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- PDB-6oaw: Crystal structure of a CRISPR Cas-related protein -

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Basic information

Entry
Database: PDB / ID: 6oaw
TitleCrystal structure of a CRISPR Cas-related protein
ComponentsWYL1
KeywordsIMMUNE SYSTEM / WYL domain / Structural Genomics / Structural Genomics Consortium / SGC
Function / homologyUncharacterized protein
Function and homology information
Biological speciesRuminococcus sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 Å
AuthorsZhang, H. / Dong, C. / Li, L. / Tempel, W. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Min, J. / Structural Genomics Consortium / Structural Genomics Consortium (SGC)
CitationJournal: Nucleic Acids Res. / Year: 2019
Title: Structural insights into the modulatory role of the accessory protein WYL1 in the Type VI-D CRISPR-Cas system.
Authors: Zhang, H. / Dong, C. / Li, L. / Wasney, G.A. / Min, J.
History
DepositionMar 18, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 10, 2019Provider: repository / Type: Initial release
Revision 1.1May 22, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jun 12, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: WYL1
B: WYL1


Theoretical massNumber of molelcules
Total (without water)91,98833
Polymers91,9882
Non-polymers031
Water1,47782
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4620 Å2
ΔGint-36 kcal/mol
Surface area36480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.768, 95.294, 77.337
Angle α, β, γ (deg.)90.000, 112.760, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010A3 - 391
2010B3 - 391

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Components

#1: Protein WYL1


Mass: 45994.215 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ruminococcus sp. (bacteria) / Gene: DCZ53_08630 / Plasmid: pET28-MKH8SUMO / Production host: Escherichia coli (E. coli) / References: UniProt: A0A352D0K5
#2: Chemical...
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 31 / Source method: obtained synthetically
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 82 / 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: 2.86 Å3/Da / Density % sol: 56.93 % / Mosaicity: 0.17 °
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1 M ammonium acetate, 0.015 M magnesium acetate, 0.05 M sodium cacodylate, 10% v/v 2-propanol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97868 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 7, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97868 Å / Relative weight: 1
ReflectionResolution: 2.1→47.65 Å / Num. obs: 59861 / % possible obs: 99.2 % / Redundancy: 6.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.077 / Rpim(I) all: 0.032 / Rrim(I) all: 0.083 / Net I/σ(I): 16
Reflection shellResolution: 2.1→2.15 Å / Redundancy: 6.6 % / Rmerge(I) obs: 1.371 / Num. unique obs: 4627 / CC1/2: 0.641 / Rpim(I) all: 0.569 / Rrim(I) all: 1.487 / % possible all: 98.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
Aimlessdata scaling
PDB_EXTRACT3.22data extraction
SHELXDEphasing
XDSdata reduction
RefinementMethod to determine structure: SAD / Resolution: 2.2→39.5 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.936 / SU B: 13.95 / SU ML: 0.166 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.237 / ESU R Free: 0.195
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflection
Rfree0.2467 2554 4.9 %
Rwork0.2115 --
obs0.2133 49263 99.22 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 129.69 Å2 / Biso mean: 46.952 Å2 / Biso min: 24.04 Å2
Baniso -1Baniso -2Baniso -3
1-2.09 Å20 Å2-1.39 Å2
2--1.17 Å20 Å2
3----1.55 Å2
Refinement stepCycle: final / Resolution: 2.2→39.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6020 0 31 82 6133
Biso mean--37.43 40.97 -
Num. residues----772
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0136160
X-RAY DIFFRACTIONr_bond_other_d0.0020.0175541
X-RAY DIFFRACTIONr_angle_refined_deg1.5761.6488357
X-RAY DIFFRACTIONr_angle_other_deg1.351.57112807
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9785770
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.75722.282298
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.90915977
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2361533
X-RAY DIFFRACTIONr_chiral_restr0.0740.2828
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.026906
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021321
X-RAY DIFFRACTIONr_mcbond_it1.5192.8783082
X-RAY DIFFRACTIONr_mcbond_other1.5192.8773081
X-RAY DIFFRACTIONr_mcangle_it2.4224.3093847
Refine LS restraints NCS

Ens-ID: 1 / Number: 11393 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.11 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.303 180 -
Rwork0.289 3612 -
all-3792 -
obs--98.7 %
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)
11.02180.52810.49262.49570.682.3166-0.1294-0.00890.1565-0.0844-0.08490.1918-0.2588-0.09150.21430.0963-0.02380.00510.0829-0.05380.094735.14742.91945.858
22.390.0696-0.20044.07261.87615.9363-0.0320.1273-0.0969-0.25620.1902-0.56320.17360.9624-0.15820.05660.00250.05680.2227-0.03670.092345.61918.54433.12
32.42680.26591.68142.15710.42316.3566-0.07210.062-0.1806-0.30790.0417-0.0950.08360.09710.03030.21010.08650.07420.05930.02390.055540.08511.28265.691
40.997-1.68580.38894.0416-0.70951.21410.0572-0.0437-0.3095-0.37840.05120.69390.3378-0.2438-0.10840.3551-0.1199-0.20440.15990.07090.29299.49223.64642.819
52.4773-0.6157-0.95522.1940.6266.1042-0.1402-0.31990.49640.29160.13780.44410.2197-0.70760.00240.25590.05740.02770.26650.01170.32699.23628.19472.254
63.602-1.2576-0.3336.30030.14553.89360.0777-0.1380.2281-0.1159-0.1553-0.1278-0.5411-0.01590.07760.19140.1001-0.00190.10830.00070.018439.37123.69278.754
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 174
2X-RAY DIFFRACTION2A175 - 302
3X-RAY DIFFRACTION3A303 - 391
4X-RAY DIFFRACTION3A392
5X-RAY DIFFRACTION4B2 - 174
6X-RAY DIFFRACTION5B175 - 302
7X-RAY DIFFRACTION6B303 - 391

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