

#1: RNA chain 25S


Mass: 1085278.125 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast)
#2: RNA chain 5S


Mass: 38943.129 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast)
#3: RNA chain 5.8S


Mass: 50683.906 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast)
#46: RNA chain 18S


Mass: 575838.625 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast)

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60S ribosomal protein ... , 38 types, 75 molecules jAWkAXlAYnBAoBBpBCqBDrBEsBFtBGuBHvBIyBLzBM0BN...

#4: Protein 60S ribosomal protein L2-B


Mass: 27366.596 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: A0A8H6F1X9
#5: Protein 60S ribosomal protein L3


Mass: 44040.848 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: Q59LS1
#6: Protein 60S ribosomal protein L4-B


Mass: 39282.352 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: A0A8H6F4H4
#8: Protein 60S ribosomal protein L6


Mass: 19798.002 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: Q9P834
#9: Protein 60S ribosomal protein L7-A


Mass: 27446.961 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: A0A8H6BVN2
#10: Protein 60S ribosomal protein L8


Mass: 28549.424 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: A0A8H6C337
#11: Protein 60S ribosomal protein L9-B


Mass: 21755.217 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: A0A8H6C3N3
#12: Protein 60S ribosomal protein L10


Mass: 25236.297 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: Q5AIB8
#13: Protein 60S ribosomal protein L11-B


Mass: 19859.805 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: A0A8H6F1S5
#14: Protein 60S ribosomal protein L13


Mass: 23105.771 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: A0A8H6F5V7
#15: Protein 60S ribosomal protein L14-B


Mass: 14748.476 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: A0A8H6F332
#16: Protein 60S ribosomal protein L15-A


Mass: 24389.256 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: Q5A6R1
#19: Protein 60S ribosomal protein L18-A


Mass: 20817.367 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: A0A8H6C4Y1
#20: Protein 60S ribosomal protein L19-A


Mass: 21942.750 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: A0A1D8PK40
#21: Protein 60S ribosomal protein L20


Mass: 20376.859 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: A0A8H6BZJ3
#22: Protein 60S ribosomal protein L21-A


Mass: 18049.945 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: A0A8H6F1C8
#23: Protein 60S ribosomal protein L22-B


Mass: 14107.862 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: A0A1D8PM41
#24: Protein 60S ribosomal protein L23-A


Mass: 14494.999 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: A0A8H6C444
#25: Protein 60S ribosomal protein L24-A


Mass: 17430.322 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: A0A8H6C4U1
#26: Protein 60S ribosomal protein L25


Mass: 15873.581 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: A0A8H6F6A1
#28: Protein 60S ribosomal protein L27


Mass: 15551.407 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: Q9P843
#29: Protein 60S ribosomal protein L28


Mass: 16703.367 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: A0A8H6BVY8
#30: Protein 60S ribosomal protein L29


Mass: 7135.336 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: A0A8H6F0G8
#31: Protein 60S ribosomal protein L30


Mass: 11520.384 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: A0A1D8PM75
#32: Protein 60S ribosomal protein L31-B


Mass: 12993.149 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: A0A8H6F1M1
#33: Protein 60S ribosomal protein L32


Mass: 14993.688 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: O94008
#34: Protein 60S ribosomal protein L33-A


Mass: 12138.237 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: A0A8H6BW57
#35: Protein 60S ribosomal protein L34-B


Mass: 13774.282 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: A0A8H6F171
#37: Protein 60S ribosomal protein L36 / L39


Mass: 11096.161 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: P47834
#38: Protein 60S ribosomal protein L37-B


Mass: 10102.830 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: A0A1D8PF45
#39: Protein 60S ribosomal protein L38


Mass: 8911.532 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: A0A1D8PG16
#40: Protein 60S ribosomal protein L39 / L46


Mass: 6347.549 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: Q96W55
#41: Protein 60S ribosomal protein L40-B


Mass: 6078.412 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: A0A1D8PL68
#42: Protein/peptide 60S ribosomal protein L41


Mass: 3396.280 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: P9WER7
#43: Protein 60S ribosomal protein L42-B


Mass: 12259.631 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: A0A8H6BR69
#44: Protein 60S ribosomal protein L43-A


Mass: 10136.844 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: A0A1D8PP14
#45: Protein 60S ribosomal protein CAALFM_C304810CA


Mass: 29126.141 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: A0A1D8PK71
#81: Protein 60S ribosomal protein L12-A


Mass: 17791.539 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: A0A8H6C5X8

-
Protein , 5 types, 10 molecules mAZhDSARDTP0p0L1l1

#7: Protein Uncharacterized protein CaJ7.0206


Mass: 34557.977 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: G1UAA6
#78: Protein Ubiquitin-40S ribosomal protein S31 fusion protein


Mass: 22615.525 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: Q5A109
#79: Protein Guanine nucleotide-binding protein subunit beta-like protein


Mass: 34593.934 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: A0A8H6C3E7
#80: Protein 60S acidic ribosomal protein P0


Mass: 33302.633 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: G1UA71
#82: Protein Ribosomal protein


Mass: 24416.736 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: A0A8H6F4E7

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Ribosomal protein ... , 10 types, 20 molecules wBJxBK9BTAICCECPFCQHCSLCWWDHZDK

#17: Protein Ribosomal protein L13


Mass: 22685.850 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: A0A8H6BZ56
#18: Protein Ribosomal protein L22


Mass: 21002.861 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: A0A8H6BUG0
#27: Protein Ribosomal protein L24


Mass: 14215.550 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: A0A8H6F3X2
#36: Protein Ribosomal protein L29


Mass: 14118.759 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: A0A8H6F6B7
#49: Protein Ribosomal protein S5


Mass: 26917.314 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: A0A8H6BZ90
#50: Protein Ribosomal protein S3


Mass: 27313.570 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: A0A8H6BYS1
#52: Protein Ribosomal protein S7


Mass: 25319.922 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: A0A8H6BS29
#56: Protein Ribosomal protein S4


Mass: 21765.146 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: A0A8H6F1X2
#67: Protein Ribosomal protein S10


Mass: 13366.540 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: A0A8H6BYJ9
#70: Protein Ribosomal protein S23 (S12)


Mass: 16000.784 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: A0A8H6F0V0

+
40S ribosomal protein ... , 25 types, 50 molecules CCNDCOGCRICTJCUKCVMCXNCYOCZPDAQDBRDCSDDTDEUDF...

#47: Protein 40S ribosomal protein S0


Mass: 28759.307 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: A0A8H6C395
#48: Protein 40S ribosomal protein S1


Mass: 29041.859 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: A0A8H6C387
#51: Protein 40S ribosomal protein S4


Mass: 29435.354 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: A0A1D8PCI6
#53: Protein 40S ribosomal protein S6


Mass: 27146.469 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: A0A8H6BZ37
#54: Protein 40S ribosomal protein S7


Mass: 21285.818 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: A0A8H6C655
#55: Protein 40S ribosomal protein S8


Mass: 22801.979 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: A0A8H6F0S0
#57: Protein 40S ribosomal protein S10-A


Mass: 13836.824 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: A0A8H6BWQ8
#58: Protein 40S ribosomal protein S11A


Mass: 17638.648 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: A0A1D8PN83
#59: Protein 40S ribosomal protein S12


Mass: 15715.855 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: A0A8H6C3A1
#60: Protein 40S ribosomal protein S13


Mass: 16976.787 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: A0A8H6F4G0
#61: Protein 40S ribosomal protein S14-A


Mass: 14052.112 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: A0A8H6F0V4
#62: Protein 40S ribosomal protein S15


Mass: 15967.796 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: A0A1D8PK22
#63: Protein 40S ribosomal protein S16


Mass: 15769.456 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: O94017
#64: Protein 40S ribosomal protein S17-B


Mass: 15770.298 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: A0A8H6BTR7
#65: Protein 40S ribosomal protein S18-B


Mass: 17023.785 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: A0A8H6F3Y8
#66: Protein 40S ribosomal protein S19-A


Mass: 16097.218 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: A0A8H6C5L4
#68: Protein 40S ribosomal protein S21


Mass: 9652.814 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: Q9P844
#69: Protein 40S ribosomal protein S22-A


Mass: 14807.189 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: A0A8H6F0N4
#71: Protein 40S ribosomal protein S24


Mass: 15546.922 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: A0A8H6C3K1
#72: Protein 40S ribosomal protein S25


Mass: 11633.762 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: A0A8H6EZQ8
#73: Protein 40S ribosomal protein S26


Mass: 13606.099 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: A0A8H6BTS1
#74: Protein 40S ribosomal protein S27


Mass: 8982.504 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: A0A8H6BWE6
#75: Protein 40S ribosomal protein S28-B


Mass: 7536.808 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: A0A8H6C0A5
#76: Protein 40S ribosomal protein S29A


Mass: 6615.582 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: A0A1D8PTR4
#77: Protein 40S ribosomal protein S30


Mass: 7127.437 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: A0A1D8PSK2

-
Non-polymers , 5 types, 1261 molecules

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


Mass: 24.305 Da / Num. of mol.: 1210 / Source method: obtained synthetically / Formula: Mg
#84: Chemical ChemComp-3K5 / 3-O-acetyl-2-O-(3-O-acetyl-6-deoxy-beta-D-glucopyranosyl)-6-deoxy-1-O-{[(2R,2'S,3a'R,4''S,5''R,6'S,7a'S)-5''-methyl-4''-{[(2E)-3-phenylprop-2-enoyl]oxy}decahydrodispiro[oxirane-2,3'-[1]benzofuran-2',2''-pyran]-6'-yl]carbonyl}-beta-D-glucopyranose / Phyllanthoside


Mass: 804.831 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C40H52O17
#85: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: Zn
#86: Chemical ChemComp-HYG / HYGROMYCIN B / HYGROMIX / ANTIHELMYCIN / HYDROMYCIN B / DESTOMYSIN / ANTIBIOTIC A-396-II


Mass: 527.520 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C20H37N3O13 / Feature type: SUBJECT OF INVESTIGATION / Comment: antibiotic*YM
#87: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 30 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 3.04 Å3/Da / Density % sol: 59.59 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 7
Details: PEG 20K, KSCN, Mg Acetate, K - acetate, Bis-Tris-Acetate, Glycerol, Spermidine, phyllanthoside

-
Data collection

DiffractionMean temperature: 173 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 19, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.05→163.72 Å / Num. obs: 1429361 / % possible obs: 99.1 % / Redundancy: 14.5 % / Biso Wilson estimate: 64.17 Å2 / CC1/2: 0.986 / CC star: 0.996 / Rmerge(I) obs: 0.838 / Rpim(I) all: 0.226 / Rrim(I) all: 0.868 / Net I/σ(I): 3.69
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
3.05-3.12.659679550.0442.7541
3.1-3.152.641639670.0442.7341
3.15-3.22.614599980.0562.7061
3.2-3.252.602564020.0562.6931
3.25-3.32.541530180.0672.6311
3.3-3.352.492499080.0792.581
3.35-3.42.41471800.0822.4961
3.4-3.452.362442460.0962.4471
3.45-3.52.263418610.1252.3441
3.5-3.62.112768780.1542.1891
3.6-3.71.939686670.2082.0111
3.7-3.81.712614300.2781.7771
3.8-3.91.536524510.3411.5971
3.9-41.43499890.4351.4811
4-4.51.1211899500.6691.161
4.5-70.6233267090.9180.6461
7-100.291784710.9880.3021
10-500.092399990.9990.0951
50-163.720.0522820.9990.0541

-
Processing

Software
NameVersionClassification
PHENIX(1.19rc4_4035: ???)refinement
XDSdata reduction
XSCALEdata scaling
REFMACphasing
RefinementMethod to determine structure: SAD / Resolution: 3.05→163.72 Å / SU ML: 0.75 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 39.15 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3068 1999 0.14 %
Rwork0.2828 --
obs0.2828 1429093 99.07 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.05→163.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms183237 224124 1443 0 408804
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003438556
X-RAY DIFFRACTIONf_angle_d0.781643246
X-RAY DIFFRACTIONf_dihedral_angle_d16.047152172
X-RAY DIFFRACTIONf_chiral_restr0.04580555
X-RAY DIFFRACTIONf_plane_restr0.00642502
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.05-3.130.42011430.4083101920X-RAY DIFFRACTION99
3.13-3.210.35551430.3874102228X-RAY DIFFRACTION100
3.21-3.310.37381430.3746102131X-RAY DIFFRACTION100
3.31-3.410.38011440.3734102321X-RAY DIFFRACTION100
3.41-3.530.40731430.3713102295X-RAY DIFFRACTION100
3.53-3.680.38961430.3553102046X-RAY DIFFRACTION99
3.68-3.840.34151410.3324101252X-RAY DIFFRACTION99
3.84-4.050.33691400.31199707X-RAY DIFFRACTION97
4.05-4.30.33031430.292102591X-RAY DIFFRACTION100
4.3-4.630.29511440.2673102682X-RAY DIFFRACTION100
4.63-5.10.31751440.2491102609X-RAY DIFFRACTION100
5.1-5.830.28831400.2248100042X-RAY DIFFRACTION97
5.83-7.350.2441440.22103063X-RAY DIFFRACTION100
7.35-163.720.19331440.1982102207X-RAY DIFFRACTION98

+
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