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- PDB-4n77: Crystal structure of Cas protein -

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Basic information

Entry
Database: PDB / ID: 4n77
TitleCrystal structure of Cas protein
ComponentsUncharacterized protein
KeywordsRNA BINDING PROTEIN / crispr / RRM
Function / homology
Function and homology information


maintenance of CRISPR repeat elements / defense response to virus / RNA binding
Similarity search - Function
Alpha-Beta Plaits - #2660 / CRISPR-associated protein, CasD / CRISPR-associated protein, Cas5 / CRISPR-associated protein (Cas_Cas5) / CRISPR-associated protein Cas5, N-terminal / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Uncharacterized protein
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.999 Å
AuthorsTian, W. / Sheng, G. / Zhao, H. / Wang, J. / Wang, Y.
CitationJournal: To be Published
Title: Crystal strucute studies of CasD
Authors: Tian, W. / Sheng, G. / Zhao, H. / Wang, J. / Wang, Y.
History
DepositionOct 15, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 15, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.2Mar 21, 2018Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.pdbx_collection_date
Revision 1.3Mar 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: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)28,0381
Polymers28,0381
Non-polymers00
Water2,504139
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)62.618, 62.618, 93.344
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Uncharacterized protein / CasD


Mass: 28038.088 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Gene: TTHB191 / Production host: Escherichia coli (E. coli) / References: UniProt: Q53WH0
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 139 / 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: 1.63 Å3/Da / Density % sol: 24.62 % / Mosaicity: 0.742 °
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1M Tris.HCl, 5% PEG8000, 28% PEG300, 10% Glycerol, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSSRF BL17U10.97
SYNCHROTRONBSRF 3W1A21.7
Detector
TypeIDDetectorDate
ADSC QUANTUM 3151CCDJun 6, 2012
MAR CCD 165 mm2CCDAug 2, 2012
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si 111 CHANNELSINGLE WAVELENGTHMx-ray1
2Si 111 CHANNELSINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.971
21.71
ReflectionResolution: 1.999→50 Å / Num. obs: 13127 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.8 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 23.5
Reflection shellResolution: 1.999→2.07 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.511 / Mean I/σ(I) obs: 5 / Num. unique all: 1275 / % possible all: 99.5

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASESphasing
PHENIX1.8.2_1309refinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
RefinementMethod to determine structure: SAD / Resolution: 1.999→20.003 Å / Occupancy max: 1 / Occupancy min: 0.65 / SU ML: 0.19 / σ(F): 1.34 / Phase error: 21.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2312 639 4.92 %RANDOM
Rwork0.1693 ---
all0.1723 12992 --
obs0.1723 12992 98.87 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 86.69 Å2 / Biso mean: 21.3517 Å2 / Biso min: 6.95 Å2
Refinement stepCycle: LAST / Resolution: 1.999→20.003 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1544 0 0 139 1683
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071584
X-RAY DIFFRACTIONf_angle_d1.2162150
X-RAY DIFFRACTIONf_chiral_restr0.084228
X-RAY DIFFRACTIONf_plane_restr0.005285
X-RAY DIFFRACTIONf_dihedral_angle_d12.855613
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.999-2.15320.25991260.16942389251598
2.1532-2.36960.24081230.17742392251598
2.3696-2.71170.26921190.18262450256999
2.7117-3.41370.24671350.17724892624100
3.4137-20.00350.19771360.157226332769100

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