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- PDB-4kzz: Rabbit 40S ribosomal subunit in complex with mRNA, initiator tRNA... -

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Basic information

Entry
Database: PDB / ID: 4kzz
TitleRabbit 40S ribosomal subunit in complex with mRNA, initiator tRNA and eIF1A
Components
  • (40S Ribosomal Protein ...) x 33
  • 18S Ribosomal RNA
  • human initiation factor eIF1A
  • initiator Met-RNA-i
  • mRNA
KeywordsRIBOSOME / translation initiation
Function / homology
Function and homology information


multi-eIF complex / eukaryotic 43S preinitiation complex / translation factor activity, RNA binding / ribosomal subunit / eukaryotic 48S preinitiation complex / Formation of the ternary complex, and subsequently, the 43S complex / laminin receptor activity / Translation initiation complex formation / Ribosomal scanning and start codon recognition / mammalian oogenesis stage ...multi-eIF complex / eukaryotic 43S preinitiation complex / translation factor activity, RNA binding / ribosomal subunit / eukaryotic 48S preinitiation complex / Formation of the ternary complex, and subsequently, the 43S complex / laminin receptor activity / Translation initiation complex formation / Ribosomal scanning and start codon recognition / mammalian oogenesis stage / activation-induced cell death of T cells / positive regulation of signal transduction by p53 class mediator / ubiquitin ligase inhibitor activity / Formation of a pool of free 40S subunits / phagocytic cup / L13a-mediated translational silencing of Ceruloplasmin expression / GTP hydrolysis and joining of the 60S ribosomal subunit / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / TOR signaling / T cell proliferation involved in immune response / ribosomal small subunit export from nucleus / erythrocyte development / translation regulator activity / cytosolic ribosome / laminin binding / rough endoplasmic reticulum / 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) / gastrulation / MDM2/MDM4 family protein binding / translational initiation / translation initiation factor activity / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / DNA-(apurinic or apyrimidinic site) lyase / ribosome assembly / rescue of stalled ribosome / 90S preribosome / 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 / positive regulation of apoptotic signaling pathway / protein kinase C binding / positive regulation of protein-containing complex assembly / placenta development / cytoplasmic ribonucleoprotein granule / modification-dependent protein catabolic process / spindle / G1/S transition of mitotic cell cycle / rRNA processing / protein tag activity / rhythmic process / positive regulation of canonical Wnt signaling pathway / 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 / perikaryon / cytosolic small ribosomal subunit / mitochondrial inner membrane / tRNA binding / cytoplasmic translation / 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 cycle / cell division / DNA repair / centrosome / mRNA binding / apoptotic process / ubiquitin protein ligase binding / synapse / dendrite / positive regulation of cell population proliferation / nucleolus / negative regulation of 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 / cytoplasm
Similarity search - Function
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 ...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 S2, eukaryotic / Ribosomal protein S21e / Ribosomal protein S21e superfamily / Ribosomal protein S21e / 40S Ribosomal protein S10 / S27a-like superfamily / Ribosomal protein S10, eukaryotic/archaeal / Plectin/S10, N-terminal / Plectin/S10 domain / Ribosomal protein S25 / S25 ribosomal protein / Ribosomal protein S2, eukaryotic/archaeal / : / Ribosomal protein S17e, conserved site / Ribosomal protein S17e signature. / Ribosomal protein S27a / Ribosomal protein S27a / Ribosomal protein S27a / 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 / 40S ribosomal protein S1/3, eukaryotes / Ribosomal protein S4e, N-terminal / RS4NT (NUC023) domain / 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 S3Ae / Ribosomal protein S28e conserved site / Ribosomal S3Ae family / Ribosomal protein S28e signature. / Ribosomal S3Ae family / Ribosomal protein S28e / Ribosomal protein S28e / Ribosomal protein S6e / Ribosomal protein S5/S7, eukaryotic/archaeal / Ribosomal protein S6e
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 ...: / : / 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 1A, X-chromosomal
Similarity search - Component
Biological speciesHomo sapiens (human)
Oryctolagus cuniculus (rabbit)
Synthetic (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 7.0305 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
j: initiator Met-RNA-i
k: mRNA
n: human initiation factor eIF1A


Theoretical massNumber of molelcules
Total (without water)1,274,24937
Polymers1,274,24937
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)297.750, 297.750, 485.160
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 , 3 types, 3 molecules ijk

#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
#35: RNA chain initiator Met-RNA-i


Mass: 24231.510 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: GenBank: 174924
#36: RNA chain mRNA


Mass: 7635.679 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: mRNA / Source: (synth.) Synthetic (others)

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Protein , 1 types, 1 molecules n

#37: Protein human initiation factor eIF1A


Mass: 16488.449 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: N-terminal His6/TEV / Source: (gene. exp.) Homo sapiens (human) / Strain: K12 / 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. For chain X, the first residue should be the ...The reference for chain A is XP_002712810.1 at NCBI. For chain X, the first residue should be the initiating M.

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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: 4.87 Å3/Da / Density % sol: 74.75 %
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: 0.97949 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 9, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 7.03→80 Å / Num. all: 39353 / Num. obs: 38696 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 9.6 % / Biso Wilson estimate: 551.17 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: 7.0305→77.529 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.6057 / SU ML: 1.62 / σ(F): 1.34 / Phase error: 43.5 / 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
Rfree0.3592 1941 5.02 %RANDOM
Rwork0.345 ---
obs0.3454 38696 98.33 %-
all-39353 --
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: 529.05 Å2 / Biso mean: 179.8919 Å2 / Biso min: 12.79 Å2
Baniso -1Baniso -2Baniso -3
1-583.8464 Å20 Å20 Å2
2--583.8464 Å20 Å2
3---498.2526 Å2
Refinement stepCycle: LAST / Resolution: 7.0305→77.529 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms39654 39394 0 0 79048
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.02684421
X-RAY DIFFRACTIONf_angle_d2.743122711
X-RAY DIFFRACTIONf_chiral_restr0.23815186
X-RAY DIFFRACTIONf_plane_restr0.0228713
X-RAY DIFFRACTIONf_dihedral_angle_d20.56738025
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 (%)
7.0305-7.20620.40191230.41632183230683
7.2062-7.40090.38091540.40082598275299
7.4009-7.61850.43651320.397926422774100
7.6185-7.86420.44341490.388926092758100
7.8642-8.1450.41181350.40826332768100
8.145-8.47070.49061270.385726502777100
8.4707-8.85570.40461370.38326552792100
8.8557-9.32190.43791230.380626852808100
9.3219-9.90480.35921360.382926522788100
9.9048-10.66780.31281300.365526762806100
10.6678-11.7380.36561530.351826502803100
11.738-13.42890.35851430.342226902833100
13.4289-16.89020.39381620.366627072869100
16.8902-77.53350.3181370.30232725286295
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)
11.5945-0.15230.11482.23851.0992.2404-0.42351.93050.375-0.49350.62660.26580.10210.54030.8230.0933-0.874-0.49184.6297-0.58930.922964.1164108.3827-127.376
20.0348-0.01760.03520.0071-0.01670.01770.35110.0258-0.09520.43840.0659-0.53160.29980.1201-0.1354.11262.0749-0.77934.4016-1.14233.33312.1581148.927855.0803
30.16480.1315-0.04890.158-0.17280.3335-0.2285-0.1874-0.01740.47780.45311.5361-0.0671-0.0147-0.07444.92650.9141.36454.8736-0.23014.12060.4331190.687717.0872
40.0592-0.14890.09010.2337-0.15730.08210.11240.50330.0499-0.2070.24710.2327-0.1904-0.3825-0.09865.49410.01510.73796.4557-0.55616.2162-20.1938123.8437-41.7898
50.96930.5795-0.31160.7386-0.81540.95560.12570.78940.15460.12260.05710.4024-1.5746-0.2997-0.12691.444-0.2491-1.0422.48321.23272.40257.6459155.1786-5.4449
61.9399-0.7401-0.18962.7569-0.33092.0472-0.48520.8479-0.31181.4319-0.15450.95091.1509-1.3696-0.706-1.5449-0.5912-0.28721.2541-0.36210.250129.7284123.2812-32.5802
70.08940.1199-0.05981.02240.20410.179-0.6952-0.21690.20290.9574-0.098-0.97640.47580.78170.23362.9461-1.12930.38846.6561-0.24486.0556107.1339108.0298-79.9485
80.2017-0.05520.11620.1847-0.07090.083-0.05050.1734-0.08630.00710.17010.2503-0.21160.51720.04462.8869-0.85281.34773.56770.00512.528879.2053140.4342-79.2595
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain D or chain F or chain K or chain M or chain P or chain Q or chain R or chain S or chain T or chain U or chain Z or chain c or chain d or chain f or chain g or (chain i and resid 1207:1683)D1 - 227
2X-RAY DIFFRACTION1chain D or chain F or chain K or chain M or chain P or chain Q or chain R or chain S or chain T or chain U or chain Z or chain c or chain d or chain f or chain g or (chain i and resid 1207:1683)F14 - 204
3X-RAY DIFFRACTION1chain D or chain F or chain K or chain M or chain P or chain Q or chain R or chain S or chain T or chain U or chain Z or chain c or chain d or chain f or chain g or (chain i and resid 1207:1683)K1 - 98
4X-RAY DIFFRACTION1chain D or chain F or chain K or chain M or chain P or chain Q or chain R or chain S or chain T or chain U or chain Z or chain c or chain d or chain f or chain g or (chain i and resid 1207:1683)M9 - 132
5X-RAY DIFFRACTION1chain D or chain F or chain K or chain M or chain P or chain Q or chain R or chain S or chain T or chain U or chain Z or chain c or chain d or chain f or chain g or (chain i and resid 1207:1683)P4 - 130
6X-RAY DIFFRACTION1chain D or chain F or chain K or chain M or chain P or chain Q or chain R or chain S or chain T or chain U or chain Z or chain c or chain d or chain f or chain g or (chain i and resid 1207:1683)Q6 - 146
7X-RAY DIFFRACTION1chain D or chain F or chain K or chain M or chain P or chain Q or chain R or chain S or chain T or chain U or chain Z or chain c or chain d or chain f or chain g or (chain i and resid 1207:1683)R1 - 126
8X-RAY DIFFRACTION1chain D or chain F or chain K or chain M or chain P or chain Q or chain R or chain S or chain T or chain U or chain Z or chain c or chain d or chain f or chain g or (chain i and resid 1207:1683)S6 - 142
9X-RAY DIFFRACTION1chain D or chain F or chain K or chain M or chain P or chain Q or chain R or chain S or chain T or chain U or chain Z or chain c or chain d or chain f or chain g or (chain i and resid 1207:1683)T4 - 144
10X-RAY DIFFRACTION1chain D or chain F or chain K or chain M or chain P or chain Q or chain R or chain S or chain T or chain U or chain Z or chain c or chain d or chain f or chain g or (chain i and resid 1207:1683)U16 - 119
11X-RAY DIFFRACTION1chain D or chain F or chain K or chain M or chain P or chain Q or chain R or chain S or chain T or chain U or chain Z or chain c or chain d or chain f or chain g or (chain i and resid 1207:1683)Z41 - 115
12X-RAY DIFFRACTION1chain D or chain F or chain K or chain M or chain P or chain Q or chain R or chain S or chain T or chain U or chain Z or chain c or chain d or chain f or chain g or (chain i and resid 1207:1683)c5 - 68
13X-RAY DIFFRACTION1chain D or chain F or chain K or chain M or chain P or chain Q or chain R or chain S or chain T or chain U or chain Z or chain c or chain d or chain f or chain g or (chain i and resid 1207:1683)d4 - 56
14X-RAY DIFFRACTION1chain D or chain F or chain K or chain M or chain P or chain Q or chain R or chain S or chain T or chain U or chain Z or chain c or chain d or chain f or chain g or (chain i and resid 1207:1683)f82 - 152
15X-RAY DIFFRACTION1chain D or chain F or chain K or chain M or chain P or chain Q or chain R or chain S or chain T or chain U or chain Z or chain c or chain d or chain f or chain g or (chain i and resid 1207:1683)g2 - 314
16X-RAY DIFFRACTION1chain D or chain F or chain K or chain M or chain P or chain Q or chain R or chain S or chain T or chain U or chain Z or chain c or chain d or chain f or chain g or (chain i and resid 1207:1683)i1207 - 1683
17X-RAY DIFFRACTION2chain i and resid 184:209i184 - 209
18X-RAY DIFFRACTION3chain i and resid 305:326i305 - 326
19X-RAY DIFFRACTION4chain i and resid 681:737i681 - 737
20X-RAY DIFFRACTION5chain i and resid 1699:1826i1699 - 1826
21X-RAY DIFFRACTION6chain A or chain B or chain C or chain E or chain G or chain H or chain I or chain J or chain L or chain N or chain O or chain V or chain W or chain X or chain Y or chain a or chain b or chain e or (chain i and not resid 184:209 and not resid 305:326 and not resid 681:737 and not resid 1207:1683 and not resid 1699:1826)A2 - 209
22X-RAY DIFFRACTION6chain A or chain B or chain C or chain E or chain G or chain H or chain I or chain J or chain L or chain N or chain O or chain V or chain W or chain X or chain Y or chain a or chain b or chain e or (chain i and not resid 184:209 and not resid 305:326 and not resid 681:737 and not resid 1207:1683 and not resid 1699:1826)B19 - 233
23X-RAY DIFFRACTION6chain A or chain B or chain C or chain E or chain G or chain H or chain I or chain J or chain L or chain N or chain O or chain V or chain W or chain X or chain Y or chain a or chain b or chain e or (chain i and not resid 184:209 and not resid 305:326 and not resid 681:737 and not resid 1207:1683 and not resid 1699:1826)C38 - 263
24X-RAY DIFFRACTION6chain A or chain B or chain C or chain E or chain G or chain H or chain I or chain J or chain L or chain N or chain O or chain V or chain W or chain X or chain Y or chain a or chain b or chain e or (chain i and not resid 184:209 and not resid 305:326 and not resid 681:737 and not resid 1207:1683 and not resid 1699:1826)E1 - 263
25X-RAY DIFFRACTION6chain A or chain B or chain C or chain E or chain G or chain H or chain I or chain J or chain L or chain N or chain O or chain V or chain W or chain X or chain Y or chain a or chain b or chain e or (chain i and not resid 184:209 and not resid 305:326 and not resid 681:737 and not resid 1207:1683 and not resid 1699:1826)G1 - 237
26X-RAY DIFFRACTION6chain A or chain B or chain C or chain E or chain G or chain H or chain I or chain J or chain L or chain N or chain O or chain V or chain W or chain X or chain Y or chain a or chain b or chain e or (chain i and not resid 184:209 and not resid 305:326 and not resid 681:737 and not resid 1207:1683 and not resid 1699:1826)H5 - 194
27X-RAY DIFFRACTION6chain A or chain B or chain C or chain E or chain G or chain H or chain I or chain J or chain L or chain N or chain O or chain V or chain W or chain X or chain Y or chain a or chain b or chain e or (chain i and not resid 184:209 and not resid 305:326 and not resid 681:737 and not resid 1207:1683 and not resid 1699:1826)I2 - 207
28X-RAY DIFFRACTION6chain A or chain B or chain C or chain E or chain G or chain H or chain I or chain J or chain L or chain N or chain O or chain V or chain W or chain X or chain Y or chain a or chain b or chain e or (chain i and not resid 184:209 and not resid 305:326 and not resid 681:737 and not resid 1207:1683 and not resid 1699:1826)J7 - 188
29X-RAY DIFFRACTION6chain A or chain B or chain C or chain E or chain G or chain H or chain I or chain J or chain L or chain N or chain O or chain V or chain W or chain X or chain Y or chain a or chain b or chain e or (chain i and not resid 184:209 and not resid 305:326 and not resid 681:737 and not resid 1207:1683 and not resid 1699:1826)L1 - 158
30X-RAY DIFFRACTION6chain A or chain B or chain C or chain E or chain G or chain H or chain I or chain J or chain L or chain N or chain O or chain V or chain W or chain X or chain Y or chain a or chain b or chain e or (chain i and not resid 184:209 and not resid 305:326 and not resid 681:737 and not resid 1207:1683 and not resid 1699:1826)N2 - 151
31X-RAY DIFFRACTION6chain A or chain B or chain C or chain E or chain G or chain H or chain I or chain J or chain L or chain N or chain O or chain V or chain W or chain X or chain Y or chain a or chain b or chain e or (chain i and not resid 184:209 and not resid 305:326 and not resid 681:737 and not resid 1207:1683 and not resid 1699:1826)O16 - 151
32X-RAY DIFFRACTION6chain A or chain B or chain C or chain E or chain G or chain H or chain I or chain J or chain L or chain N or chain O or chain V or chain W or chain X or chain Y or chain a or chain b or chain e or (chain i and not resid 184:209 and not resid 305:326 and not resid 681:737 and not resid 1207:1683 and not resid 1699:1826)V1 - 82
33X-RAY DIFFRACTION6chain A or chain B or chain C or chain E or chain G or chain H or chain I or chain J or chain L or chain N or chain O or chain V or chain W or chain X or chain Y or chain a or chain b or chain e or (chain i and not resid 184:209 and not resid 305:326 and not resid 681:737 and not resid 1207:1683 and not resid 1699:1826)W2 - 130
34X-RAY DIFFRACTION6chain A or chain B or chain C or chain E or chain G or chain H or chain I or chain J or chain L or chain N or chain O or chain V or chain W or chain X or chain Y or chain a or chain b or chain e or (chain i and not resid 184:209 and not resid 305:326 and not resid 681:737 and not resid 1207:1683 and not resid 1699:1826)X1 - 142
35X-RAY DIFFRACTION6chain A or chain B or chain C or chain E or chain G or chain H or chain I or chain J or chain L or chain N or chain O or chain V or chain W or chain X or chain Y or chain a or chain b or chain e or (chain i and not resid 184:209 and not resid 305:326 and not resid 681:737 and not resid 1207:1683 and not resid 1699:1826)Y3 - 128
36X-RAY DIFFRACTION6chain A or chain B or chain C or chain E or chain G or chain H or chain I or chain J or chain L or chain N or chain O or chain V or chain W or chain X or chain Y or chain a or chain b or chain e or (chain i and not resid 184:209 and not resid 305:326 and not resid 681:737 and not resid 1207:1683 and not resid 1699:1826)a2 - 108
37X-RAY DIFFRACTION6chain A or chain B or chain C or chain E or chain G or chain H or chain I or chain J or chain L or chain N or chain O or chain V or chain W or chain X or chain Y or chain a or chain b or chain e or (chain i and not resid 184:209 and not resid 305:326 and not resid 681:737 and not resid 1207:1683 and not resid 1699:1826)b1 - 84
38X-RAY DIFFRACTION6chain A or chain B or chain C or chain E or chain G or chain H or chain I or chain J or chain L or chain N or chain O or chain V or chain W or chain X or chain Y or chain a or chain b or chain e or (chain i and not resid 184:209 and not resid 305:326 and not resid 681:737 and not resid 1207:1683 and not resid 1699:1826)e75 - 133
39X-RAY DIFFRACTION6chain A or chain B or chain C or chain E or chain G or chain H or chain I or chain J or chain L or chain N or chain O or chain V or chain W or chain X or chain Y or chain a or chain b or chain e or (chain i and not resid 184:209 and not resid 305:326 and not resid 681:737 and not resid 1207:1683 and not resid 1699:1826)i1 - 183
40X-RAY DIFFRACTION6chain A or chain B or chain C or chain E or chain G or chain H or chain I or chain J or chain L or chain N or chain O or chain V or chain W or chain X or chain Y or chain a or chain b or chain e or (chain i and not resid 184:209 and not resid 305:326 and not resid 681:737 and not resid 1207:1683 and not resid 1699:1826)i210 - 304
41X-RAY DIFFRACTION6chain A or chain B or chain C or chain E or chain G or chain H or chain I or chain J or chain L or chain N or chain O or chain V or chain W or chain X or chain Y or chain a or chain b or chain e or (chain i and not resid 184:209 and not resid 305:326 and not resid 681:737 and not resid 1207:1683 and not resid 1699:1826)i327 - 680
42X-RAY DIFFRACTION6chain A or chain B or chain C or chain E or chain G or chain H or chain I or chain J or chain L or chain N or chain O or chain V or chain W or chain X or chain Y or chain a or chain b or chain e or (chain i and not resid 184:209 and not resid 305:326 and not resid 681:737 and not resid 1207:1683 and not resid 1699:1826)i738 - 1206
43X-RAY DIFFRACTION6chain A or chain B or chain C or chain E or chain G or chain H or chain I or chain J or chain L or chain N or chain O or chain V or chain W or chain X or chain Y or chain a or chain b or chain e or (chain i and not resid 184:209 and not resid 305:326 and not resid 681:737 and not resid 1207:1683 and not resid 1699:1826)i1684 - 1698
44X-RAY DIFFRACTION6chain A or chain B or chain C or chain E or chain G or chain H or chain I or chain J or chain L or chain N or chain O or chain V or chain W or chain X or chain Y or chain a or chain b or chain e or (chain i and not resid 184:209 and not resid 305:326 and not resid 681:737 and not resid 1207:1683 and not resid 1699:1826)i1827 - 1863
45X-RAY DIFFRACTION7chain j or chain kj1 - 75
46X-RAY DIFFRACTION7chain j or chain kk10 - 22
47X-RAY DIFFRACTION8chain nn32 - 113

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