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- PDB-2j85: B116 of Sulfolobus turreted icosahedral virus (STIV) -

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Basic information

Entry
Database: PDB / ID: 2j85
TitleB116 of Sulfolobus turreted icosahedral virus (STIV)
ComponentsSTIV B116
KeywordsVIRAL PROTEIN / ARCHAEAL VIRUS / CRENARCHAEAL VIRUS / B116 / STIV / ARCHAEA / SULFOLOBUS / CRENARCHAEA / SULFOLOBUS TURRETED ICOSAHEDRAL VIRUS / HYPOTHETICAL PROTEIN
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
Function and homology information
Biological speciesSULFOLOBUS TURRETED ICOSAHEDRAL VIRUS
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.39 Å
AuthorsLarson, E.T. / Reiter, D. / Young, M.J. / Lawrence, C.M.
CitationJournal: Virology / Year: 2007
Title: A New DNA Binding Protein Highly Conserved in Diverse Crenarchaeal Viruses
Authors: Larson, E.T. / Eilers, B.J. / Reiter, D. / Ortmann, A.C. / Young, M.J. / Lawrence, C.M.
History
DepositionOct 19, 2006Deposition site: PDBE / Processing site: PDBE
SupersessionNov 2, 2006ID: 2BLK
Revision 1.0Nov 2, 2006Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2May 8, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Experimental preparation / Other
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / pdbx_seq_map_depositor_info / struct_conn
Item: _exptl_crystal_grow.method / _exptl_crystal_grow.temp ..._exptl_crystal_grow.method / _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval / _pdbx_seq_map_depositor_info.one_letter_code_mod / _struct_conn.pdbx_leaving_atom_flag
Revision 1.3Nov 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: STIV B116
B: STIV B116


Theoretical massNumber of molelcules
Total (without water)28,8192
Polymers28,8192
Non-polymers00
Water1,29772
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)48.573, 83.317, 89.501
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein STIV B116


Mass: 14409.745 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SULFOLOBUS TURRETED ICOSAHEDRAL VIRUS / Strain: ISOLATE YNPRC179
Description: STIV WAS ISOLATED FROM SULFOLOBUS SPECIES IN ACIDIC HOT SPRINGS (PH 2.9-3.9, 72-92 DEGREES C) IN THE RABBIT CREEK THERMAL AREA WITHIN MIDWAY GEYSER BASIN INYELLOWSTONE NATIONAL PARK ...Description: STIV WAS ISOLATED FROM SULFOLOBUS SPECIES IN ACIDIC HOT SPRINGS (PH 2.9-3.9, 72-92 DEGREES C) IN THE RABBIT CREEK THERMAL AREA WITHIN MIDWAY GEYSER BASIN INYELLOWSTONE NATIONAL PARK (RICE, ET AL. PNAS. MAY 18, 2004 VOL. 101 NO. 20. PP. 7716-7720.)
Plasmid: PEXP14-STIVB116 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): B834(DE3)PLYSS / References: UniProt: Q6Q0K9
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 72 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsC-TERMINUS 6XHIS TAG WAS ADDED DURING CLONING.

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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: 3.3 Å3/Da / Density % sol: 62.4 %
Description: DATA WERE COLLECTED DURING RAPIDATA 2004 COURSE AT NSLS.
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 6.5 MG/ML PROTEIN WAS CRYSTALLIZED BY HANGING DROP VAPOR DIFFUSION IN 0.1 M TRIS-HCL (PH 8.0), 1.95 M NH4H2PO4 AT 17 DEGREES C.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X9B / Wavelength: 0.97946
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 27, 2004 / Details: MIRRORS
RadiationMonochromator: CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.4→30 Å / Num. obs: 14911 / % possible obs: 99.9 % / Observed criterion σ(I): 3 / Redundancy: 5.1 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 22
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.26 / Mean I/σ(I) obs: 5 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.39→29.81 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.918 / SU B: 12.526 / SU ML: 0.152 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.283 / ESU R Free: 0.218 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. TLS GROUP SELECTIONS WERE MADE WITH THE AID OF TLS MOTION DETERMINATION SERVER. PAINTER AND MERRITT. 2005. ACTA CRYST D61, 465-471. CHAIN A ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. TLS GROUP SELECTIONS WERE MADE WITH THE AID OF TLS MOTION DETERMINATION SERVER. PAINTER AND MERRITT. 2005. ACTA CRYST D61, 465-471. CHAIN A AND CHAIN B TOGETHER MAKE UP THE BIOLOGICAL MOLECULE.
RfactorNum. reflection% reflectionSelection details
Rfree0.24 758 5.1 %RANDOM
Rwork0.208 ---
obs0.21 14067 99.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 28.3 Å2
Baniso -1Baniso -2Baniso -3
1-0.61 Å20 Å20 Å2
2--0.13 Å20 Å2
3----0.74 Å2
Refinement stepCycle: LAST / Resolution: 2.39→29.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1878 0 0 72 1950
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0221903
X-RAY DIFFRACTIONr_bond_other_d0.0010.021298
X-RAY DIFFRACTIONr_angle_refined_deg1.3521.9712559
X-RAY DIFFRACTIONr_angle_other_deg0.833.0033190
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.265231
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.72725.93491
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.99215385
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.28158
X-RAY DIFFRACTIONr_chiral_restr0.0740.2297
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022067
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02347
X-RAY DIFFRACTIONr_nbd_refined0.1930.2327
X-RAY DIFFRACTIONr_nbd_other0.1850.21251
X-RAY DIFFRACTIONr_nbtor_refined0.1710.2877
X-RAY DIFFRACTIONr_nbtor_other0.0860.21054
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1470.275
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3560.28
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1810.217
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.120.25
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0521.51197
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.39321870
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.0483796
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.1424.5689
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: 2.39→2.45 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.222 53
Rwork0.225 982
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)
11.06450.6462-1.15320.6221-1.66185.2740.0259-0.0523-0.02680.1357-0.0559-0.021-0.05510.22870.03010.15210.0171-0.01620.11660.03340.113143.443643.69819.5156
21.8821-0.5503-0.45123.6822-0.86294.6721-0.0507-0.0586-0.12980.0593-0.3673-0.44330.35010.90690.4180.01680.060.01560.19010.09810.087954.429742.297214.5873
33.7134-1.2461-2.985128.242510.97428.1877-0.1728-0.2836-0.03691.12420.2402-0.01460.39580.1512-0.06740.19730.0085-0.02970.22310.05710.11144.682143.607620.7553
45.30623.2905-1.96135.04970.34172.5238-0.1194-0.0242-0.7506-0.7104-0.3786-0.22871.19170.62780.4980.3620.26960.03960.00790.0060.20550.423226.70039.0048
53.44070.5665-1.13794.0228-2.13835.2833-0.124-0.1996-0.0519-0.20890.20510.11120.3518-0.1809-0.08110.1885-0.029-0.00750.19940.08640.124339.943339.84218.7345
60.17720.2947-0.90211.4376-2.10454.978-0.01410.2086-0.0061-0.20760.15840.04050.2491-0.2522-0.14430.12080.001-0.00610.16410.02620.094635.539833.497729.3291
72.26520.42230.43522.46140.62412.9150.0901-0.10190.08710.1475-0.0216-0.0827-0.0962-0.0122-0.06840.12670.01980.02150.1321-0.00580.112134.733433.467945.8828
83.2484-0.42152.15712.326-1.05553.37630.04530.1443-0.0708-0.13970.00770.07310.107-0.0212-0.0530.12550.0010.02120.1441-0.0060.1239.959625.824240.0193
946.4548-11.3096-6.582121.7375-3.933217.3410.10561.7427-1.082-0.3186-0.978-0.65860.58690.89830.87240.1492-0.0096-0.01290.15760.03990.155253.489631.811939.0161
102.7304-2.25281.4812.7043-1.50552.1882-0.1436-0.1790.27810.29230.099-0.262-0.25140.0620.04460.1503-0.01310.00730.0923-0.00060.138248.893934.159545.5519
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 40
2X-RAY DIFFRACTION2A41 - 75
3X-RAY DIFFRACTION3A76 - 86
4X-RAY DIFFRACTION4A87 - 108
5X-RAY DIFFRACTION5A109 - 119
6X-RAY DIFFRACTION6B2 - 24
7X-RAY DIFFRACTION7B25 - 46
8X-RAY DIFFRACTION8B47 - 84
9X-RAY DIFFRACTION9B85 - 89
10X-RAY DIFFRACTION10B90 - 118

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