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- PDB-7zal: FNIP family proteins from Cafeteria roenbergensis virus (CroV): l... -

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Basic information

Entry
Database: PDB / ID: 7zal
TitleFNIP family proteins from Cafeteria roenbergensis virus (CroV): leucine-rich repeats with novel structural features
ComponentsCrov539
KeywordsUNKNOWN FUNCTION / FNIP IP22 LRR
Function / homologyFNIP / : / FNIP Repeat / Leucine-rich repeat domain superfamily / FNIP repeat-containing protein
Function and homology information
Biological speciesCafeteria roenbergensis virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.732 Å
AuthorsHuyton, T. / Goerlich, D.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Federal Ministry for Education and Research Germany
CitationJournal: Sci Rep / Year: 2022
Title: Crystal structures of FNIP/FGxxFN motif-containing leucine-rich repeat proteins.
Authors: Huyton, T. / Jaiswal, M. / Taxer, W. / Fischer, M. / Gorlich, D.
History
DepositionMar 22, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 24, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 26, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2May 1, 2024Group: 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
AAA: Crov539
BBB: Crov539
CCC: Crov539
DDD: Crov539
EEE: Crov539
FFF: Crov539


Theoretical massNumber of molelcules
Total (without water)204,5226
Polymers204,5226
Non-polymers00
Water5,477304
1
AAA: Crov539

EEE: Crov539


Theoretical massNumber of molelcules
Total (without water)68,1742
Polymers68,1742
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y+1/2,-z+1/21
Buried area3400 Å2
ΔGint-22 kcal/mol
Surface area27270 Å2
2
BBB: Crov539
CCC: Crov539


Theoretical massNumber of molelcules
Total (without water)68,1742
Polymers68,1742
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3420 Å2
ΔGint-26 kcal/mol
Surface area27280 Å2
3
DDD: Crov539
FFF: Crov539


Theoretical massNumber of molelcules
Total (without water)68,1742
Polymers68,1742
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3370 Å2
ΔGint-22 kcal/mol
Surface area27450 Å2
Unit cell
Length a, b, c (Å)101.012, 113.453, 236.242
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11CCC
21BBB
31DDD
41AAA
51EEE
61FFF

NCS domain segments:

Ens-ID: 1 / Beg auth comp-ID: LEU / Beg label comp-ID: LEU / End auth comp-ID: GLN / End label comp-ID: GLN / Auth seq-ID: 40 - 250 / Label seq-ID: 42 - 252

Dom-IDComponent-IDAuth asym-IDLabel asym-ID
11CCCC
22BBBB
33DDDD
44AAAA
55EEEE
66FFFF

NCS ensembles : (Details: Global NCS restraints between domains: 1 2 3 4 5 6)

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Components

#1: Protein
Crov539


Mass: 34087.035 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cafeteria roenbergensis virus / Strain: BV-PW1 / Gene: crov539 / Production host: Escherichia coli (E. coli) / References: UniProt: E3T5W0
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 304 / 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: 3.31 Å3/Da / Density % sol: 63 % / Description: rods
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1M Bis-TRIS pH 6.5, 10% PEG10,000, 0.2M Potassium Sodium Tartrate tetrahydrate.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER2 S 16M / Detector: PIXEL / Date: Jun 14, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.73→49.46 Å / Num. obs: 999128 / % possible obs: 99.7 % / Redundancy: 13.8 % / CC1/2: 0.99 / Rpim(I) all: 0.034 / Net I/σ(I): 14.4
Reflection shellResolution: 2.73→2.79 Å / Redundancy: 13.6 % / Mean I/σ(I) obs: 1 / Num. unique obs: 57315 / CC1/2: 0.44 / Rpim(I) all: 0.788 / % possible all: 95

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: homology model

Resolution: 2.732→49.439 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.93 / SU B: 37.395 / SU ML: 0.34 / Cross valid method: FREE R-VALUE / ESU R: 0.753 / ESU R Free: 0.344
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2666 3577 4.931 %
Rwork0.2197 68959 -
all0.222 --
obs-72536 99.662 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 89.209 Å2
Baniso -1Baniso -2Baniso -3
1-9.787 Å20 Å2-0 Å2
2---9.174 Å20 Å2
3----0.613 Å2
Refinement stepCycle: LAST / Resolution: 2.732→49.439 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14496 0 0 304 14800
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.01314934
X-RAY DIFFRACTIONr_bond_other_d0.0010.01614196
X-RAY DIFFRACTIONr_angle_refined_deg1.1121.64320382
X-RAY DIFFRACTIONr_angle_other_deg1.2491.57232856
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.27151746
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.58125.826690
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.268152598
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.531156
X-RAY DIFFRACTIONr_chiral_restr0.0490.22028
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0216542
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023366
X-RAY DIFFRACTIONr_nbd_refined0.1690.22637
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1890.213698
X-RAY DIFFRACTIONr_nbtor_refined0.170.27172
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0720.27046
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2170.2429
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0770.210
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.380.265
X-RAY DIFFRACTIONr_nbd_other0.340.2229
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.3020.219
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0630.21
X-RAY DIFFRACTIONr_mcbond_it0.6384.5817002
X-RAY DIFFRACTIONr_mcbond_other0.6384.5817001
X-RAY DIFFRACTIONr_mcangle_it1.1526.8728742
X-RAY DIFFRACTIONr_mcangle_other1.1526.8728743
X-RAY DIFFRACTIONr_scbond_it0.4374.6317931
X-RAY DIFFRACTIONr_scbond_other0.4374.6317932
X-RAY DIFFRACTIONr_scangle_it0.8156.92511640
X-RAY DIFFRACTIONr_scangle_other0.8156.92511641
X-RAY DIFFRACTIONr_lrange_it4.99186.13758183
X-RAY DIFFRACTIONr_lrange_other4.95786.05358116
Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION / Type: loose positional; loose thermal / Weight Biso : 10 / Weight position: 5

Dom-IDAuth asym-IDRms dev Biso (Å2)Rms dev position (Å)
1CCC14.456070.61698
2BBB3.356350.74988
3DDD5.093350.75031
4AAA11.141230.67554
5EEE11.200790.71189
6FFF17.489920.86597
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.732-2.8030.3742340.364858X-RAY DIFFRACTION95.8043
2.803-2.8790.3752500.3544925X-RAY DIFFRACTION100
2.879-2.9630.3462250.3524786X-RAY DIFFRACTION100
2.963-3.0540.382620.3244653X-RAY DIFFRACTION100
3.054-3.1540.3292310.3034546X-RAY DIFFRACTION100
3.154-3.2650.3172140.2944375X-RAY DIFFRACTION100
3.265-3.3880.2852130.264216X-RAY DIFFRACTION100
3.388-3.5260.2982190.2474065X-RAY DIFFRACTION99.9767
3.526-3.6830.322020.2473906X-RAY DIFFRACTION100
3.683-3.8620.2991980.2293746X-RAY DIFFRACTION100
3.862-4.0710.2841930.223585X-RAY DIFFRACTION100
4.071-4.3170.2461690.1973365X-RAY DIFFRACTION100
4.317-4.6150.2341990.1793180X-RAY DIFFRACTION100
4.615-4.9840.1671650.1632942X-RAY DIFFRACTION99.9678
4.984-5.4590.2191420.1722769X-RAY DIFFRACTION100
5.459-6.1020.2731150.1912533X-RAY DIFFRACTION100
6.102-7.0420.2771180.22212X-RAY DIFFRACTION100
7.042-8.6170.337970.231907X-RAY DIFFRACTION100
8.617-12.1550.17890.161500X-RAY DIFFRACTION100
12.155-49.430.248420.184890X-RAY DIFFRACTION97.7964
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)
11.2242-0.5522-0.41741.72691.05253.20820.20980.09060.0292-0.2014-0.0628-0.2625-0.07150.3791-0.1470.04520.02960.0310.64570.0230.2863.51552.66262.181
21.33391.72041.31383.67241.97982.3523-0.235-0.04370.7688-0.5909-0.24020.7849-0.1797-0.12230.47520.11350.0817-0.1080.71380.06870.620929.95951.82326.727
30.86030.6824-0.53571.6826-1.04432.99210.0001-0.032-0.1747-0.1541-0.1662-0.2545-0.0660.31720.16610.03190.03820.02130.76450.01450.278221.1931.42830.38
40.9030.78140.7052.04692.01924.97620.3915-0.00940.09640.49040.0802-0.11380.41340.4141-0.47170.18810.0256-0.00030.7661-0.02980.586651.88457.99454.594
50.75611.31860.78983.63621.79432.2212-0.0168-0.0009-0.16420.02040.1184-0.41950.25850.1039-0.10160.10210.0587-0.05890.76710.03490.216122.78710.95297.514
61.1551.5355-0.98895.5407-1.54550.9670.20080.00790.445-0.11330.21780.9223-0.29850.072-0.41870.3514-0.0571-0.04020.7505-0.03220.386124.69846.68697.411
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLAAA-1 - 290
2X-RAY DIFFRACTION2ALLBBB-1 - 290
3X-RAY DIFFRACTION3ALLCCC-1 - 290
4X-RAY DIFFRACTION4ALLDDD-1 - 290
5X-RAY DIFFRACTION5ALLEEE-1 - 290
6X-RAY DIFFRACTION6ALLFFF-1 - 290

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