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- PDB-1zpw: Crystal structure of a hypothetical protein TT1823 from Thermus t... -

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Basic information

Entry
Database: PDB / ID: 1zpw
TitleCrystal structure of a hypothetical protein TT1823 from Thermus thermophilus
Componentshypothetical protein TT1823
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / hyphotetical protein / Thermus thermophilus / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


maintenance of CRISPR repeat elements / RNA endonuclease activity / defense response to virus / Hydrolases; Acting on ester bonds / metal ion binding
Similarity search - Function
CRISPR-associated endonuclease Cas2 / Virulence-associated protein D / CRISPR associated protein Cas2 / CRISPR associated protein Cas2 / Alpha-Beta Plaits - #240 / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
CRISPR-associated endonuclease Cas2 2
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / molecular replacement, MAD / Resolution: 1.64 Å
AuthorsIhsanawati / Murayama, K. / Shirouzu, M. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Crystal structure of a hypothetical protein TT1823 from Thermus thermophilus
Authors: Ihsanawati / Murayama, K. / Shirouzu, M. / Yokoyama, S.
History
DepositionMay 18, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 18, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Mar 13, 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
X: hypothetical protein TT1823


Theoretical massNumber of molelcules
Total (without water)10,3991
Polymers10,3991
Non-polymers00
Water2,324129
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
X: hypothetical protein TT1823

X: hypothetical protein TT1823


Theoretical massNumber of molelcules
Total (without water)20,7982
Polymers20,7982
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Buried area3130 Å2
ΔGint-14 kcal/mol
Surface area8460 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)44.234, 55.964, 74.937
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein hypothetical protein TT1823


Mass: 10399.093 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: Q746F4
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 129 / 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: 2

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Sample preparation

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
12.244.4
2
Crystal grow
Temperature (K)Crystal-IDMethodpHDetails
2931vapor diffusion, hanging drop7.622% PEG 3350, 0.1M TrisCl pH 7.6, 0.2M NaF, VAPOR DIFFUSION, HANGING DROP, temperature 293K
2932vapor diffusion, hanging drop7.618% PEG 3350, 0.1M TrisCl pH 7.6, 0.2M NaF, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
1,21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSPring-8 BL26B111
SYNCHROTRONPhoton Factory AR-NW12A20.97908, 0.97971, 0.98359
Detector
TypeIDDetectorDate
RIGAKU JUPITER 2101CCDNov 5, 2004
ADSC QUANTUM 42CCDApr 11, 2005
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2MADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
111
20.979081
30.979711
40.983591
ReflectionResolution: 1.64→50 Å / Num. all: 11711 / Num. obs: 11711 / % possible obs: 99.8 % / Observed criterion σ(I): 18.69
Reflection shellResolution: 1.64→1.7 Å / % possible all: 99.7

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
MOLREPphasing
RefinementMethod to determine structure: molecular replacement, MAD / Resolution: 1.64→25.46 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.95 / SU B: 1.635 / SU ML: 0.057 / Cross valid method: THROUGHOUT / ESU R: 0.098 / ESU R Free: 0.095 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.21259 555 4.7 %RANDOM
Rwork0.18455 ---
all0.18595 11711 --
obs0.18595 11156 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 21.153 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å20 Å20 Å2
2---0.39 Å20 Å2
3---0.41 Å2
Refinement stepCycle: LAST / Resolution: 1.64→25.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms663 0 0 129 792
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.021684
X-RAY DIFFRACTIONr_angle_refined_deg1.5872.011923
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.698581
X-RAY DIFFRACTIONr_chiral_restr0.1180.2104
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02519
X-RAY DIFFRACTIONr_nbd_refined0.2220.2277
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1690.291
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2160.247
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1330.218
X-RAY DIFFRACTIONr_mcbond_it1.0221.5408
X-RAY DIFFRACTIONr_mcangle_it1.8332657
X-RAY DIFFRACTIONr_scbond_it2.793276
X-RAY DIFFRACTIONr_scangle_it4.4584.5266
LS refinement shellResolution: 1.641→1.684 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.248 36
Rwork0.229 817

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