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- PDB-4l6u: Crystal structure of AF1868: Cmr1 subunit of the Cmr RNA silencin... -

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Basic information

Entry
Database: PDB / ID: 4l6u
TitleCrystal structure of AF1868: Cmr1 subunit of the Cmr RNA silencing complex
ComponentsPutative uncharacterized protein
KeywordsUNKNOWN FUNCTION / ferredoxin
Function / homologyCRISPR-associated protein TM1795 / CRISPR type III-associated protein / RAMP superfamily / defense response to virus / Uncharacterized protein
Function and homology information
Biological speciesArchaeoglobus fulgidus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.5 Å
AuthorsSun, J. / Jeon, J.H. / Shin, M. / Shin, H.C. / Oh, B.H. / Kim, J.S.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2014
Title: Crystal structure and CRISPR RNA-binding site of the Cmr1 subunit of the Cmr interference complex
Authors: Sun, J. / Jeon, J.H. / Shin, M. / Shin, H.C. / Oh, B.H. / Kim, J.S.
History
DepositionJun 12, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 12, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 25, 2015Group: Database references
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative uncharacterized protein
B: Putative uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)76,0342
Polymers76,0342
Non-polymers00
Water905
1
A: Putative uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)38,0171
Polymers38,0171
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Putative uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)38,0171
Polymers38,0171
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)70.695, 64.162, 79.278
Angle α, β, γ (deg.)90.00, 93.79, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Putative uncharacterized protein


Mass: 38016.969 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Archaeoglobus fulgidus (archaea)
Strain: ATCC 49558 / VC-16 / DSM 4304 / JCM 9628 / NBRC 100126
Gene: AF_1868 / Production host: Escherichia coli (E. coli) / References: UniProt: O28411
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: H2O

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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: 47.87 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS.
Crystal growTemperature: 295 K / Method: vapor diffusion / pH: 5.5
Details: 20%(w/v) polyethyleneglycol 6000, 0.1M NaCl, 0.1M Bis-Tris, 60mM beta-mercaptoethanol, pH 5.5, VAPOR DIFFUSION, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.2 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 20, 2012
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2 Å / Relative weight: 1
ReflectionResolution: 2.5→79.1 Å / Num. all: 24701 / Num. obs: 24479 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Rmerge(I) obs: 0.058
Reflection shellResolution: 2.5→2.64 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.673 / Mean I/σ(I) obs: 1.4 / Num. unique all: 3549 / % possible all: 98.8

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SOLVEphasing
PHENIX(phenix.refine: 1.8.1_1168)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: SAD / Resolution: 2.5→79.1 Å / SU ML: 0.35 / σ(F): 1.34 / Phase error: 33.45 / Stereochemistry target values: ML
Details: SF FILE CONTAINS FRIEDEL PAIRS UNDER I/F_MINUS AND I/F_PLUS COLUMNS.
RfactorNum. reflection% reflectionSelection details
Rfree0.2533 1317 4.99 %RANDOM
Rwork0.23 ---
obs0.2313 24395 96.37 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.5→79.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4633 0 0 5 4638
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034739
X-RAY DIFFRACTIONf_angle_d0.7026388
X-RAY DIFFRACTIONf_chiral_restr0.0521717
X-RAY DIFFRACTIONf_improper_angle_d0.002715
X-RAY DIFFRACTIONf_dihedral_angle_d10.814797
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 17

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.5-2.55120.38511370.3773260695
2.5512-2.60670.35241270.3409252795
2.6067-2.66730.37241500.3302257595
2.6673-2.7340.36361070.3288261396
2.734-2.80790.32951640.3034253096
2.8079-2.89060.30511370.2808256996
2.8906-2.98390.33431420.2698256997
2.9839-3.09050.33271400.2443262997
3.0905-3.21430.29511290.2431262797
3.2143-3.36050.28261280.2283259997
3.3605-3.53770.26421300.2268263297
3.5377-3.75940.26461410.2196261197
3.7594-4.04960.25371250.211259397
4.0496-4.45710.23271500.1942260697
4.4571-5.1020.19621350.1851262597
5.102-6.42750.23121360.2499257696
6.4275-79.14430.22231360.2202257396
Refinement TLS params.Method: refined / Origin x: 48.1959 Å / Origin y: 42.9001 Å / Origin z: 59.702 Å
111213212223313233
T0.4219 Å2-0.0182 Å2-0.0348 Å2-0.3915 Å2-0.0789 Å2--0.5575 Å2
L0.824 °2-0.1736 °20.0129 °2-2.05 °2-1.0537 °2--3.2256 °2
S0.0579 Å °0.0018 Å °0.0351 Å °0.0931 Å °-0.1903 Å °-0.2192 Å °-0.0399 Å °0.5718 Å °0.1173 Å °
Refinement TLS groupSelection details: all

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