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- PDB-4kzy: Rabbit 40S ribosomal subunit in complex with eIF1 and eIF1A. -

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Basic information

Entry
Database: PDB / ID: 4kzy
TitleRabbit 40S ribosomal subunit in complex with eIF1 and eIF1A.
Components
  • (40S Ribosomal Protein ...) x 33
  • (human initiation factor ...) x 2
  • 18S Ribosomal RNA
KeywordsRIBOSOME / 40S / translation initiation
Function / homology
Function and homology information


positive regulation of mRNA cis splicing, via spliceosome / multi-eIF complex / eukaryotic 43S preinitiation complex / translation factor activity, RNA binding / eukaryotic 48S preinitiation complex / regulation of translational initiation / Formation of the ternary complex, and subsequently, the 43S complex / laminin receptor activity / Ribosomal scanning and start codon recognition / Translation initiation complex formation ...positive regulation of mRNA cis splicing, via spliceosome / multi-eIF complex / eukaryotic 43S preinitiation complex / translation factor activity, RNA binding / eukaryotic 48S preinitiation complex / regulation of translational initiation / Formation of the ternary complex, and subsequently, the 43S complex / laminin receptor activity / Ribosomal scanning and start codon recognition / Translation initiation complex formation / mammalian oogenesis stage / activation-induced cell death of T cells / positive regulation of signal transduction by p53 class mediator / Formation of a pool of free 40S subunits / phagocytic cup / ubiquitin ligase inhibitor activity / ribosomal small subunit binding / GTP hydrolysis and joining of the 60S ribosomal subunit / TOR signaling / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / L13a-mediated translational silencing of Ceruloplasmin expression / 90S preribosome / T cell proliferation involved in immune response / erythrocyte development / translation regulator activity / ribosomal small subunit export from nucleus / cytosolic ribosome / laminin binding / endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / rough endoplasmic reticulum / gastrulation / MDM2/MDM4 family protein binding / translation initiation factor activity / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / DNA-(apurinic or apyrimidinic site) lyase / rescue of stalled ribosome / ribosome assembly / positive regulation of apoptotic signaling pathway / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / cellular response to leukemia inhibitory factor / maturation of SSU-rRNA / small-subunit processome / translational initiation / protein kinase C binding / positive regulation of protein-containing complex assembly / placenta development / modification-dependent protein catabolic process / spindle / cytoplasmic ribonucleoprotein granule / rRNA processing / G1/S transition of mitotic cell cycle / protein tag activity / positive regulation of canonical Wnt signaling pathway / rhythmic process / ribosome binding / glucose homeostasis / regulation of translation / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / cell body / T cell differentiation in thymus / cytosolic small ribosomal subunit / perikaryon / cytoplasmic translation / mitochondrial inner membrane / tRNA binding / postsynaptic density / cell differentiation / rRNA binding / ribosome / protein ubiquitination / structural constituent of ribosome / ribonucleoprotein complex / translation / positive regulation of protein phosphorylation / positive regulation of apoptotic process / cell division / DNA repair / mRNA binding / centrosome / ubiquitin protein ligase binding / synapse / dendrite / positive regulation of cell population proliferation / nucleolus / negative regulation of apoptotic process / apoptotic process / protein kinase binding / perinuclear region of cytoplasm / Golgi apparatus / endoplasmic reticulum / DNA binding / RNA binding / zinc ion binding / membrane / nucleus / metal ion binding / plasma membrane
Similarity search - Function
Eukaryotic translation initiation factor SUI1 / SUI1 domain superfamily / Translation initiation factor SUI1 / Translation initiation factor SUI1 family profile. / SUI1 domain / Translation initiation factor 1A (eIF-1A), conserved site / Eukaryotic initiation factor 1A signature. / eukaryotic translation initiation factor 1A / Translation initiation factor 1A (eIF-1A) / RNA-binding domain, S1, IF1 type ...Eukaryotic translation initiation factor SUI1 / SUI1 domain superfamily / Translation initiation factor SUI1 / Translation initiation factor SUI1 family profile. / SUI1 domain / Translation initiation factor 1A (eIF-1A), conserved site / Eukaryotic initiation factor 1A signature. / eukaryotic translation initiation factor 1A / Translation initiation factor 1A (eIF-1A) / RNA-binding domain, S1, IF1 type / Translation initiation factor 1A / IF-1 / S1 domain IF1 type profile. / 40S ribosomal protein SA / 40S ribosomal protein SA, C-terminal domain / 40S ribosomal protein SA C-terminus / Ubiquitin-like protein FUBI / : / Ribosomal protein S26e signature. / : / Ribosomal protein S26e / Ribosomal protein S26e superfamily / Ribosomal protein S26e / Ribosomal protein S21e, conserved site / Ribosomal protein S21e signature. / Ribosomal protein S12e signature. / Ribosomal protein S12e / Ribosomal protein S5, eukaryotic/archaeal / Ribosomal protein S19e, conserved site / Ribosomal protein S19e signature. / Small (40S) ribosomal subunit Asc1/RACK1 / Ribosomal protein S21e / Ribosomal protein S2, eukaryotic / Ribosomal protein S21e superfamily / Ribosomal protein S21e / S27a-like superfamily / 40S Ribosomal protein S10 / Ribosomal protein S10, eukaryotic/archaeal / Plectin/S10, N-terminal / Plectin/S10 domain / Ribosomal protein S25 / S25 ribosomal protein / Ribosomal protein S27a / Ribosomal protein S2, eukaryotic/archaeal / : / Ribosomal protein S27a / Ribosomal protein S27a / Ribosomal protein S17e, conserved site / Ribosomal protein S17e signature. / Ribosomal protein S8e subdomain, eukaryotes / Ribosomal protein S30 / Ribosomal protein S30 / 40S ribosomal protein S29/30S ribosomal protein S14 type Z / Ribosomal protein S7e signature. / Ribosomal protein S3, eukaryotic/archaeal / : / Ribosomal protein S19e / Ribosomal protein S3Ae, conserved site / Ribosomal protein S19e / Ribosomal protein S3Ae signature. / Ribosomal_S19e / Ribosomal protein S27e signature. / Ribosomal protein S4e, N-terminal, conserved site / Ribosomal protein S4e signature. / 40S ribosomal protein S4, C-terminal domain / 40S ribosomal protein S4 C-terminus / Ribosomal protein S19A/S15e / Ribosomal protein S8e, conserved site / Ribosomal protein S8e signature. / Ribosomal protein S17e / Ribosomal protein S17e-like superfamily / Ribosomal S17 / Ribosomal protein S6, eukaryotic / Ribosomal protein S4e, N-terminal / RS4NT (NUC023) domain / 40S ribosomal protein S1/3, eukaryotes / Ribosomal S24e conserved site / Ribosomal protein S24e signature. / 40S ribosomal protein S11, N-terminal / Ribosomal_S17 N-terminal / Ribosomal protein S7e / Ribosomal protein S7e / Ribosomal protein S4, KOW domain / Ribosomal protein S4e / Ribosomal protein S4e, central region / Ribosomal protein S4e, central domain superfamily / Ribosomal family S4e / Ribosomal protein S27, zinc-binding domain superfamily / Ribosomal protein S24e / Ribosomal protein S23, eukaryotic/archaeal / Ribosomal protein S24e / Ribosomal protein S6/S6e/A/B/2, conserved site / Ribosomal protein S6e signature. / Ribosomal protein S27 / Ribosomal protein S27 / Ribosomal protein S8e / Ribosomal protein S17, archaeal/eukaryotic / Ribosomal protein S28e conserved site / Ribosomal protein S28e signature. / Ribosomal protein S3Ae / Ribosomal S3Ae family
Similarity search - Domain/homology
: / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein uS4 / Small ribosomal subunit protein eS12 / Small ribosomal subunit protein uS9 / Small ribosomal subunit protein uS10 / Small ribosomal subunit protein RACK1 ...: / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein uS4 / Small ribosomal subunit protein eS12 / Small ribosomal subunit protein uS9 / Small ribosomal subunit protein uS10 / Small ribosomal subunit protein RACK1 / Ubiquitin-ribosomal protein eS31 fusion protein / Small ribosomal subunit protein uS15 / Small ribosomal subunit protein eS7 / Small ribosomal subunit protein uS12 / Small ribosomal subunit protein eS10 / Ubiquitin-like FUBI-ribosomal protein eS30 fusion protein / Small ribosomal subunit protein eS25 / Small ribosomal subunit protein eS26 / Small ribosomal subunit protein uS7 / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein uS2 / Small ribosomal subunit protein eS28 / Small ribosomal subunit protein eS8 / Small ribosomal subunit protein eS4 / Small ribosomal subunit protein eS6 / Small ribosomal subunit protein eS21 / Small ribosomal subunit protein eS19 / Small ribosomal subunit protein eS1 / Small ribosomal subunit protein uS3 / Small ribosomal subunit protein uS13 / Small ribosomal subunit protein uS17 / 40S ribosomal protein S24 / Small ribosomal subunit protein eS17 / Small ribosomal subunit protein eS27 / Small ribosomal subunit protein uS19 / Small ribosomal subunit protein uS5 / Small ribosomal subunit protein uS11 / Small ribosomal subunit protein uS14 / Eukaryotic translation initiation factor 1 / Eukaryotic translation initiation factor 1A, X-chromosomal
Similarity search - Component
Biological speciesHomo sapiens (human)
Oryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 7.01 Å
AuthorsLomakin, I.B. / Steitz, T.A.
CitationJournal: Nature / Year: 2013
Title: The initiation of mammalian protein synthesis and mRNA scanning mechanism.
Authors: Lomakin, I.B. / Steitz, T.A.
History
DepositionMay 30, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 24, 2013Provider: repository / Type: Initial release
Revision 1.1Aug 7, 2013Group: Database references
Revision 1.2Sep 4, 2013Group: Database references
Revision 1.3Sep 20, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 40S Ribosomal Protein SA
B: 40S Ribosomal Protein S3A
C: 40S Ribosomal Protein S2
D: 40S Ribosomal Protein S3
E: 40S Ribosomal Protein S4X
F: 40S Ribosomal Protein S5
G: 40S Ribosomal Protein S6
H: 40S Ribosomal Protein S7
I: 40S Ribosomal Protein S8
J: 40S Ribosomal Protein S9
K: 40S Ribosomal Protein S10
L: 40S Ribosomal Protein S11
M: 40S Ribosomal Protein S12
N: 40S Ribosomal Protein S13
O: 40S Ribosomal Protein S14
P: 40S Ribosomal Protein S15
Q: 40S Ribosomal Protein S16
R: 40S Ribosomal Protein S17
S: 40S Ribosomal Protein S18
T: 40S Ribosomal Protein S19
U: 40S Ribosomal Protein S20
V: 40S Ribosomal Protein S21
W: 40S Ribosomal Protein S15A
X: 40S Ribosomal Protein S23
Y: 40S Ribosomal Protein S24
Z: 40S Ribosomal Protein S25
a: 40S Ribosomal Protein S26
b: 40S Ribosomal Protein S27
c: 40S Ribosomal Protein S28
d: 40S Ribosomal Protein S29
e: 40S Ribosomal Protein S30
f: 40S Ribosomal Protein S27A
g: 40S Ribosomal Protein RACK1
i: 18S Ribosomal RNA
l: human initiation factor eIF1
n: human initiation factor eIF1A


Theoretical massNumber of molelcules
Total (without water)1,255,13436
Polymers1,255,13436
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)296.897, 296.897, 478.305
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

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40S Ribosomal Protein ... , 33 types, 33 molecules ABCDEFGHIJKLMNOPQRSTUVWXYZabcd...

#1: Protein 40S Ribosomal Protein SA


Mass: 32927.988 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TGI6*PLUS
#2: Protein 40S Ribosomal Protein S3A


Mass: 29928.967 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TN72
#3: Protein 40S Ribosomal Protein S2


Mass: 29575.578 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1U2Z9
#4: Protein 40S Ribosomal Protein S3


Mass: 26715.344 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TNM3
#5: Protein 40S Ribosomal Protein S4X


Mass: 29658.920 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TK17
#6: Protein 40S Ribosomal Protein S5


Mass: 22913.453 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TFM5
#7: Protein 40S Ribosomal Protein S6


Mass: 28751.906 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TM55
#8: Protein 40S Ribosomal Protein S7


Mass: 22168.914 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SVB0
#9: Protein 40S Ribosomal Protein S8


Mass: 24163.244 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TJW1
#10: Protein 40S Ribosomal Protein S9


Mass: 22641.564 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: B7NZS8
#11: Protein 40S Ribosomal Protein S10


Mass: 18933.846 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1T168
#12: Protein 40S Ribosomal Protein S11


Mass: 18468.826 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TRM4
#13: Protein 40S Ribosomal Protein S12


Mass: 14538.987 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SFR8
#14: Protein 40S Ribosomal Protein S13


Mass: 17259.389 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SP51
#15: Protein 40S Ribosomal Protein S14


Mass: 16302.772 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1U472
#16: Protein 40S Ribosomal Protein S15


Mass: 17049.182 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1U0Q2
#17: Protein 40S Ribosomal Protein S16


Mass: 16477.377 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SGX4
#18: Protein 40S Ribosomal Protein S17


Mass: 15552.119 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TU13
#19: Protein 40S Ribosomal Protein S18


Mass: 17759.777 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TPG3
#20: Protein 40S Ribosomal Protein S19


Mass: 16235.796 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TN62
#21: Protein 40S Ribosomal Protein S20


Mass: 13398.763 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SIZ2
#22: Protein 40S Ribosomal Protein S21


Mass: 9043.276 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TM82
#23: Protein 40S Ribosomal Protein S15A


Mass: 14865.555 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TG89
#24: Protein 40S Ribosomal Protein S23


Mass: 15844.666 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SZ47
#25: Protein 40S Ribosomal Protein S24


Mass: 15434.267 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TS40
#26: Protein 40S Ribosomal Protein S25


Mass: 13776.224 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TDB3
#27: Protein 40S Ribosomal Protein S26


Mass: 12961.455 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TFE8
#28: Protein 40S Ribosomal Protein S27


Mass: 9480.186 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TZ76
#29: Protein 40S Ribosomal Protein S28


Mass: 7855.052 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TIB4
#30: Protein 40S Ribosomal Protein S29


Mass: 6690.821 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1U7M4
#31: Protein 40S Ribosomal Protein S30


Mass: 14498.884 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1T8A2
#32: Protein 40S Ribosomal Protein S27A


Mass: 18004.041 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SK22
#33: Protein 40S Ribosomal Protein RACK1


Mass: 35115.652 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SJB4

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RNA chain , 1 types, 1 molecules i

#34: RNA chain 18S Ribosomal RNA


Mass: 600900.562 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: GenBank: 283837872

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Human initiation factor ... , 2 types, 2 molecules ln

#35: Protein human initiation factor eIF1


Mass: 12752.498 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EIF1 / Plasmid: pET28a-heIF1tev / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P41567
#36: Protein human initiation factor eIF1A


Mass: 16488.449 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EIF1AX / Plasmid: pET28a-heIF1Atev / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P47813

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Details

Sequence detailsThe reference for chain A is XP_002712810.1 at NCBI which indicates Met at position 1 instead of Ala

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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: 4.85 Å3/Da / Density % sol: 74.63 %
Crystal growTemperature: 292 K / Method: vapor diffusion / pH: 8.5
Details: 0.1M Ammonium acetate, 0.05M Tris-HCl pH 8.5, 2.5% PEG-20K, 4-6% MPD, 5.0mM Mg acetate, 2.0mM TCEP, vapor diffusion, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9789 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 18, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 7.01→120 Å / Num. all: 39111 / Num. obs: 38929 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 464.07 Å2

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Processing

Software
NameVersionClassificationNB
PHENIX1.7.3_928refinement
PDB_EXTRACT3.11data extraction
ADSCQuantumdata collection
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3J3A AND 3J3D

3j3a
PDB Unreleased entry

3j3d
PDB Unreleased entry


Resolution: 7.01→113.236 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.592 / SU ML: 1.01 / σ(F): 1.34 / Phase error: 44.53 / Stereochemistry target values: ML
Details: AUTHORS PERFORMED RIGID BODY REFINEMENT USING THE HUMAN PROTEINS WITH SIDECHAINS FROM PDB ENTRIES 3J3A AND 3J3D. THIS RESULTS IN CLOSE CONTACTS BETWEEN SIDECHAINS
RfactorNum. reflection% reflectionSelection details
Rfree0.3478 1921 5.03 %RANDOM
Rwork0.3662 ---
all0.3653 39111 --
obs0.3653 38188 98.03 %-
Solvent computationShrinkage radii: 1.2 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 100 Å2 / ksol: 0.334 e/Å3
Displacement parametersBiso max: 456.93 Å2 / Biso mean: 235.3539 Å2 / Biso min: 20 Å2
Baniso -1Baniso -2Baniso -3
1-582.5633 Å20 Å20 Å2
2--582.5633 Å20 Å2
3---371.4953 Å2
Refinement stepCycle: LAST / Resolution: 7.01→113.236 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms40341 38071 0 0 78412
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.02683615
X-RAY DIFFRACTIONf_angle_d2.784121263
X-RAY DIFFRACTIONf_chiral_restr0.2414955
X-RAY DIFFRACTIONf_plane_restr0.0228763
X-RAY DIFFRACTIONf_dihedral_angle_d20.72337597
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
7.0103-7.18560.47811210.5072133225481
7.1856-7.37990.47181210.46892548266998
7.3799-7.5970.42911410.43932564270598
7.597-7.84210.40021500.43212563271399
7.8421-8.12230.44361380.42052576271499
8.1223-8.44740.35791370.419526262763100
8.4474-8.83180.42081340.407526142748100
8.8318-9.29720.38221260.423526392765100
9.2972-9.87940.40261340.415326392773100
9.8794-10.64160.40581520.390926092761100
10.6416-11.71160.37241260.38726682794100
11.7116-13.40390.33481490.37226312780100
13.4039-16.87850.37661420.3882669281199
16.8785-113.25060.28421500.3082788293898
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)
12.4224-0.5196-0.41022.1888-0.00682.40090.37670.82080.6629-2.41850.3948-0.2637-0.28660.20852.05065.1136-1.1010.79251.4155-0.26092.81-61.9434110.3641-47.0715
20.0117-0.01330.00340.0046-0.0008-0.0003-0.18670.0427-0.36690.18720.2465-0.18880.13210.313203.2911-0.9493-0.15765.2223-0.89893.1037-127.684577.3705132.3764
30.02390.03310.01740.02630.00760.0053-0.05930.1798-0.4161-0.66350.4136-0.0649-0.28850.071804.3261-0.64620.95884.47030.34073.9466-164.381295.212896.2891
4-0.0145-0.00220.0019-0.029-0.0011-0.0047-0.0960.1135-0.1244-0.31460.3481-0.28220.0853-0.00505.7709-0.60841.02094.29090.37865.1004-120.402145.587239.297
50.0009-0.0168-0.00210.01410.01070.0047-0.2665-0.4093-0.3236-0.0037-0.13370.45730.0098-0.030905.69660.4231-0.14645.36430.00415.2935-103.13538.1583101.7462
60.5848-0.02730.72841.7517-0.46211.0914-0.71960.0582-0.4944-0.45030.3487-0.42320.0247-0.9908-0.0462.9382-1.0437-1.72572.2015-0.44263.2091-106.8181126.806574.1411
73.4553-0.3690.00031.05360.15881.2755-0.5784-0.5677-0.8248-0.30120.20370.23661.30060.1354-1.27151.5749-0.97750.20520.5422-0.2560.5718-91.809487.722747.2796
80.0387-0.00840.03220.0480.00620.05470.00320.0105-0.02640.15070.06310.0513-0.1307-0.0496-03.77020.11930.42823.5530.13412.8946-82.612138.8370.2624
90.07740.0133-0.04330.0480.00610.0282-0.06140.0381-0.10880.03630.0012-0.1011-0.0870.079203.0018-1.18470.86083.07070.92574.4677-53.0411140.716410.0833
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1segid S03A or segid S05A or segid S10A or segid S12A or segid S15A or segid S16A or segid S17A or segid S18A or segid S19A or segid S20A or segid S25A or segid S28A or segid S29A or segid 27aA or segid RACA or (segid 18SA and resid 1207:1683)D1 - 227
2X-RAY DIFFRACTION1segid S03A or segid S05A or segid S10A or segid S12A or segid S15A or segid S16A or segid S17A or segid S18A or segid S19A or segid S20A or segid S25A or segid S28A or segid S29A or segid 27aA or segid RACA or (segid 18SA and resid 1207:1683)F14 - 204
3X-RAY DIFFRACTION1segid S03A or segid S05A or segid S10A or segid S12A or segid S15A or segid S16A or segid S17A or segid S18A or segid S19A or segid S20A or segid S25A or segid S28A or segid S29A or segid 27aA or segid RACA or (segid 18SA and resid 1207:1683)K1 - 98
4X-RAY DIFFRACTION1segid S03A or segid S05A or segid S10A or segid S12A or segid S15A or segid S16A or segid S17A or segid S18A or segid S19A or segid S20A or segid S25A or segid S28A or segid S29A or segid 27aA or segid RACA or (segid 18SA and resid 1207:1683)M9 - 132
5X-RAY DIFFRACTION1segid S03A or segid S05A or segid S10A or segid S12A or segid S15A or segid S16A or segid S17A or segid S18A or segid S19A or segid S20A or segid S25A or segid S28A or segid S29A or segid 27aA or segid RACA or (segid 18SA and resid 1207:1683)P4 - 130
6X-RAY DIFFRACTION1segid S03A or segid S05A or segid S10A or segid S12A or segid S15A or segid S16A or segid S17A or segid S18A or segid S19A or segid S20A or segid S25A or segid S28A or segid S29A or segid 27aA or segid RACA or (segid 18SA and resid 1207:1683)Q6 - 146
7X-RAY DIFFRACTION1segid S03A or segid S05A or segid S10A or segid S12A or segid S15A or segid S16A or segid S17A or segid S18A or segid S19A or segid S20A or segid S25A or segid S28A or segid S29A or segid 27aA or segid RACA or (segid 18SA and resid 1207:1683)R1 - 126
8X-RAY DIFFRACTION1segid S03A or segid S05A or segid S10A or segid S12A or segid S15A or segid S16A or segid S17A or segid S18A or segid S19A or segid S20A or segid S25A or segid S28A or segid S29A or segid 27aA or segid RACA or (segid 18SA and resid 1207:1683)S6 - 142
9X-RAY DIFFRACTION1segid S03A or segid S05A or segid S10A or segid S12A or segid S15A or segid S16A or segid S17A or segid S18A or segid S19A or segid S20A or segid S25A or segid S28A or segid S29A or segid 27aA or segid RACA or (segid 18SA and resid 1207:1683)T4 - 144
10X-RAY DIFFRACTION1segid S03A or segid S05A or segid S10A or segid S12A or segid S15A or segid S16A or segid S17A or segid S18A or segid S19A or segid S20A or segid S25A or segid S28A or segid S29A or segid 27aA or segid RACA or (segid 18SA and resid 1207:1683)U16 - 119
11X-RAY DIFFRACTION1segid S03A or segid S05A or segid S10A or segid S12A or segid S15A or segid S16A or segid S17A or segid S18A or segid S19A or segid S20A or segid S25A or segid S28A or segid S29A or segid 27aA or segid RACA or (segid 18SA and resid 1207:1683)Z41 - 115
12X-RAY DIFFRACTION1segid S03A or segid S05A or segid S10A or segid S12A or segid S15A or segid S16A or segid S17A or segid S18A or segid S19A or segid S20A or segid S25A or segid S28A or segid S29A or segid 27aA or segid RACA or (segid 18SA and resid 1207:1683)c5 - 68
13X-RAY DIFFRACTION1segid S03A or segid S05A or segid S10A or segid S12A or segid S15A or segid S16A or segid S17A or segid S18A or segid S19A or segid S20A or segid S25A or segid S28A or segid S29A or segid 27aA or segid RACA or (segid 18SA and resid 1207:1683)d4 - 56
14X-RAY DIFFRACTION1segid S03A or segid S05A or segid S10A or segid S12A or segid S15A or segid S16A or segid S17A or segid S18A or segid S19A or segid S20A or segid S25A or segid S28A or segid S29A or segid 27aA or segid RACA or (segid 18SA and resid 1207:1683)f82 - 152
15X-RAY DIFFRACTION1segid S03A or segid S05A or segid S10A or segid S12A or segid S15A or segid S16A or segid S17A or segid S18A or segid S19A or segid S20A or segid S25A or segid S28A or segid S29A or segid 27aA or segid RACA or (segid 18SA and resid 1207:1683)g2 - 314
16X-RAY DIFFRACTION1segid S03A or segid S05A or segid S10A or segid S12A or segid S15A or segid S16A or segid S17A or segid S18A or segid S19A or segid S20A or segid S25A or segid S28A or segid S29A or segid 27aA or segid RACA or (segid 18SA and resid 1207:1683)i1 - 1863
17X-RAY DIFFRACTION2segid 18SA and resid 184:209i184 - 209
18X-RAY DIFFRACTION3segid 18SA and resid 305:326i305 - 326
19X-RAY DIFFRACTION4segid 18SA and resid 681:737i681 - 737
20X-RAY DIFFRACTION5segid 18SA and resid 745:787i745 - 787
21X-RAY DIFFRACTION6segid 18SA and resid 1699:1826i1699 - 1826
22X-RAY DIFFRACTION7segid S0aA or segid S3aA or segid S02A or segid S4xA or segid S06A or segid S07A or segid S08A or segid S09A or segid S11A or segid S13A or segid S14A or segid S21A or segid 15aA or segid S23A or segid S24A or segid S26A or segid S27A or segid S30A or (segid 18SA and not resid 184:209 and not resid 305:326 and not resid 681:737 and not resid 745:787 and not resid 1207:1683 and not resid 1699:1826)A2 - 209
23X-RAY DIFFRACTION7segid S0aA or segid S3aA or segid S02A or segid S4xA or segid S06A or segid S07A or segid S08A or segid S09A or segid S11A or segid S13A or segid S14A or segid S21A or segid 15aA or segid S23A or segid S24A or segid S26A or segid S27A or segid S30A or (segid 18SA and not resid 184:209 and not resid 305:326 and not resid 681:737 and not resid 745:787 and not resid 1207:1683 and not resid 1699:1826)B19 - 233
24X-RAY DIFFRACTION7segid S0aA or segid S3aA or segid S02A or segid S4xA or segid S06A or segid S07A or segid S08A or segid S09A or segid S11A or segid S13A or segid S14A or segid S21A or segid 15aA or segid S23A or segid S24A or segid S26A or segid S27A or segid S30A or (segid 18SA and not resid 184:209 and not resid 305:326 and not resid 681:737 and not resid 745:787 and not resid 1207:1683 and not resid 1699:1826)C38 - 263
25X-RAY DIFFRACTION7segid S0aA or segid S3aA or segid S02A or segid S4xA or segid S06A or segid S07A or segid S08A or segid S09A or segid S11A or segid S13A or segid S14A or segid S21A or segid 15aA or segid S23A or segid S24A or segid S26A or segid S27A or segid S30A or (segid 18SA and not resid 184:209 and not resid 305:326 and not resid 681:737 and not resid 745:787 and not resid 1207:1683 and not resid 1699:1826)E1 - 263
26X-RAY DIFFRACTION7segid S0aA or segid S3aA or segid S02A or segid S4xA or segid S06A or segid S07A or segid S08A or segid S09A or segid S11A or segid S13A or segid S14A or segid S21A or segid 15aA or segid S23A or segid S24A or segid S26A or segid S27A or segid S30A or (segid 18SA and not resid 184:209 and not resid 305:326 and not resid 681:737 and not resid 745:787 and not resid 1207:1683 and not resid 1699:1826)G1 - 237
27X-RAY DIFFRACTION7segid S0aA or segid S3aA or segid S02A or segid S4xA or segid S06A or segid S07A or segid S08A or segid S09A or segid S11A or segid S13A or segid S14A or segid S21A or segid 15aA or segid S23A or segid S24A or segid S26A or segid S27A or segid S30A or (segid 18SA and not resid 184:209 and not resid 305:326 and not resid 681:737 and not resid 745:787 and not resid 1207:1683 and not resid 1699:1826)H5 - 194
28X-RAY DIFFRACTION7segid S0aA or segid S3aA or segid S02A or segid S4xA or segid S06A or segid S07A or segid S08A or segid S09A or segid S11A or segid S13A or segid S14A or segid S21A or segid 15aA or segid S23A or segid S24A or segid S26A or segid S27A or segid S30A or (segid 18SA and not resid 184:209 and not resid 305:326 and not resid 681:737 and not resid 745:787 and not resid 1207:1683 and not resid 1699:1826)I2 - 207
29X-RAY DIFFRACTION7segid S0aA or segid S3aA or segid S02A or segid S4xA or segid S06A or segid S07A or segid S08A or segid S09A or segid S11A or segid S13A or segid S14A or segid S21A or segid 15aA or segid S23A or segid S24A or segid S26A or segid S27A or segid S30A or (segid 18SA and not resid 184:209 and not resid 305:326 and not resid 681:737 and not resid 745:787 and not resid 1207:1683 and not resid 1699:1826)J7 - 188
30X-RAY DIFFRACTION7segid S0aA or segid S3aA or segid S02A or segid S4xA or segid S06A or segid S07A or segid S08A or segid S09A or segid S11A or segid S13A or segid S14A or segid S21A or segid 15aA or segid S23A or segid S24A or segid S26A or segid S27A or segid S30A or (segid 18SA and not resid 184:209 and not resid 305:326 and not resid 681:737 and not resid 745:787 and not resid 1207:1683 and not resid 1699:1826)L1 - 158
31X-RAY DIFFRACTION7segid S0aA or segid S3aA or segid S02A or segid S4xA or segid S06A or segid S07A or segid S08A or segid S09A or segid S11A or segid S13A or segid S14A or segid S21A or segid 15aA or segid S23A or segid S24A or segid S26A or segid S27A or segid S30A or (segid 18SA and not resid 184:209 and not resid 305:326 and not resid 681:737 and not resid 745:787 and not resid 1207:1683 and not resid 1699:1826)N2 - 151
32X-RAY DIFFRACTION7segid S0aA or segid S3aA or segid S02A or segid S4xA or segid S06A or segid S07A or segid S08A or segid S09A or segid S11A or segid S13A or segid S14A or segid S21A or segid 15aA or segid S23A or segid S24A or segid S26A or segid S27A or segid S30A or (segid 18SA and not resid 184:209 and not resid 305:326 and not resid 681:737 and not resid 745:787 and not resid 1207:1683 and not resid 1699:1826)O16 - 151
33X-RAY DIFFRACTION7segid S0aA or segid S3aA or segid S02A or segid S4xA or segid S06A or segid S07A or segid S08A or segid S09A or segid S11A or segid S13A or segid S14A or segid S21A or segid 15aA or segid S23A or segid S24A or segid S26A or segid S27A or segid S30A or (segid 18SA and not resid 184:209 and not resid 305:326 and not resid 681:737 and not resid 745:787 and not resid 1207:1683 and not resid 1699:1826)V1 - 82
34X-RAY DIFFRACTION7segid S0aA or segid S3aA or segid S02A or segid S4xA or segid S06A or segid S07A or segid S08A or segid S09A or segid S11A or segid S13A or segid S14A or segid S21A or segid 15aA or segid S23A or segid S24A or segid S26A or segid S27A or segid S30A or (segid 18SA and not resid 184:209 and not resid 305:326 and not resid 681:737 and not resid 745:787 and not resid 1207:1683 and not resid 1699:1826)W2 - 130
35X-RAY DIFFRACTION7segid S0aA or segid S3aA or segid S02A or segid S4xA or segid S06A or segid S07A or segid S08A or segid S09A or segid S11A or segid S13A or segid S14A or segid S21A or segid 15aA or segid S23A or segid S24A or segid S26A or segid S27A or segid S30A or (segid 18SA and not resid 184:209 and not resid 305:326 and not resid 681:737 and not resid 745:787 and not resid 1207:1683 and not resid 1699:1826)X1 - 142
36X-RAY DIFFRACTION7segid S0aA or segid S3aA or segid S02A or segid S4xA or segid S06A or segid S07A or segid S08A or segid S09A or segid S11A or segid S13A or segid S14A or segid S21A or segid 15aA or segid S23A or segid S24A or segid S26A or segid S27A or segid S30A or (segid 18SA and not resid 184:209 and not resid 305:326 and not resid 681:737 and not resid 745:787 and not resid 1207:1683 and not resid 1699:1826)Y3 - 128
37X-RAY DIFFRACTION7segid S0aA or segid S3aA or segid S02A or segid S4xA or segid S06A or segid S07A or segid S08A or segid S09A or segid S11A or segid S13A or segid S14A or segid S21A or segid 15aA or segid S23A or segid S24A or segid S26A or segid S27A or segid S30A or (segid 18SA and not resid 184:209 and not resid 305:326 and not resid 681:737 and not resid 745:787 and not resid 1207:1683 and not resid 1699:1826)a2 - 108
38X-RAY DIFFRACTION7segid S0aA or segid S3aA or segid S02A or segid S4xA or segid S06A or segid S07A or segid S08A or segid S09A or segid S11A or segid S13A or segid S14A or segid S21A or segid 15aA or segid S23A or segid S24A or segid S26A or segid S27A or segid S30A or (segid 18SA and not resid 184:209 and not resid 305:326 and not resid 681:737 and not resid 745:787 and not resid 1207:1683 and not resid 1699:1826)b1 - 84
39X-RAY DIFFRACTION7segid S0aA or segid S3aA or segid S02A or segid S4xA or segid S06A or segid S07A or segid S08A or segid S09A or segid S11A or segid S13A or segid S14A or segid S21A or segid 15aA or segid S23A or segid S24A or segid S26A or segid S27A or segid S30A or (segid 18SA and not resid 184:209 and not resid 305:326 and not resid 681:737 and not resid 745:787 and not resid 1207:1683 and not resid 1699:1826)e75 - 133
40X-RAY DIFFRACTION7segid S0aA or segid S3aA or segid S02A or segid S4xA or segid S06A or segid S07A or segid S08A or segid S09A or segid S11A or segid S13A or segid S14A or segid S21A or segid 15aA or segid S23A or segid S24A or segid S26A or segid S27A or segid S30A or (segid 18SA and not resid 184:209 and not resid 305:326 and not resid 681:737 and not resid 745:787 and not resid 1207:1683 and not resid 1699:1826)i1 - 1863
41X-RAY DIFFRACTION8segid f1aAn32 - 113
42X-RAY DIFFRACTION9segid eF1Al29 - 113

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