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- PDB-2zop: X-ray crystal structure of a CRISPR-associated Cmr5 family protei... -

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Basic information

Entry
Database: PDB / ID: 2zop
TitleX-ray crystal structure of a CRISPR-associated Cmr5 family protein from Thermus thermophilus HB8
ComponentsPutative uncharacterized protein TTHB164
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / All alpha proteins / Plasmid / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


defense response to virus / cytoplasm
Similarity search - Function
AF1862-like domain / CRISPR-associated protein (Cas_Cmr5) / CRISPR-associated protein, Cmr5 / AF1862-like domain superfamily / Peroxidase; domain 1 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
CRISPR system Cmr subunit Cmr5
Similarity search - Component
Biological speciesThermus thermophilus HB8 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 Å
AuthorsSakamoto, K. / Agari, Y. / Shinkai, A. / Yokoyama, S. / Kuramitsu, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: Proteins / Year: 2009
Title: X-ray crystal structure of a CRISPR-associated RAMP superfamily protein, Cmr5, from Thermus thermophilus HB8
Authors: Sakamoto, K. / Agari, Y. / Agari, K. / Yokoyama, S. / Kuramitsu, S. / Shinkai, A.
History
DepositionMay 28, 2008Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 10, 2009Provider: 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative uncharacterized protein TTHB164
B: Putative uncharacterized protein TTHB164
C: Putative uncharacterized protein TTHB164
D: Putative uncharacterized protein TTHB164
E: Putative uncharacterized protein TTHB164
F: Putative uncharacterized protein TTHB164
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,12613
Polymers78,4546
Non-polymers6727
Water3,909217
1
A: Putative uncharacterized protein TTHB164
B: Putative uncharacterized protein TTHB164
C: Putative uncharacterized protein TTHB164
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,8039
Polymers39,2273
Non-polymers5766
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: Putative uncharacterized protein TTHB164
E: Putative uncharacterized protein TTHB164
F: Putative uncharacterized protein TTHB164
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,3234
Polymers39,2273
Non-polymers961
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Putative uncharacterized protein TTHB164
B: Putative uncharacterized protein TTHB164
C: Putative uncharacterized protein TTHB164
hetero molecules

D: Putative uncharacterized protein TTHB164
E: Putative uncharacterized protein TTHB164
F: Putative uncharacterized protein TTHB164
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,12613
Polymers78,4546
Non-polymers6727
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555-x+1/2,y+1/2,-z+1/21
Buried area8000 Å2
ΔGint-125 kcal/mol
Surface area32550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.122, 114.801, 122.845
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-207-

HOH

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Components

#1: Protein
Putative uncharacterized protein TTHB164 / CRISPR-associated Cmr5 family protein


Mass: 13075.657 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus HB8 (bacteria) / Gene: TTHB164 / Plasmid: pET-11a / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: Q53W05
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 217 / 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: 2.29 Å3/Da / Density % sol: 46.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 0.1M sodium acetate, 1.7M ammonium sulfate, 0.03M DTT, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 0.979 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 21, 2007
Details: A fixed exit Si double crystal monochromator followed by a two dimensional focusing mirror which is coated in rhodium.
RadiationMonochromator: Fixed exit Si double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.05→50 Å / Num. all: 45600 / Num. obs: 45600 / % possible obs: 99.9 % / Redundancy: 10.4 % / Biso Wilson estimate: 21.2 Å2 / Rmerge(I) obs: 0.064 / Net I/σ(I): 51.1
Reflection shellResolution: 2.05→2.12 Å / Redundancy: 10.6 % / Rmerge(I) obs: 0.314 / Mean I/σ(I) obs: 9.4 / Num. unique all: 4488 / % 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: 2.1→43.62 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 4139235.16 / 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
Rfree0.249 4261 10.1 %RANDOM
Rwork0.235 ---
all0.236 42225 --
obs0.235 42225 99.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 44.4646 Å2 / ksol: 0.379875 e/Å3
Displacement parametersBiso mean: 31.1 Å2
Baniso -1Baniso -2Baniso -3
1-4.23 Å20 Å20 Å2
2---5.22 Å20 Å2
3---1 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.28 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.14 Å0.14 Å
Refinement stepCycle: LAST / Resolution: 2.1→43.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5293 0 35 217 5545
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
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
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d15.4
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.63
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it2.211.5
X-RAY DIFFRACTIONc_mcangle_it2.932
X-RAY DIFFRACTIONc_scbond_it3.362
X-RAY DIFFRACTIONc_scangle_it4.872.5
LS refinement shellResolution: 2.1→2.23 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.262 671 9.7 %
Rwork0.234 6224 -
obs-6895 98.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top

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