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- PDB-3wvo: Crystal structure of Thermobifida fusca Cse1 -

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Basic information

Entry
Database: PDB / ID: 3wvo
TitleCrystal structure of Thermobifida fusca Cse1
ComponentsCRISPR-associated protein, Cse1 family
KeywordsCELL INVASION / CRISPR / Cascade / CasA
Function / homologyTopoisomerase I; Chain A, domain 4 - #100 / CRISPR-associated protein Cse1 / CRISPR-associated protein Cse1 (CRISPR_cse1) / Topoisomerase I; Chain A, domain 4 / Orthogonal Bundle / Mainly Alpha / CRISPR-associated protein, Cse1 family
Function and homology information
Biological speciesThermobifida fusca (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.31 Å
AuthorsYuan, Y.A. / Tay, M.
CitationJournal: Protein Sci. / Year: 2015
Title: Crystal structure of Thermobifida fusca Cse1 reveals target DNA binding site.
Authors: Tay, M. / Liu, S. / Yuan, Y.A.
History
DepositionJun 2, 2014Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 14, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 24, 2022Group: Database references / Category: citation / database_2 / struct_ref_seq_dif
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.2Nov 8, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_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 protein, Cse1 family
B: CRISPR-associated protein, Cse1 family
C: CRISPR-associated protein, Cse1 family


Theoretical massNumber of molelcules
Total (without water)185,4853
Polymers185,4853
Non-polymers00
Water50428
1
A: CRISPR-associated protein, Cse1 family
B: CRISPR-associated protein, Cse1 family


Theoretical massNumber of molelcules
Total (without water)123,6572
Polymers123,6572
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2960 Å2
ΔGint-12 kcal/mol
Surface area45070 Å2
MethodPISA
2
C: CRISPR-associated protein, Cse1 family

C: CRISPR-associated protein, Cse1 family


Theoretical massNumber of molelcules
Total (without water)123,6572
Polymers123,6572
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area3080 Å2
ΔGint-11 kcal/mol
Surface area44690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)207.304, 132.529, 102.962
Angle α, β, γ (deg.)90.00, 93.75, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13B
23C

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: MET / Beg label comp-ID: MET / Refine code: _

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ALAALAAA1 - 5454 - 548
21ALAALABB1 - 5454 - 548
12THRTHRAA1 - 5464 - 549
22THRTHRCC1 - 5464 - 549
13THRTHRBB1 - 5464 - 549
23THRTHRCC1 - 5464 - 549

NCS ensembles :
ID
1
2
3

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Components

#1: Protein CRISPR-associated protein, Cse1 family


Mass: 61828.496 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermobifida fusca (bacteria) / Strain: YX / Gene: Tfu_1600 / Production host: Escherichia coli (E. coli) / References: UniProt: Q47PI4
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 28 / 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: 3.8 Å3/Da / Density % sol: 67.67 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: PEG8000, Cacodylate, potassium chloride, magnesium sulphate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 13, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 3.3→50 Å / Num. all: 39600 / Num. obs: 35245 / % possible obs: 89.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 3.3→3.36 Å / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC5.7.0029refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4H3T

4h3t


Resolution: 3.31→48.37 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.919 / SU B: 40.337 / SU ML: 0.299 / Cross valid method: THROUGHOUT / ESU R Free: 0.442 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.20974 1873 5 %RANDOM
Rwork0.15627 ---
all0.162 ---
obs0.15895 35245 89.43 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 73.488 Å2
Baniso -1Baniso -2Baniso -3
1-2.93 Å20 Å2-1.73 Å2
2---0.91 Å20 Å2
3----1.89 Å2
Refinement stepCycle: LAST / Resolution: 3.31→48.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12756 0 0 28 12784
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.01913068
X-RAY DIFFRACTIONr_angle_refined_deg1.7971.95417793
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.44151619
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.86223.25637
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.662152064
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.60715125
X-RAY DIFFRACTIONr_chiral_restr0.1120.21932
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02110202
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A6540.08
12B6540.08
21A6610.09
22C6610.09
31B6540.09
32C6540.09
LS refinement shellResolution: 3.31→3.396 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.259 57 -
Rwork0.229 1275 -
obs--43.83 %
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)
12.40661.3124-0.01452.24530.58811.79410.04120.06050.0858-0.23250.11-0.3593-0.24210.1482-0.15120.07540.00670.1020.135-0.01210.196246.510427.084150.4153
20.9580.47620.33874.147-0.55422.81810.3693-0.2294-0.17260.605-0.1172-0.11550.2072-0.248-0.25210.2463-0.2133-0.08310.33250.10430.206145.730434.087288.6593
33.11341.23130.37641.49080.33212.67290.07430.0924-0.16410.0790.09450.0230.37140.1568-0.16880.07950.0657-0.03080.0787-0.0220.0297-0.6995-0.693219.2732
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 547
2X-RAY DIFFRACTION2B1 - 546
3X-RAY DIFFRACTION3C1 - 546

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