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- PDB-6opm: Casposase bound to integration product -

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Basic information

Entry
Database: PDB / ID: 6opm
TitleCasposase bound to integration product
Components
  • CRISPR-associated endonuclease Cas1
  • DNA 21-mer
  • unknown
KeywordsHYDROLASE/DNA / Transposition / casposase / HYDROLASE-DNA complex
Function / homology
Function and homology information


maintenance of CRISPR repeat elements / endonuclease activity / defense response to virus / Hydrolases; Acting on ester bonds / DNA binding / metal ion binding
Similarity search - Function
CRISPR-associated endonuclease Cas1, N-terminal domain / CRISPR-associated protein Cas1 / CRISPR-associated endonuclease Cas1, C-terminal domain / CRISPR associated protein Cas1
Similarity search - Domain/homology
DNA / DNA (> 10) / CRISPR-associated endonuclease Cas1
Similarity search - Component
Biological speciesMethanosarcina mazei (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 3.1 Å
AuthorsDyda, F. / Hickman, A.B. / Kailasan, S.
CitationJournal: Elife / Year: 2020
Title: Casposase structure and the mechanistic link between DNA transposition and spacer acquisition by CRISPR-Cas.
Authors: Hickman, A.B. / Kailasan, S. / Genzor, P. / Haase, A.D. / Dyda, F.
History
DepositionApr 25, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 12, 2020Provider: repository / Type: Initial release
Revision 1.1Aug 26, 2020Group: Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / pdbx_struct_conn_angle / struct_conn
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CRISPR-associated endonuclease Cas1
B: CRISPR-associated endonuclease Cas1
C: CRISPR-associated endonuclease Cas1
D: CRISPR-associated endonuclease Cas1
E: DNA 21-mer
F: DNA 21-mer
H: unknown
J: unknown
hetero molecules


Theoretical massNumber of molelcules
Total (without water)215,10114
Polymers214,8618
Non-polymers2406
Water64936
1
A: CRISPR-associated endonuclease Cas1
B: CRISPR-associated endonuclease Cas1
C: CRISPR-associated endonuclease Cas1
D: CRISPR-associated endonuclease Cas1
E: DNA 21-mer
F: DNA 21-mer
hetero molecules


Theoretical massNumber of molelcules
Total (without water)212,85312
Polymers212,6126
Non-polymers2406
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20040 Å2
ΔGint-147 kcal/mol
Surface area64520 Å2
MethodPISA
2
H: unknown


Theoretical massNumber of molelcules
Total (without water)1,1241
Polymers1,1241
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area1160 Å2
MethodPISA
3
J: unknown


Theoretical massNumber of molelcules
Total (without water)1,1241
Polymers1,1241
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area1240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.390, 106.390, 423.360
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein
CRISPR-associated endonuclease Cas1 / casposase


Mass: 49961.492 Da / Num. of mol.: 4 / Mutation: C184S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanosarcina mazei (archaea)
Gene: cas1, DU30_01425, DU33_00735, DU42_16395, DU43_06520, DU45_00060, DU52_05410, DU56_00015, DU57_15540, DU59_17660, DU64_01200, DU66_03140, DU67_00910, DU68_00045, DU71_17290, DU72_02185, DU87_01695
Production host: Escherichia coli (E. coli)
References: UniProt: A0A0F8IEL4, Hydrolases; Acting on ester bonds
#2: DNA chain DNA 21-mer


Mass: 6383.137 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Methanosarcina mazei (archaea)
#3: Protein/peptide unknown


Mass: 1124.378 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanosarcina mazei (archaea) / Production host: Escherichia coli (E. coli)
#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 36 / 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: 2.79 Å3/Da / Density % sol: 55.92 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.15-0.185 M calcium acetate, 84 mM sodium acetate, pH 3.8-4.4, 7.5-9.0% PEG8000, 0.5 M potassium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.9792966, 0.9791605,0.9680223
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 25, 2019
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792966 Å / Relative weight: 1
ReflectionResolution: 3.1→30 Å / Num. obs: 45362 / % possible obs: 99.8 % / Redundancy: 14.54 % / Biso Wilson estimate: 106.13 Å2 / Net I/σ(I): 13.3
Reflection shellResolution: 3.1→3.18 Å / Num. unique obs: 3309

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSdata reduction
XSCALEdata scaling
SHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 3.1→29.89 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.905 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.406
RfactorNum. reflection% reflectionSelection details
Rfree0.256 1135 2.5 %RANDOM
Rwork0.198 ---
obs0.2 45362 100 %-
Displacement parametersBiso mean: 142.33 Å2
Baniso -1Baniso -2Baniso -3
1--20.9925 Å20 Å20 Å2
2---20.9925 Å20 Å2
3---41.985 Å2
Refine analyzeLuzzati coordinate error obs: 0.4 Å
Refinement stepCycle: 1 / Resolution: 3.1→29.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11442 846 6 36 12330
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0112620HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.1717170HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d4416SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes1982HARMONIC5
X-RAY DIFFRACTIONt_it12620HARMONIC5
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.47
X-RAY DIFFRACTIONt_other_torsion23.88
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1642SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact14801SEMIHARMONIC4
LS refinement shellResolution: 3.1→3.12 Å / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.2934 -2.53 %
Rwork0.2551 885 -
all0.256 908 -
obs--100 %
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)
12.5226-0.9437-0.63521.24830.19982.65960.24320.6343-0.0163-0.14990.1289-0.33550.47591.0885-0.3721-0.15950.2609-0.08450.5982-0.2104-0.416165.0905-6.257412.2317
21.6189-0.26970.34691.26520.43194.31840.17350.40920.1053-0.21050.10840.4119-0.3627-0.7669-0.2819-0.10150.1334-0.0654-0.03070.1832-0.121230.00116.551328.378
31.69970.38850.4592.45910.2933.66990.3622-0.24660.25360.5141-0.1580.0421-0.91270.5195-0.20420.3649-0.29190.1273-0.17710.0322-0.356752.432310.514272.4259
41.24650.5835-0.60391.9823-0.66323.22110.1478-0.2323-0.4445-0.0477-0.1143-0.09681.08850.6195-0.03340.340.2494-0.2097-0.30180.0923-0.16951.9914-26.483655.7602
53.1865-0.4838-0.24.64680.20437.06210.2080.1092-0.15920.1579-0.05650.16760.25280.1287-0.15150.17180.1792-0.0895-0.11560.0041-0.274949.2472-7.577645.314
63.1959-1.0884-0.53893.77470.44055.64090.04530.266-0.1725-0.12150.08020.08130.82440.4927-0.12540.09630.1828-0.0335-0.05020.0284-0.180146.6766-3.618938.8936
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }
3X-RAY DIFFRACTION3{ C|* }
4X-RAY DIFFRACTION4{ D|* }
5X-RAY DIFFRACTION5{ E|* }
6X-RAY DIFFRACTION6{ F|* }

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