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- PDB-6nys: The crystal structure of CroV588 a novel circular LRR protein str... -

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Basic information

Entry
Database: PDB / ID: 6nys
TitleThe crystal structure of CroV588 a novel circular LRR protein structure
Componentscrov588
KeywordsUNKNOWN FUNCTION / Leucine rich repeat
Function / homologyFNIP / FNIP Repeat / Leucine-rich repeat domain superfamily / 6-tungstotellurate(VI) / Crov588
Function and homology information
Biological speciesCafeteria roenbergensis virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.1 Å
AuthorsHuyton, T. / Jaiswal, M. / Gorlich, D.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Federal Ministry for Education and ResearchSFB Germany
CitationJournal: To Be Published
Title: The crystal structure of CroV588 a novel circular LRR protein structure
Authors: Huyton, T. / Jaiswal, M. / Gorlich, D.
History
DepositionFeb 12, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 12, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 13, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
B: crov588
A: crov588
hetero molecules


Theoretical massNumber of molelcules
Total (without water)179,15416
Polymers156,5502
Non-polymers22,60514
Water00
1
B: crov588
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,5778
Polymers78,2751
Non-polymers11,3027
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
A: crov588
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,5778
Polymers78,2751
Non-polymers11,3027
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)65.289, 171.757, 92.031
Angle α, β, γ (deg.)90.00, 90.12, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11B
21A

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: GLU / Beg label comp-ID: GLU / End auth comp-ID: LYS / End label comp-ID: LYS / Refine code: _ / Auth seq-ID: 2 - 680 / Label seq-ID: 2 - 680

Dom-IDAuth asym-IDLabel asym-ID
1BA
2AB

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Components

#1: Protein crov588


Mass: 78274.750 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cafeteria roenbergensis virus / Production host: Escherichia coli (E. coli) / References: UniProt: A0A4D6WFR4*PLUS
#2: Chemical
ChemComp-TEW / 6-tungstotellurate(VI)


Mass: 1614.626 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: O24TeW6

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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: 3.3 Å3/Da / Density % sol: 62.68 %
Crystal growTemperature: 293 K / Method: vapor diffusion / Details: 0.1M mes PH 6.0, PEG 8000, 0.2M MgCl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.2108 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Mar 18, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2108 Å / Relative weight: 1
ReflectionResolution: 3.1→46.02 Å / Num. obs: 36749 / % possible obs: 99.81 % / Redundancy: 13.8 % / Net I/σ(I): 15.11
Reflection shellResolution: 3.1→3.211 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 3.1→46.02 Å / Cor.coef. Fo:Fc: 0.908 / Cor.coef. Fo:Fc free: 0.89 / SU B: 45.27 / SU ML: 0.422 / Cross valid method: THROUGHOUT / ESU R Free: 0.536 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29559 1851 5 %RANDOM
Rwork0.26099 ---
obs0.26266 34884 99.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 104.174 Å2
Baniso -1Baniso -2Baniso -3
1--11.62 Å2-0 Å2-0.77 Å2
2--3.89 Å20 Å2
3---7.73 Å2
Refinement stepCycle: 1 / Resolution: 3.1→46.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11042 0 434 0 11476
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.01311902
X-RAY DIFFRACTIONr_bond_other_d0.0010.01710092
X-RAY DIFFRACTIONr_angle_refined_deg2.0751.76817095
X-RAY DIFFRACTIONr_angle_other_deg1.2361.55923632
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.75151364
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.15426.02608
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.707151924
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.5861510
X-RAY DIFFRACTIONr_chiral_restr0.0740.21516
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212634
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022188
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.8284.4185450
X-RAY DIFFRACTIONr_mcbond_other2.8274.4175449
X-RAY DIFFRACTIONr_mcangle_it4.6246.6236816
X-RAY DIFFRACTIONr_mcangle_other4.6236.6256817
X-RAY DIFFRACTIONr_scbond_it5.5915.9936452
X-RAY DIFFRACTIONr_scbond_other2.5184.6615907
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.3086.9128657
X-RAY DIFFRACTIONr_long_range_B_refined10.92388.846034
X-RAY DIFFRACTIONr_long_range_B_other10.51585.01745497
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 22584 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.03 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1B
2A
LS refinement shellResolution: 3.1→3.18 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.365 147 -
Rwork0.349 2542 -
obs--99.96 %
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)
11.7642-1.16250.13742.43620.15990.6269-0.0479-0.3161-0.09020.11380.126-0.3622-0.1530.1014-0.07811.3846-0.06470.14330.09460.03140.1301-62.898421.8373-18.3205
21.56971.14150.09452.1340.30720.6331-0.04090.29580.0445-0.15570.0946-0.3530.08950.1368-0.05371.32250.08150.10440.11480.04850.1191-30.1634-24.8259-27.6334
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 416
2X-RAY DIFFRACTION1A417 - 680
3X-RAY DIFFRACTION2B2 - 367
4X-RAY DIFFRACTION2B368 - 680

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