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- PDB-4h3t: Crystal structure of CRISPR-associated protein Cse1 from Acidimic... -

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Basic information

Entry
Database: PDB / ID: 4h3t
TitleCrystal structure of CRISPR-associated protein Cse1 from Acidimicrobium ferrooxidans
ComponentsCRISPR-associated protein, Cse1 family
KeywordsCELL INVASION / Structural Genomics / PSI-Biology / Midwest Center for Structural Genomics / MCSG / CASCADE
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 speciesAcidimicrobium ferrooxidans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.03 Å
AuthorsMichalska, K. / Stols, L. / Clancy, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal structure of CRISPR-associated protein Cse1 from Acidimicrobium ferrooxidans
Authors: Michalska, K. / Stols, L. / Clancy, S. / Joachimiak, A.
History
DepositionSep 14, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 26, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 16, 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_ref_seq_dif / 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_ref_seq_dif.details / _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

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Assembly

Deposited unit
A: CRISPR-associated protein, Cse1 family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,5943
Polymers60,4101
Non-polymers1842
Water4,846269
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)137.017, 137.017, 203.537
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122
Components on special symmetry positions
IDModelComponents
11A-701-

HOH

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Components

#1: Protein CRISPR-associated protein, Cse1 family


Mass: 60410.285 Da / Num. of mol.: 1 / Mutation: L456I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acidimicrobium ferrooxidans (bacteria) / Strain: DSM 10331 / Gene: Afer_0988 / Plasmid: pMCSG48 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) Magic / References: UniProt: C7LYW9
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 269 / 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: 3.95 Å3/Da / Density % sol: 68.89 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2 M proline, 0.1 M HEPES/NaOH, 10% PEG3350, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97915 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 3, 2011 / Details: mirrors
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.03→50 Å / Num. all: 62743 / Num. obs: 62132 / % possible obs: 99 % / Observed criterion σ(I): -3 / Redundancy: 12 % / Biso Wilson estimate: 41.2 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 25.3
Reflection shellResolution: 2.03→2.07 Å / Redundancy: 9.6 % / Rmerge(I) obs: 0.73 / Mean I/σ(I) obs: 2.4 / Num. unique all: 3130 / % possible all: 99.9

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
SHELXmodel building
MLPHAREphasing
DMmodel building
ARP/wARPmodel building
Cootmodel building
BUSTER2.10.0refinement
HKL-3000data reduction
HKL-3000data scaling
SHELXphasing
DMphasing
RefinementMethod to determine structure: SAD / Resolution: 2.03→29.72 Å / Cor.coef. Fo:Fc: 0.9532 / Cor.coef. Fo:Fc free: 0.9502 / SU R Cruickshank DPI: 0.147 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Details: HYDROGEN ATOMS HAVE BEEN ADDED AT RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1991 1260 2.04 %RANDOM
Rwork0.1816 ---
all0.182 61879 --
obs0.182 61879 99.04 %-
Displacement parametersBiso mean: 52.61 Å2
Baniso -1Baniso -2Baniso -3
1--3.0899 Å20 Å20 Å2
2---3.0899 Å20 Å2
3---6.1798 Å2
Refine analyzeLuzzati coordinate error obs: 0.262 Å
Refinement stepCycle: LAST / Resolution: 2.03→29.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4060 0 12 269 4341
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0148342HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.1115053HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2299SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes94HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1247HARMONIC5
X-RAY DIFFRACTIONt_it8342HARMONIC20
X-RAY DIFFRACTIONt_omega_torsion4.46
X-RAY DIFFRACTIONt_other_torsion2.9
X-RAY DIFFRACTIONt_chiral_improper_torsion518SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact8889SEMIHARMONIC4
LS refinement shellResolution: 2.03→2.08 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2047 90 1.98 %
Rwork0.1858 4458 -
all0.1861 4548 -
obs--99.04 %
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)
12.293-0.1265-0.45331.2466-0.12821.9303-0.1145-0.49250.03590.05930.1318-0.1820.03660.2362-0.0173-0.14580.0231-0.0140.04820.0242-0.1266-2.899647.1136-3.9257
22.0253-0.356-0.33010.8176-0.07151.3915-0.135-0.1662-0.2221-0.05220.1264-0.02070.25830.00630.0086-0.0712-0.02030.0268-0.01860.0523-0.0833-9.311740.9766-11.7942
30.9634-0.3254-0.5491.9808-0.37190.9584-0.0969-0.3196-0.1392-0.09920.09090.32550.1341-0.11370.0061-0.1157-0.01520.02220.0820.0751-0.0441-29.897847.7952-4.8788
42.9209-0.14660.260700.92362.2640.05210.3775-0.0781-0.21750.0450.1622-0.1945-0.1552-0.0970.05110.0620.00470.0280.0713-0.1324-20.42452.0796-20.0792
51.5906-0.72291.00730.7419-0.77191.6771-0.1439-0.31860.01480.09130.07330.1252-0.0792-0.21890.0706-0.12370.03110.00590.0574-0.0293-0.0186-40.551266.7405-11.0553
62.4309-1.29611.72911.5616-1.85113.3927-0.3383-0.45250.19150.2640.20590.1465-0.4638-0.54420.1324-0.09530.1072-0.02870.0465-0.0802-0.0254-46.618475.7916-14.056
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{A|2 - 150}A2 - 150
2X-RAY DIFFRACTION2{A|151 - 294}A151 - 294
3X-RAY DIFFRACTION3{A|295 - 360}A295 - 360
4X-RAY DIFFRACTION4{A|361 - 379}A361 - 379
5X-RAY DIFFRACTION5{A|380 - 486}A380 - 486
6X-RAY DIFFRACTION6{A|487 - 531}A487 - 531

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