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- PDB-2x4i: ORF 114a from Sulfolobus islandicus rudivirus 1 -

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Basic information

Entry
Database: PDB / ID: 2x4i
TitleORF 114a from Sulfolobus islandicus rudivirus 1
ComponentsUNCHARACTERIZED PROTEIN 114
KeywordsUNKNOWN FUNCTION / DUF1874 / ARCHEAL VIRUS
Function / homologyUncharacterised protein PF08960, DUF1874 / STIV B116-like / STIV B116-like superfamily / STIV B116-like / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / Uncharacterized protein 114
Function and homology information
Biological speciesSULFOLOBUS ISLANDICUS RUDIVIRUS 1 VARIANT XX
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
DepositionJan 31, 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 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / 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_ncs_dom_lim
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_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
Revision 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: UNCHARACTERIZED PROTEIN 114
B: UNCHARACTERIZED PROTEIN 114
C: UNCHARACTERIZED PROTEIN 114
D: UNCHARACTERIZED PROTEIN 114


Theoretical massNumber of molelcules
Total (without water)52,9734
Polymers52,9734
Non-polymers00
Water55831
1
C: UNCHARACTERIZED PROTEIN 114
D: UNCHARACTERIZED PROTEIN 114


Theoretical massNumber of molelcules
Total (without water)26,4872
Polymers26,4872
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1570 Å2
ΔGint-12.4 kcal/mol
Surface area11790 Å2
MethodPISA
2
A: UNCHARACTERIZED PROTEIN 114
B: UNCHARACTERIZED PROTEIN 114


Theoretical massNumber of molelcules
Total (without water)26,4872
Polymers26,4872
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1620 Å2
ΔGint-12.1 kcal/mol
Surface area12000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.790, 48.790, 195.270
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:

Ens-ID: 1 / Refine code: 5

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LEULEUVALVALAA6 - 806 - 80
21LEULEUVALVALBB6 - 806 - 80
31LEULEUVALVALCC6 - 806 - 80
41LEULEUVALVALDD6 - 806 - 80
12GLNGLNILEILEAA107 - 111107 - 111
22GLNGLNILEILEBB107 - 111107 - 111
32GLNGLNILEILECC107 - 111107 - 111
42GLNGLNILEILEDD107 - 111107 - 111

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Components

#1: Protein
UNCHARACTERIZED PROTEIN 114 / CAG38848


Mass: 13243.285 Da / Num. of mol.: 4
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) / Strain (production host): BL21(DE3) / References: UniProt: Q8QL27
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 31 / 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: 2.21 Å3/Da / Density % sol: 44.29 % / Description: NONE
Crystal growpH: 7.5 / Details: 31% PEG1500, 0.1M HEPES, PH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.939
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: May 13, 2006
RadiationMonochromator: DIAMOND CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.939 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.927
11-H, K, -L20.073
ReflectionResolution: 2.2→27.08 Å / Num. obs: 16793 / % possible obs: 76.8 % / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 11.6
Reflection shellResolution: 2.2→2.26 Å / Redundancy: 3 % / Rmerge(I) obs: 0.66 / Mean I/σ(I) obs: 2.1 / % possible all: 32.4

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Processing

Software
NameVersionClassification
REFMAC5.5.0102refinement
MOSFLMdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2BLK

2blk
PDB Unreleased entry


Resolution: 2.2→27.08 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.902 / SU B: 19.784 / SU ML: 0.205 / Cross valid method: THROUGHOUT / ESU R: 0.125 / ESU R Free: 0.064 / 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
Rfree0.27736 947 5.3 %RANDOM
Rwork0.24122 ---
obs0.24319 16793 76.84 %-
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: 11.673 Å2
Baniso -1Baniso -2Baniso -3
1-3.85 Å20 Å2-0 Å2
2--3.85 Å20 Å2
3----7.7 Å2
Refinement stepCycle: LAST / Resolution: 2.2→27.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3329 0 0 31 3360
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0223374
X-RAY DIFFRACTIONr_bond_other_d0.0010.022266
X-RAY DIFFRACTIONr_angle_refined_deg0.9861.9724542
X-RAY DIFFRACTIONr_angle_other_deg0.76235614
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4475402
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.16726.584161
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.1115684
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.986158
X-RAY DIFFRACTIONr_chiral_restr0.060.2551
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.023591
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02601
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_it0.3251.52033
X-RAY DIFFRACTIONr_mcbond_other0.0731.5822
X-RAY DIFFRACTIONr_mcangle_it0.5923336
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.79531341
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.2544.51205
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
Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A475medium positional0.20.5
2B475medium positional0.180.5
3C475medium positional0.20.5
4D475medium positional0.210.5
1A607loose positional0.765
2B607loose positional0.595
3C607loose positional0.795
4D607loose positional0.675
1A475medium thermal0.332
2B475medium thermal0.252
3C475medium thermal0.292
4D475medium thermal0.352
1A607loose thermal0.3610
2B607loose thermal0.2910
3C607loose thermal0.2810
4D607loose thermal0.2910
LS refinement shellResolution: 2.198→2.255 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.39 30 -
Rwork0.267 512 -
obs--32.44 %
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)
14.4338-1.9009-3.30093.56943.213713.07220.08960.19370.0674-0.04170.129-0.4105-0.03850.7746-0.21860.1915-0.03290.01310.29450.00120.1451-23.47917.9-7.352
26.7914-1.369-3.50524.02393.652311.2910.08310.24780.3637-0.4991-0.1116-0.1172-1.2362-0.09170.02850.5077-0.0224-0.01160.27940.00110.1688-29.15827.58-3.026
315.6789-6.1559-5.85824.83164.787316.7455-0.3052-0.3151-0.45040.1495-0.33520.38120.3291-1.43420.64040.2201-0.0294-0.01150.287-0.05740.1129-36.49319.2011.877
41.8180.4396-0.94572.32131.044317.257-0.10060.0501-0.01950.160.1677-0.07791.6262-0.2008-0.06720.5191-0.0677-0.0190.288-0.0270.1366-28.4396.843-12.063
54.89751.8822-1.97585.301-1.260315.9767-0.28280.1735-0.3302-0.11130.26430.07731.7386-1.2260.01850.6512-0.24780.04150.5433-0.04120.0755-32.7424.349-24.158
63.2054-1.75551.29221.3896-0.630912.26310.2631-0.00840.1567-0.051-0.120.1743-0.0155-0.2285-0.14310.4503-0.11580.13070.4642-0.0760.14-28.46514.207-29.709
75.92530.1343-0.3053.0818-0.27768.66110.10070.25990.26420.4825-0.2040.2129-0.24270.49240.10330.3857-0.0578-0.01860.32660.01970.1164-11.10510.0095.609
86.93030.7245-0.56237.86312.88919.90270.18460.53670.12060.2644-0.078-0.36640.22322.1403-0.10660.41720.0801-0.08741.0790.03360.0868-1.4628.0020.421
920.9368-10.2687-2.853615.76095.96135.740.86890.328-1.07990.0884-0.82360.39620.74950.7555-0.04530.57680.1021-0.06440.939-0.0005-0.0342-4.719-2.184-1.628
100.9394-0.01931.78124.4179-1.057321.28670.5138-0.097-0.01240.529-0.20020.49750.40330.2478-0.31360.4215-0.1380.03760.3947-0.06880.2259-19.7723.17412.862
115.08132.43953.3286.483-2.028812.82630.5638-0.3456-0.59560.7579-0.07950.1797-0.0412-0.1435-0.48430.6458-0.15510.06260.53820.00090.2819-19.0780.37425.523
127.7523-1.519911.05282.8236-3.566717.85360.11860.91930.14860.9368-0.6738-0.2531-0.90962.37570.55520.8404-0.401-0.04010.8963-0.01730.1868-8.8917.31226.876
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 30
2X-RAY DIFFRACTION2A31 - 95
3X-RAY DIFFRACTION3A96 - 113
4X-RAY DIFFRACTION4B2 - 27
5X-RAY DIFFRACTION5B28 - 83
6X-RAY DIFFRACTION6B93 - 113
7X-RAY DIFFRACTION7C2 - 30
8X-RAY DIFFRACTION8C31 - 82
9X-RAY DIFFRACTION9C92 - 114
10X-RAY DIFFRACTION10D2 - 27
11X-RAY DIFFRACTION11D28 - 83
12X-RAY DIFFRACTION12D95 - 113

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