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- PDB-2x5g: Crystal structure of the ORF131L51M mutant from Sulfolobus island... -

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Basic information

Entry
Database: PDB / ID: 2x5g
TitleCrystal structure of the ORF131L51M mutant from Sulfolobus islandicus rudivirus 1
ComponentsORF 131
KeywordsVIRAL PROTEIN
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 / MAD / Resolution: 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.Genom. / 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 8, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 21, 2010Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / struct_conn / 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 / _pdbx_entry_details.has_protein_modification / _struct_conn.pdbx_leaving_atom_flag / _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)11,4076
Polymers11,0971
Non-polymers3105
Water48627
1
A: ORF 131
hetero molecules

A: ORF 131
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,81412
Polymers22,1932
Non-polymers62110
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_765-x+2,-x+y+1,-z+1/31
Buried area3250 Å2
ΔGint-76.1 kcal/mol
Surface area11480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.453, 58.453, 68.113
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-2003-

HOH

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Components

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


Mass: 11096.696 Da / Num. of mol.: 1 / Fragment: TRUNCATED VERSION, RESIDUES 1-96 / Mutation: YES
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-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H2O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 27 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, LEU 51 TO MSE
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: 3.2 Å3/Da / Density % sol: 60 % / 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: Sep 10, 2006 / Details: MIRRORS
RadiationMonochromator: SI(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.6 Å / Relative weight: 1
ReflectionResolution: 2→25.31 Å / Num. obs: 9346 / % possible obs: 99 % / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 0 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 20.9
Reflection shellResolution: 2→2.1 Å / Redundancy: 2 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 1.7 / % possible all: 92

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
MOSFLMdata reduction
SCALAdata scaling
SHELXDEphasing
SOLVEphasing
RESOLVEphasing
RefinementMethod to determine structure: MAD
Starting model: NONE

Resolution: 2→25.311 Å / SU ML: 0.26 / σ(F): 1.36 / Phase error: 27.56 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2489 457 4.9 %
Rwork0.2104 --
obs0.2123 9346 98.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 54.997 Å2 / ksol: 0.441 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.2218 Å2-0 Å2-0 Å2
2--1.2218 Å20 Å2
3----2.4437 Å2
Refinement stepCycle: LAST / Resolution: 2→25.311 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms741 0 17 27 785
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.018791
X-RAY DIFFRACTIONf_angle_d1.7411061
X-RAY DIFFRACTIONf_dihedral_angle_d18.056322
X-RAY DIFFRACTIONf_chiral_restr0.1120
X-RAY DIFFRACTIONf_plane_restr0.018136
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0002-2.28950.35451410.25482886X-RAY DIFFRACTION98
2.2895-2.88380.27161570.20572959X-RAY DIFFRACTION100
2.8838-25.31290.22291590.20123044X-RAY DIFFRACTION99
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)
11.1566-1.22070.1832.4520.2482.48270.14780.3519-0.1344-0.0799-0.32160.458-0.525-1.51690.11260.51280.2068-0.02170.6068-0.04350.385725.023624.2474-1.8271
22.8962-0.6389-0.62933.29162.06832.16780.4343-0.06720.0099-0.3209-0.3463-0.3566-0.24930.002-0.08950.33190.02740.07930.3652-0.04060.401833.709323.70497.6402
33.66431.2205-0.72054.11530.01573.5689-0.33480.0861.01640.98880.31321.2179-0.38960.5646-0.02190.37090.010.08570.3120.16340.582938.432629.230618.1822
41.00410.5460.75240.4841-0.31664.93030.05240.0324-0.31360.1648-0.1695-0.0041.06210.44870.08580.330.0199-0.01560.2589-0.04150.387542.526915.83797.0907
51.5524-0.4384-0.65922.71211.1993.38650.63120.3516-0.0818-0.6675-0.1146-0.5891-1.18140.2387-0.11070.5384-0.09040.07040.4231-0.00750.425138.000422.4015-6.3796
600-0000-00-969457.3228000969457.3000.3376-0.05050.05440.4785-0.05310.35438.100130.009320.4145
70000000000000001.6143-0.1225-0.13160.8301-0.45170.820340.400511.7006-3.3619
80000000000000000.53620.0356-0.02720.3953-0.00580.58133.821519.31111.3029
91.99991.46767.41262.0003-5.84487.9326-0.26740.48690.3079-0.15840.12960.0109-0.1087-0.3297-0.04291.4523-0.14310.22710.5054-0.25620.48537.028911.48277.4627
102.00011.9992-5.06591.99941.99951.99991.13683.5836-2.4829-5.1618-0.74931.08562.62550.858-0.41841.2966-0.2041-0.12721.22880.17560.495732.150914.2035.8105
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 2:23)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 24:57)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 58:68)
4X-RAY DIFFRACTION4(CHAIN A AND RESID 69:86)
5X-RAY DIFFRACTION5(CHAIN A AND RESID 87:95)
6X-RAY DIFFRACTION6(CHAIN B AND RESID 1:1)
7X-RAY DIFFRACTION7(CHAIN B AND RESID 2:2)
8X-RAY DIFFRACTION8(CHAIN B AND RESID 3:3)
9X-RAY DIFFRACTION9(CHAIN D AND RESID 201:201)
10X-RAY DIFFRACTION10(CHAIN D AND RESID 202:202)

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