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- PDB-4qts: Crystal structure of Csm3-Csm4 subcomplex in the type III-A CRISP... -

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Basic information

Entry
Database: PDB / ID: 4qts
TitleCrystal structure of Csm3-Csm4 subcomplex in the type III-A CRISPR-Cas interference complex
Components
  • CRISPR type III-associated RAMP protein Csm3
  • CRISPR type III-associated RAMP protein Csm4
KeywordsRNA BINDING PROTEIN / CRISPR-associated protein / ferredoxin-like fold / Type III-A CRISPR-Cas system
Function / homology
Function and homology information


defense response to virus / endonuclease activity / Hydrolases; Acting on ester bonds / RNA binding / metal ion binding
Similarity search - Function
Csm4, C-terminal / CRISPR Csm4 C-terminal domain / CRISPR-associated RAMP Csm3 / CRISPR type III-associated RAMP protein Csm4 / : / CRISPR type III-associated protein / RAMP superfamily
Similarity search - Domain/homology
CRISPR system Cms protein Csm4 / CRISPR system Cms endoribonuclease Csm3
Similarity search - Component
Biological speciesMethanocaldococcus jannaschii DSM 2661 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.105 Å
AuthorsNumata, T. / Inanaga, H. / Osawa, T.
CitationJournal: J.Mol.Biol. / Year: 2015
Title: Crystal structure of the Csm3-Csm4 subcomplex in the type III-A CRISPR-Cas interference complex.
Authors: Numata, T. / Inanaga, H. / Sato, C. / Osawa, T.
History
DepositionJul 9, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 24, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 24, 2022Group: Database references / Derived calculations
Category: citation / database_2 ...citation / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CRISPR type III-associated RAMP protein Csm4
B: CRISPR type III-associated RAMP protein Csm4
C: CRISPR type III-associated RAMP protein Csm3
D: CRISPR type III-associated RAMP protein Csm3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)148,7316
Polymers148,6014
Non-polymers1312
Water00
1
A: CRISPR type III-associated RAMP protein Csm4
C: CRISPR type III-associated RAMP protein Csm3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,3663
Polymers74,3002
Non-polymers651
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1920 Å2
ΔGint-4 kcal/mol
Surface area25880 Å2
MethodPISA
2
B: CRISPR type III-associated RAMP protein Csm4
D: CRISPR type III-associated RAMP protein Csm3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,3663
Polymers74,3002
Non-polymers651
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1920 Å2
ΔGint-4 kcal/mol
Surface area25770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.653, 96.319, 194.797
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein CRISPR type III-associated RAMP protein Csm4 / CRISPR type III-A/Mtube-associated RAMP protein Csm4


Mass: 43922.531 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanocaldococcus jannaschii DSM 2661 (archaea)
Gene: csm4, MJ1668 / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus (DE3)-RIL / References: UniProt: Q59062
#2: Protein CRISPR type III-associated RAMP protein Csm3 / CRISPR type III-A/Mtube-associated RAMP protein Csm3


Mass: 30377.734 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanocaldococcus jannaschii DSM 2661 (archaea)
Gene: csm3, MJ1669 / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus (DE3)-RIL / References: UniProt: Q59063
#3: Chemical ChemComp-ZN / ZINC ION


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

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.36 Å3/Da / Density % sol: 47.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: 50mM HEPES-Na (pH 6.8), 200mM potassium chrolide, 30% v/v Pentaerythritol propoxylate (5/4 PO/OH), VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 11, 2012
RadiationMonochromator: Numerical link type Si(111) double crystal monochromator, liquid nitrogen cooling
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 3.1→50 Å / Num. obs: 25906 / % possible obs: 99.2 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.058 / Net I/σ(I): 15.1
Reflection shellResolution: 3.1→3.29 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.557 / Mean I/σ(I) obs: 2.7 / Num. unique all: 30283 / % possible all: 99.4

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Processing

Software
NameVersionClassification
XDSdata scaling
SHARPphasing
PHENIX(phenix.refine: 1.8.4_1496)refinement
XDSdata reduction
RefinementMethod to determine structure: SAD / Resolution: 3.105→43.46 Å / SU ML: 0.46 / σ(F): 1.37 / Phase error: 30.17 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2882 1296 5 %RANDOM
Rwork0.2251 ---
obs0.2282 25882 99.32 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.105→43.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8020 0 2 0 8022
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0038154
X-RAY DIFFRACTIONf_angle_d0.70410896
X-RAY DIFFRACTIONf_dihedral_angle_d13.1123185
X-RAY DIFFRACTIONf_chiral_restr0.0291196
X-RAY DIFFRACTIONf_plane_restr0.0031359
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.1047-3.2290.34261400.299266499
3.229-3.37590.33291430.28542707100
3.3759-3.55380.31751430.27392728100
3.5538-3.77630.3191430.25292701100
3.7763-4.06770.32591430.2362732100
4.0677-4.47660.31371440.21782720100
4.4766-5.12350.24971460.18932776100
5.1235-6.45170.27351470.23092795100
6.4517-43.46430.271470.2092278795

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