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- PDB-2x3g: Crystal Structure of the hypothetical protein ORF119 from Sulfolo... -

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Basic information

Entry
Database: PDB / ID: 2x3g
TitleCrystal Structure of the hypothetical protein ORF119 from Sulfolobus islandicus rod-shaped virus 1
ComponentsSIRV1 HYPOTHETICAL PROTEIN ORF119
KeywordsVIRAL PROTEIN / HOST MEMBRANE
Function / homologyAlpha-Beta Plaits - #1910 / : / : / Virus, 117-like / Replication-associated protein ORF2/G2P / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta / Replication-associated protein ORF2/G2P domain-containing protein
Function and homology information
Biological speciesSULFOLOBUS ISLANDICUS RUDIVIRUS 1 VARIANT XX
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å
AuthorsOke, M. / Carter, L.G. / Johnson, K.A. / Liu, H. / Mcmahon, S.A. / White, M.F. / Naismith, J.H.
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
DepositionJan 24, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 21, 2010Provider: repository / Type: Initial release
Revision 1.1May 7, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 24, 2018Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name ..._entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain / _entity_src_gen.pdbx_host_org_variant
Revision 1.4Nov 13, 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
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_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SIRV1 HYPOTHETICAL PROTEIN ORF119


Theoretical massNumber of molelcules
Total (without water)14,5201
Polymers14,5201
Non-polymers00
Water1,58588
1
A: SIRV1 HYPOTHETICAL PROTEIN ORF119

A: SIRV1 HYPOTHETICAL PROTEIN ORF119


Theoretical massNumber of molelcules
Total (without water)29,0412
Polymers29,0412
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area1990 Å2
ΔGint-9.6 kcal/mol
Surface area13150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.380, 46.170, 40.020
Angle α, β, γ (deg.)90.00, 101.83, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein SIRV1 HYPOTHETICAL PROTEIN ORF119


Mass: 14520.341 Da / Num. of mol.: 1 / Fragment: RESIDUES 2-119
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SULFOLOBUS ISLANDICUS RUDIVIRUS 1 VARIANT XX
Plasmid: PDEST14 / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / Variant (production host): C43 / References: UniProt: Q5TJA9
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 88 / Source method: isolated from a natural source / Formula: H2O
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: 2.31 Å3/Da / Density % sol: 47 % / Description: NONE
Crystal growpH: 6
Details: 20% PEG 4000, 0.1 M SODIUM CITRATE PH 6.0. CRYSTALS WERE CRYOPROTECTED WITH 25% PEG400 IN A SOLUTION CONTAINING 22% PEG 4000, 0.1 M SODIUM CITRATE PH 6.0.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.9537
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 21, 2008 / Details: MIRRORS
RadiationMonochromator: SI(III) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.8→38.84 Å / Num. obs: 11671 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 6.5 % / Biso Wilson estimate: 0 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 15.8
Reflection shellResolution: 1.8→1.85 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.54 / Mean I/σ(I) obs: 3.8 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
SCALEPACKdata scaling
SHELXDphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 1.8→38.84 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.926 / SU B: 6.192 / SU ML: 0.104 / Cross valid method: THROUGHOUT / ESU R: 0.137 / ESU R Free: 0.133 / 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 RESIDUES 57-59 ARE DISORDERED.
RfactorNum. reflection% reflectionSelection details
Rfree0.23786 592 4.8 %RANDOM
Rwork0.19355 ---
obs0.19587 11671 99.97 %-
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: 21.839 Å2
Baniso -1Baniso -2Baniso -3
1-2.94 Å20 Å2-1.61 Å2
2---1.58 Å20 Å2
3----2.02 Å2
Refinement stepCycle: LAST / Resolution: 1.8→38.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms992 0 0 88 1080
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0221027
X-RAY DIFFRACTIONr_bond_other_d0.0020.02722
X-RAY DIFFRACTIONr_angle_refined_deg1.1831.9381378
X-RAY DIFFRACTIONr_angle_other_deg0.75831757
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3575114
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.14423.06149
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.11915201
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.274154
X-RAY DIFFRACTIONr_chiral_restr0.0690.2148
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021085
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02223
X-RAY DIFFRACTIONr_nbd_refined0.2080.2172
X-RAY DIFFRACTIONr_nbd_other0.1750.2697
X-RAY DIFFRACTIONr_nbtor_refined0.1920.2492
X-RAY DIFFRACTIONr_nbtor_other0.0830.2549
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.140.265
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1060.211
X-RAY DIFFRACTIONr_symmetry_vdw_other0.20.239
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1510.214
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9221.5702
X-RAY DIFFRACTIONr_mcbond_other0.1691.5232
X-RAY DIFFRACTIONr_mcangle_it1.1312953
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.9883524
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.4454.5425
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: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3 34 -
Rwork0.239 869 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: 19.627 Å / Origin y: 14.44 Å / Origin z: 8.829 Å
111213212223313233
T-0.1209 Å20.0016 Å20.0091 Å2--0.0959 Å20.009 Å2---0.1102 Å2
L1.5131 °20.153 °20.1555 °2-3.0256 °20.1935 °2--1.9367 °2
S-0.0188 Å °-0.1869 Å °0.1005 Å °0.3744 Å °0.0683 Å °0.0065 Å °-0.1499 Å °-0.0059 Å °-0.0495 Å °

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