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- PDB-4uw2: Crystal structure of Csm1 in T.onnurineus -

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Basic information

Entry
Database: PDB / ID: 4uw2
TitleCrystal structure of Csm1 in T.onnurineus
ComponentsCSM1
KeywordsIMMUNE SYSTEM / BACTERIAL IMMUNITY / CRISPR / CSM INTERFERENCE CSM1 / HD DOMAIN
Function / homology
Function and homology information


exonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / transferase activity / endonuclease activity / defense response to virus / Hydrolases; Acting on ester bonds / ATP binding / identical protein binding
Similarity search - Function
: / CRISPR system single-strand-specific deoxyribonuclease Cas10/Csm1 / Csm1, subunit domain B / Csm1 subunit domain B / : / Cas10/Cmr2, second palm domain / HD domain profile. / HD domain / GGDEF domain profile. / GGDEF domain ...: / CRISPR system single-strand-specific deoxyribonuclease Cas10/Csm1 / Csm1, subunit domain B / Csm1 subunit domain B / : / Cas10/Cmr2, second palm domain / HD domain profile. / HD domain / GGDEF domain profile. / GGDEF domain / HD domain / Reverse transcriptase/Diguanylate cyclase domain / Reverse transcriptase/Diguanylate cyclase domain / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
CRISPR system single-strand-specific deoxyribonuclease Cas10/Csm1 (subtype III-A)
Similarity search - Component
Biological speciesTHERMOCOCCUS ONNURINEUS NA1 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.632 Å
AuthorsJung, T.Y. / An, Y. / Park, K.H. / Lee, M.H. / Oh, B.H. / Woo, E.J.
CitationJournal: Structure / Year: 2015
Title: Crystal Structure of the Csm1 Subunit of the Csm Complex and its Single-Stranded DNA-Specific Nuclease Activity.
Authors: Jung, T. / An, Y. / Park, K. / Lee, M. / Oh, B. / Woo, E.
History
DepositionAug 8, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 25, 2015Provider: repository / Type: Initial release
Revision 1.1Apr 22, 2015Group: Database references
Revision 1.2Sep 23, 2015Group: Data collection
Revision 1.3Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CSM1
B: CSM1
C: CSM1
D: CSM1


Theoretical massNumber of molelcules
Total (without water)356,1504
Polymers356,1504
Non-polymers00
Water10,989610
1
A: CSM1


Theoretical massNumber of molelcules
Total (without water)89,0381
Polymers89,0381
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: CSM1


Theoretical massNumber of molelcules
Total (without water)89,0381
Polymers89,0381
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: CSM1


Theoretical massNumber of molelcules
Total (without water)89,0381
Polymers89,0381
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: CSM1


Theoretical massNumber of molelcules
Total (without water)89,0381
Polymers89,0381
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)57.894, 158.292, 299.275
Angle α, β, γ (deg.)90.00, 89.97, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
CSM1


Mass: 89037.617 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) THERMOCOCCUS ONNURINEUS NA1 (archaea) / Plasmid: PPROEX HTB / Production host: ESCHERICHIA COLI B (bacteria) / Strain (production host): B834 DE3 RIL / References: UniProt: B6YWB8
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 610 / 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: 2.6 Å3/Da / Density % sol: 52.67 % / Description: NONE
Crystal growpH: 7 / Details: 0.2 M AMMONIUM CITRATE PH 7.0, 20% PEG3350

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.97918
DetectorType: ADSC CCD / Detector: CCD / Date: Jul 10, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
Reflection twinOperator: h,-k,-l / Fraction: 0.5
ReflectionResolution: 2.63→50 Å / Num. obs: 78224 / % possible obs: 98.2 % / Redundancy: 6.8 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 40.84
Reflection shellResolution: 2.63→2.68 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.07 / Mean I/σ(I) obs: 4.67 / % possible all: 98.5

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 2.632→30.657 Å / σ(F): 0.19 / Phase error: 27.26 / Stereochemistry target values: TWIN_LSQ_F
Details: CHAIN C AND D CONTAINS ONLY A PARTIAL DOMAIN OF FULL STRUCTURE DUE TO SPONTANEOUS PARTIAL DIGESTION DURING CRYSTALLIZATION.
RfactorNum. reflection% reflection
Rfree0.2609 2016 2.6 %
Rwork0.2035 --
obs0.2061 78224 98.18 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.632→30.657 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13698 0 0 610 14308
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00213963
X-RAY DIFFRACTIONf_angle_d0.60818821
X-RAY DIFFRACTIONf_dihedral_angle_d11.4575182
X-RAY DIFFRACTIONf_chiral_restr0.0232005
X-RAY DIFFRACTIONf_plane_restr0.0032407
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6343-2.70010.33681330.22295089X-RAY DIFFRACTION91
2.7001-2.7730.32051380.22415368X-RAY DIFFRACTION95
2.773-2.85450.27011430.21945346X-RAY DIFFRACTION95
2.8545-2.94660.30781390.21425456X-RAY DIFFRACTION96
2.9466-3.05170.28041400.21775457X-RAY DIFFRACTION96
3.0517-3.17370.36521410.2115458X-RAY DIFFRACTION97
3.1737-3.31790.25891420.20565470X-RAY DIFFRACTION97
3.3179-3.49250.25161430.1995528X-RAY DIFFRACTION97
3.4925-3.71080.21491430.19535476X-RAY DIFFRACTION97
3.7108-3.99650.25081480.19535532X-RAY DIFFRACTION97
3.9965-4.39710.24581470.17955508X-RAY DIFFRACTION97
4.3971-5.02990.24211460.17985477X-RAY DIFFRACTION96
5.0299-6.32360.23261400.22175566X-RAY DIFFRACTION97
6.3236-27.00240.24971460.22315442X-RAY DIFFRACTION94

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