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- PDB-4w8k: Crystal structure of a putative Cas1 enzyme from Vibrio phage ICP1 -

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Basic information

Entry
Database: PDB / ID: 4w8k
TitleCrystal structure of a putative Cas1 enzyme from Vibrio phage ICP1
ComponentsCas1 protein
KeywordsVIRAL PROTEIN / immunity / CRISPR-associated / vibrio / phage / Center for Structuaral Genomics of Infectious Diseases / CSGID / National Institute of Allergy and Infectious Diseases / NIAID / Structural Genomics / Center for Structural Genomics of Infectious Diseases
Function / homology
Function and homology information


maintenance of CRISPR repeat elements / DNA endonuclease activity / defense response to virus / DNA binding / metal ion binding
Similarity search - Function
CRISPR-associated protein Cas1, YPEST subtype / CRISPR-associated endonuclease Cas1, N-terminal domain / CRISPR-associated endonuclease Cas1, C-terminal domain / CRISPR-associated endonuclease Cas1, N-terminal domain / CRISPR-associated protein Cas1 / CRISPR-associated endonuclease Cas1, C-terminal domain / CRISPR associated protein Cas1 / Ribosomal Protein L15; Chain: K; domain 2 / Ribosomal Protein L15; Chain: K; domain 2 / Four Helix Bundle (Hemerythrin (Met), subunit A) ...CRISPR-associated protein Cas1, YPEST subtype / CRISPR-associated endonuclease Cas1, N-terminal domain / CRISPR-associated endonuclease Cas1, C-terminal domain / CRISPR-associated endonuclease Cas1, N-terminal domain / CRISPR-associated protein Cas1 / CRISPR-associated endonuclease Cas1, C-terminal domain / CRISPR associated protein Cas1 / Ribosomal Protein L15; Chain: K; domain 2 / Ribosomal Protein L15; Chain: K; domain 2 / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
: / Uncharacterized protein
Similarity search - Component
Biological speciesVibrio phage ICP1_2005_A (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.13 Å
AuthorsStogios, P.J. / Wawrzak, Z. / Onopriyeno, O. / Yim, V. / Savchenko, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To Be Published
Title: To be published
Authors: Savchenko, A.
History
DepositionAug 25, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 17, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Refinement description / Source and taxonomy
Category: diffrn_detector / entity_src_gen ...diffrn_detector / entity_src_gen / pdbx_database_status / pdbx_struct_oper_list / software
Item: _diffrn_detector.detector / _entity_src_gen.pdbx_alt_source_flag ..._diffrn_detector.detector / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_oper_list.symmetry_operation / _software.pdbx_ordinal
Revision 1.2Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cas1 protein
B: Cas1 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,4753
Polymers73,4352
Non-polymers391
Water5,855325
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3900 Å2
ΔGint-23 kcal/mol
Surface area25150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.590, 83.320, 133.980
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Cas1 protein /


Mass: 36717.715 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio phage ICP1_2005_A (virus) / Gene: TUST1-15_00465 / Plasmid: pMCSG53 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: F1D4K1
#2: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 325 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.68 Å3/Da / Density % sol: 54.15 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 25% PEG 3350, 0.01 M Phenol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Jun 2, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 2.13→39.78 Å / Num. obs: 44744 / % possible obs: 99.5 % / Redundancy: 14.6 % / Biso Wilson estimate: 42.5 Å2 / Rmerge(I) obs: 0.069 / Net I/σ(I): 27.1
Reflection shellResolution: 2.13→2.19 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.623 / Mean I/σ(I) obs: 2.9 / % possible all: 98.3

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimlessdata scaling
MrBUMPphasing
PHENIXphenix.autobuildmodel building
PHENIX(phenix.refine: 1.9_1692)refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3GOD

3god


Resolution: 2.13→39.78 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.92 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2072 2166 4.85 %random selection
Rwork0.1736 ---
obs0.1752 44680 99.45 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.13→39.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4662 0 1 325 4988
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034786
X-RAY DIFFRACTIONf_angle_d0.6466468
X-RAY DIFFRACTIONf_dihedral_angle_d12.3121747
X-RAY DIFFRACTIONf_chiral_restr0.024716
X-RAY DIFFRACTIONf_plane_restr0.002820
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.13-2.17960.30051310.26092743X-RAY DIFFRACTION98
2.1796-2.23410.2991540.23682749X-RAY DIFFRACTION98
2.2341-2.29450.23871410.23552744X-RAY DIFFRACTION98
2.2945-2.3620.27041550.21422795X-RAY DIFFRACTION99
2.362-2.43820.25041450.20432808X-RAY DIFFRACTION100
2.4382-2.52540.25641450.20282816X-RAY DIFFRACTION100
2.5254-2.62640.21381360.2072806X-RAY DIFFRACTION100
2.6264-2.7460.29021260.20652846X-RAY DIFFRACTION100
2.746-2.89070.22351500.20532820X-RAY DIFFRACTION100
2.8907-3.07170.27151310.20382860X-RAY DIFFRACTION100
3.0717-3.30880.23011320.19162859X-RAY DIFFRACTION100
3.3088-3.64160.21661550.17432854X-RAY DIFFRACTION100
3.6416-4.1680.16991550.1492878X-RAY DIFFRACTION100
4.168-5.24940.17091630.13352893X-RAY DIFFRACTION100
5.2494-39.78820.17181470.15153043X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.78581.76-0.3045.7578-1.05278.41960.01850.15370.02660.1093-0.0721-0.19810.0809-0.00730.10520.15720.00820.00360.3588-0.00910.288730.0055104.309912.3869
22.50942.24830.78774.14710.58261.06410.32-0.5090.18860.9256-0.31930.15060.0471-0.07760.00160.4987-0.03250.02150.4739-0.0360.295226.149107.725237.2848
34.70924.032-0.94276.7322-1.53653.59710.1627-0.19420.14390.3926-0.1379-0.0832-0.02850.1987-0.00370.31250.0108-0.09230.3644-0.03580.249631.646107.026832.2349
42.50440.44251.17395.44760.31092.6451-0.1604-0.01780.2344-0.0690.17710.5699-0.0304-0.4663-0.01030.2219-0.0154-0.01310.55240.04490.36049.7623103.9696.4183
52.61691.149-0.5193.86740.97853.8428-0.18810.1943-0.3471-0.0399-0.00320.17990.7616-0.34080.19330.4329-0.10070.03850.48120.02950.40755.723176.722617.7882
63.10550.82910.69694.18840.26235.1926-0.1030.3331-0.2145-0.34280.10780.07970.6848-0.33560.02080.3985-0.13470.03470.43790.01520.38776.609180.894710.8846
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and resid 4:85
2X-RAY DIFFRACTION2chain A and resid 86:228
3X-RAY DIFFRACTION3chain A and resid 229:296
4X-RAY DIFFRACTION4chain B and resid -1:85
5X-RAY DIFFRACTION5chain B and resid 86:228
6X-RAY DIFFRACTION6chain B and resid 229:295

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