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- PDB-4ej3: Crystal structure of a CRISPR associated protein from Thermus the... -

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Basic information

Entry
Database: PDB / ID: 4ej3
TitleCrystal structure of a CRISPR associated protein from Thermus thermophilus HB8
ComponentsCRISPR associated protein
KeywordsSIGNALING PROTEIN / CRISPR / cascade protein
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 / SAD / Resolution: 2.52 Å
AuthorsHuang, Q.Q.
CitationJournal: To be Published
Title: Crystal structure of a CRISPR associated protein from Thermus thermophilus HB8
Authors: Huang, Q.Q.
History
DepositionApr 6, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 20, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CRISPR associated protein
B: CRISPR associated protein


Theoretical massNumber of molelcules
Total (without water)115,3572
Polymers115,3572
Non-polymers00
Water2,828157
1
A: CRISPR associated protein


Theoretical massNumber of molelcules
Total (without water)57,6791
Polymers57,6791
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: CRISPR associated protein


Theoretical massNumber of molelcules
Total (without water)57,6791
Polymers57,6791
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)93.776, 47.829, 129.178
Angle α, β, γ (deg.)90.00, 97.34, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein CRISPR associated protein


Mass: 57678.680 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.: 157 / 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: 2.49 Å3/Da / Density % sol: 50.62 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 2.5M sodium formate, 0.1M Mes, 5% DMSO, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONCHESS A110.978
SYNCHROTRONCHESS F220.979
Detector
TypeIDDetectorDate
ADSC QUANTUM 2101CCDMar 5, 2012
ADSC QUANTUM 2102CCDNov 17, 2011
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Horizontal focusing 5.05 asymmetric cut Si(111)SINGLE WAVELENGTHMx-ray1
2Double-bounce downward, offset 25.4 mmSADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.9781
20.9791
ReflectionResolution: 2.5→50 Å / Num. all: 38600 / Num. obs: 38561 / % possible obs: 99.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shellResolution: 2.5→2.54 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 36.2 / Num. unique all: 1896 / Rsym value: 0.331 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
SOLVEphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.52→49.86 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.888 / SU B: 11.392 / SU ML: 0.255 / Cross valid method: THROUGHOUT / σ(F): 1 / ESU R: 0.708 / ESU R Free: 0.331 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27693 2000 5.4 %RANDOM
Rwork0.21754 ---
all0.225 38600 --
obs0.22079 34889 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.765 Å2
Baniso -1Baniso -2Baniso -3
1--0.74 Å20 Å20.7 Å2
2---0.79 Å2-0 Å2
3---1.71 Å2
Refinement stepCycle: LAST / Resolution: 2.52→49.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7388 0 0 157 7545
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0227570
X-RAY DIFFRACTIONr_bond_other_d0.0010.025349
X-RAY DIFFRACTIONr_angle_refined_deg1.1511.98710284
X-RAY DIFFRACTIONr_angle_other_deg0.85312919
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9565928
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.18322.753356
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.139151251
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.8921581
X-RAY DIFFRACTIONr_chiral_restr0.0620.21116
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0218423
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021584
X-RAY DIFFRACTIONr_mcbond_it0.5211.54656
X-RAY DIFFRACTIONr_mcbond_other0.0631.51874
X-RAY DIFFRACTIONr_mcangle_it127430
X-RAY DIFFRACTIONr_scbond_it1.19632914
X-RAY DIFFRACTIONr_scangle_it2.1034.52854
LS refinement shellResolution: 2.52→2.588 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.353 119 -
Rwork0.262 2075 -
obs--100 %

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