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- PDB-2zca: Crystal Structure of TTHB189, a CRISPR-associated protein, Cse2 f... -

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Basic information

Entry
Database: PDB / ID: 2zca
TitleCrystal Structure of TTHB189, a CRISPR-associated protein, Cse2 family from Thermus thermophilus HB8
ComponentsPutative uncharacterized protein TTHB189
KeywordsStructural Genomics / UNKNOWN FUNCTION / CRISPR / Cse2 / Thermus thermophilus / Plasmid / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homologyCRISPR-associated protein Cse2 / CRISPR-associated protein Cse2 / Cse2 superfamily / CRISPR-associated protein Cse2 (CRISPR_cse2) / Peroxidase; domain 1 / defense response to virus / Orthogonal Bundle / Mainly Alpha / CRISPR-associated protein Cse2
Function and homology information
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å
AuthorsAgari, Y. / Shinkai, A. / Yokoyama, S. / Kuramitsu, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: Proteins / Year: 2008
Title: X-ray crystal structure of a CRISPR-associated protein, Cse2, from Thermus thermophilus HB8
Authors: Agari, Y. / Yokoyama, S. / Kuramitsu, S. / Shinkai, A.
History
DepositionNov 8, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 7, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative uncharacterized protein TTHB189
B: Putative uncharacterized protein TTHB189


Theoretical massNumber of molelcules
Total (without water)39,0602
Polymers39,0602
Non-polymers00
Water4,324240
1
A: Putative uncharacterized protein TTHB189


Theoretical massNumber of molelcules
Total (without water)19,5301
Polymers19,5301
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Putative uncharacterized protein TTHB189


Theoretical massNumber of molelcules
Total (without water)19,5301
Polymers19,5301
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)52.081, 71.238, 53.753
Angle α, β, γ (deg.)90.00, 115.78, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Putative uncharacterized protein TTHB189 / CRISPR-associated protein / Cse2 family


Mass: 19529.867 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Plasmid: pET-11a / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: Q53VY0
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 240 / 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: 2.3 Å3/Da / Density % sol: 46.49 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.9
Details: 30% PEG 600, 5% PEG 1000, 0.1M Sodium Cacodylate, 10% Glycerol, pH 5.9, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 0.97897 Å
DetectorType: RIGAKU JUPITER 210 / Detector: CCD / Date: Jul 18, 2007
Details: two dimensional focusing mirror which is coated in rhodium.
RadiationMonochromator: A fixed exit Si double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97897 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. all: 32767 / Num. obs: 32767 / % possible obs: 99.9 % / Redundancy: 5.5 % / Biso Wilson estimate: 14.8 Å2 / Rmerge(I) obs: 0.071 / Net I/σ(I): 27.8
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.278 / Mean I/σ(I) obs: 3.92 / Num. unique all: 3255 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.1refinement
BSSdata collection
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.8→39.17 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 95562.87 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.215 3209 10 %RANDOM
Rwork0.186 ---
all0.189 32169 --
obs0.186 32169 97.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 43.216 Å2 / ksol: 0.370733 e/Å3
Displacement parametersBiso mean: 17.1 Å2
Baniso -1Baniso -2Baniso -3
1--1.12 Å20 Å2-1.75 Å2
2--2.09 Å20 Å2
3----0.96 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.22 Å0.18 Å
Luzzati d res low-5 Å
Luzzati sigma a0.13 Å0.07 Å
Refinement stepCycle: LAST / Resolution: 1.8→39.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2567 0 0 240 2807
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d18.7
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.74
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.251.5
X-RAY DIFFRACTIONc_mcangle_it1.92
X-RAY DIFFRACTIONc_scbond_it2.282
X-RAY DIFFRACTIONc_scangle_it3.392.5
LS refinement shellResolution: 1.8→1.91 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.236 471 9.3 %
Rwork0.209 4573 -
obs-5044 93 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top

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