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- PDB-4f3e: Crystal Structure of Thermus thermophilus HB8 CasA -

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Basic information

Entry
Database: PDB / ID: 4f3e
TitleCrystal Structure of Thermus thermophilus HB8 CasA
ComponentsCasA
KeywordsIMMUNE SYSTEM / four helix bundle / cascade complex
Function / homologyTopoisomerase I; Chain A, domain 4 - #100 / CRISPR-associated protein Cse1 / CRISPR-associated protein Cse1 (CRISPR_cse1) / Topoisomerase I; Chain A, domain 4 / defense response to virus / Orthogonal Bundle / Mainly Alpha / CRISPR-associated protein CasA/Cse1
Function and homology information
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.4 Å
AuthorsBailey, S. / Mulepati, S.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Crystal Structure of the Largest Subunit of a Bacterial RNA-guided Immune Complex and Its Role in DNA Target Binding.
Authors: Mulepati, S. / Orr, A. / Bailey, S.
History
DepositionMay 9, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 23, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 6, 2012Group: Database references
Revision 1.2Jul 18, 2012Group: Database references
Revision 1.3Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CasA
B: CasA


Theoretical massNumber of molelcules
Total (without water)112,5462
Polymers112,5462
Non-polymers00
Water5,783321
1
A: CasA


Theoretical massNumber of molelcules
Total (without water)56,2731
Polymers56,2731
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: CasA


Theoretical massNumber of molelcules
Total (without water)56,2731
Polymers56,2731
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)93.888, 47.926, 129.168
Angle α, β, γ (deg.)90.00, 97.52, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLUGLULEULEUchain A and (resseq 5:128 or resseq 143:404 or resseq 410:496 )AA5 - 1285 - 128
12GLUGLUASPASPchain A and (resseq 5:128 or resseq 143:404 or resseq 410:496 )AA143 - 404143 - 404
13SERSERLEULEUchain A and (resseq 5:128 or resseq 143:404 or resseq 410:496 )AA410 - 496410 - 496
21GLUGLULEULEUchain B and (resseq 5:128 or resseq 143:404 or resseq 410:496 )BB5 - 1285 - 128
22GLUGLUASPASPchain B and (resseq 5:128 or resseq 143:404 or resseq 410:496 )BB143 - 404143 - 404
23SERSERLEULEUchain B and (resseq 5:128 or resseq 143:404 or resseq 410:496 )BB410 - 496410 - 496

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Components

#1: Protein CasA / protein TTHB188


Mass: 56273.125 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / ATCC 27634 / DSM 579 / Gene: TTHB188 / Production host: Escherichia coli (E. coli) / References: UniProt: Q53VY1
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 321 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.56 Å3/Da / Density % sol: 51.95 %
Crystal growTemperature: 300 K / Method: vapor diffusion, sitting drop / pH: 7.4
Details: 2.3 M sodium acetate, 0.1 M MOPS, pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 300K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 1 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Sep 1, 2010
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.984→128.058 Å / Num. all: 78866 / Num. obs: 57797 / % possible obs: 98.5 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Rmerge(I) obs: 0.101 / Net I/σ(I): 11.162
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 3.6 % / Rmerge(I) obs: 1 / Mean I/σ(I) obs: 1.025 / % possible all: 98

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Processing

Software
NameVersionClassification
Blu-Icedata collection
SOLVEphasing
PHENIX(phenix.refine: 1.7.1_743)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MIR / Resolution: 2.4→45.703 Å / SU ML: 0.69 / σ(F): 0 / Phase error: 25.93 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.251 2261 5.06 %RANDOM
Rwork0.1948 ---
all0.1976 46944 --
obs0.1976 44683 98.73 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 64.819 Å2 / ksol: 0.354 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--2.1382 Å2-0 Å20.9995 Å2
2---0.424 Å2-0 Å2
3---5.1407 Å2
Refinement stepCycle: LAST / Resolution: 2.4→45.703 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7514 0 0 321 7835
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0087699
X-RAY DIFFRACTIONf_angle_d1.09410452
X-RAY DIFFRACTIONf_dihedral_angle_d15.3542912
X-RAY DIFFRACTIONf_chiral_restr0.0731128
X-RAY DIFFRACTIONf_plane_restr0.0051380
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A3757X-RAY DIFFRACTIONPOSITIONAL0.046
12B3757X-RAY DIFFRACTIONPOSITIONAL0.046
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.45220.33641270.26122594X-RAY DIFFRACTION98
2.4522-2.50920.35611500.25852588X-RAY DIFFRACTION98
2.5092-2.5720.30071380.25582609X-RAY DIFFRACTION98
2.572-2.64150.35011460.25042584X-RAY DIFFRACTION98
2.6415-2.71920.32291420.25572607X-RAY DIFFRACTION98
2.7192-2.8070.33841340.23662672X-RAY DIFFRACTION99
2.807-2.90730.27931390.21362601X-RAY DIFFRACTION99
2.9073-3.02370.26771230.21552702X-RAY DIFFRACTION99
3.0237-3.16120.2981430.21322644X-RAY DIFFRACTION100
3.1612-3.32790.33861440.21472675X-RAY DIFFRACTION100
3.3279-3.53630.24471480.20712671X-RAY DIFFRACTION100
3.5363-3.80920.25451410.18052693X-RAY DIFFRACTION100
3.8092-4.19230.25041430.172699X-RAY DIFFRACTION100
4.1923-4.79840.211410.15512713X-RAY DIFFRACTION100
4.7984-6.04330.19161450.17242717X-RAY DIFFRACTION100
6.0433-45.71110.20881570.192653X-RAY DIFFRACTION94
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)
12.80220.0818-1.10622.1760.34973.75670.07640.0554-0.137-0.1628-0.15370.4091-0.0665-0.37460.06030.18250.0289-0.0620.2532-0.01090.354859.601524.056659.154
24.7554-4.09190.59487.7064-0.02313.02190.28860.2021-0.0926-0.61570.0008-0.55720.260.1549-0.25270.2999-0.03550.03380.4099-0.13040.327388.68254.477344.3981
34.29810.7117-0.72622.6153-0.65652.80770.1532-0.20810.00120.4955-0.1153-0.0266-0.4349-0.0617-0.02920.57390.0153-0.0190.3340.01480.204839.945550.872725.2472
43.12981.5737-0.79076.1861-2.44243.7269-0.1488-0.3021-0.0077-0.0098-0.0239-0.658-0.56990.17330.16920.5462-0.1194-0.04320.5916-0.05440.364665.987970.40225.5459
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 5:367)
2X-RAY DIFFRACTION2(chain A and resid 368:496)
3X-RAY DIFFRACTION3(chain B and resid 5:367)
4X-RAY DIFFRACTION4(chain B and resid 368:496)

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