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- PDB-2x5t: Crystal structure of ORF131 from Sulfolobus islandicus rudivirus 1 -

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Basic information

Entry
Database: PDB / ID: 2x5t
TitleCrystal structure of ORF131 from Sulfolobus islandicus rudivirus 1
ComponentsORF 131
KeywordsVIRAL PROTEIN / DOMAIN-SWAP / ARCHEAL VIRUS
Function / homologySignal recognition particle alu RNA binding heterodimer, srp9/1 - #60 / : / PHA01746-like protein / Signal recognition particle alu RNA binding heterodimer, srp9/1 / 2-Layer Sandwich / Alpha Beta / MALONATE ION / Uncharacterized protein 131
Function and homology information
Biological speciesSULFOLOBUS ISLANDICUS RUDIVIRUS 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsOke, M. / Carter, L.G. / Johnson, K.A. / Liu, H. / Mcmahon, S.A. / Naismith, J.H. / White, M.F.
CitationJournal: J.Struct.Funct.Genomics / Year: 2010
Title: The Scottish Structural Proteomics Facility: Targets, Methods and Outputs.
Authors: Oke, M. / Carter, L.G. / Johnson, K.A. / Liu, H. / Mcmahon, S.A. / Yan, X. / Kerou, M. / Weikart, N.D. / Kadi, N. / Sheikh, M.A. / Schmelz, S. / Dorward, M. / Zawadzki, M. / Cozens, C. / ...Authors: Oke, M. / Carter, L.G. / Johnson, K.A. / Liu, H. / Mcmahon, S.A. / Yan, X. / Kerou, M. / Weikart, N.D. / Kadi, N. / Sheikh, M.A. / Schmelz, S. / Dorward, M. / Zawadzki, M. / Cozens, C. / Falconer, H. / Powers, H. / Overton, I.M. / Van Niekerk, C.A.J. / Peng, X. / Patel, P. / Garrett, R.A. / Prangishvili, D. / Botting, C.H. / Coote, P.J. / Dryden, D.T.F. / Barton, G.J. / Schwarz-Linek, U. / Challis, G.L. / Taylor, G.L. / White, M.F. / Naismith, J.H.
History
DepositionFeb 10, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 28, 2010Provider: repository / Type: Initial release
Revision 1.1Aug 10, 2011Group: Database references / Refinement description ...Database references / Refinement description / Structure summary / Version format compliance
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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: ORF 131
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,1342
Polymers11,0321
Non-polymers1021
Water54030
1
A: ORF 131
hetero molecules

A: ORF 131
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,2684
Polymers22,0642
Non-polymers2042
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+2/31
Buried area2890 Å2
ΔGint-13.8 kcal/mol
Surface area10850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.810, 57.810, 69.600
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-2004-

HOH

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Components

#1: Protein ORF 131 / UNCHARACTERIZED PROTEIN 131 / CAG38830


Mass: 11031.764 Da / Num. of mol.: 1 / Fragment: TRUNCATED VERSION, RESIDUES 2-96
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SULFOLOBUS ISLANDICUS RUDIVIRUS 1 / Variant: XX / Plasmid: PDEST14 / Production host: ESCHERICHIA COLI (E. coli) / Variant (production host): BL21 / References: UniProt: Q8QL44
#2: Chemical ChemComp-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H2O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 30 / 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: 2.5 Å3/Da / Density % sol: 51 % / Description: NONE
Crystal growDetails: 2.1 M SODIUM MALONATE AND CRYOPROTECTED WITH 2.4 M MALONATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.6
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Dec 12, 2005 / Details: MIRRORS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.6 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 6828 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 11.8 % / Biso Wilson estimate: 0 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 25.5
Reflection shellResolution: 2.2→2.3 Å / Redundancy: 12 % / Rmerge(I) obs: 0.61 / Mean I/σ(I) obs: 4.1 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2X5G

2x5g


Resolution: 2.2→50.06 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.89 / SU B: 12.682 / SU ML: 0.161 / Cross valid method: THROUGHOUT / ESU R: 0.233 / ESU R Free: 0.21 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS.
RfactorNum. reflection% reflectionSelection details
Rfree0.27493 337 4.7 %RANDOM
Rwork0.22146 ---
obs0.22379 6828 99.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 42.914 Å2
Baniso -1Baniso -2Baniso -3
1-1.09 Å20.55 Å20 Å2
2--1.09 Å20 Å2
3----1.64 Å2
Refinement stepCycle: LAST / Resolution: 2.2→50.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms758 0 7 30 795
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.022779
X-RAY DIFFRACTIONr_bond_other_d0.0060.02554
X-RAY DIFFRACTIONr_angle_refined_deg1.21.9841044
X-RAY DIFFRACTIONr_angle_other_deg0.7953.0011363
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.014593
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.61725.67637
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.94915161
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.139154
X-RAY DIFFRACTIONr_chiral_restr0.0730.2119
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02833
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02139
X-RAY DIFFRACTIONr_nbd_refined0.2110.2125
X-RAY DIFFRACTIONr_nbd_other0.1830.2498
X-RAY DIFFRACTIONr_nbtor_refined0.1750.2356
X-RAY DIFFRACTIONr_nbtor_other0.0850.2430
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1420.230
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1890.212
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2040.222
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1810.27
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2231.5638
X-RAY DIFFRACTIONr_mcbond_other0.1041.5186
X-RAY DIFFRACTIONr_mcangle_it0.9762757
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.123385
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.5964.5286
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.295 25 -
Rwork0.269 503 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: 26.516 Å / Origin y: -9.337 Å / Origin z: 16.949 Å
111213212223313233
T-0.214 Å2-0.0029 Å20.0202 Å2--0.1999 Å20.01 Å2---0.2137 Å2
L3.0398 °20.4218 °2-1.3675 °2-4.541 °22.9115 °2--8.0239 °2
S-0.1643 Å °0.2742 Å °-0.219 Å °-0.0193 Å °-0.0563 Å °0.162 Å °0.2544 Å °-0.5988 Å °0.2206 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 94
2X-RAY DIFFRACTION1A1096

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