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- PDB-2wbt: The Structure of a Double C2H2 Zinc Finger Protein from a Hyperth... -

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Basic information

Entry
Database: PDB / ID: 2wbt
TitleThe Structure of a Double C2H2 Zinc Finger Protein from a Hyperthermophilic Archaeal Virus in the Absence of DNA
ComponentsB-129
KeywordsDNA BINDING PROTEIN / DNA-BINDING PROTEIN / ZINC FINGER / METAL-BINDING / DNA-BINDING PROTEIN SSV
Function / homology
Function and homology information


Light-harvesting Protein - #10 / : / Uncharacterized protein B-129, C2H2 zinc finger / Light-harvesting Protein / ZN622/Rei1/Reh1, zinc finger C2H2-type / C2H2 type zinc-finger (2 copies) / Classic Zinc Finger / Other non-globular / Double Stranded RNA Binding Domain / zinc finger ...Light-harvesting Protein - #10 / : / Uncharacterized protein B-129, C2H2 zinc finger / Light-harvesting Protein / ZN622/Rei1/Reh1, zinc finger C2H2-type / C2H2 type zinc-finger (2 copies) / Classic Zinc Finger / Other non-globular / Double Stranded RNA Binding Domain / zinc finger / Zinc finger C2H2 type domain profile. / Zinc finger C2H2 superfamily / Zinc finger C2H2 type domain signature. / Zinc finger C2H2-type / Special / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Uncharacterized protein B-129
Similarity search - Component
Biological speciesSULFOLOBUS VIRUS 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.7 Å
AuthorsEilers, B.J. / Menon, S. / Windham, A.B. / Kraft, P. / Dlakic, M. / Young, M.J. / Lawrence, C.M.
CitationJournal: To be Published
Title: The Structure of a Double C2H2 Zinc Finger Protein from a Hyperthermophilic Archaeal Virus in the Absence of DNA
Authors: Eilers, B.J. / Menon, S. / Windham, A.B. / Kraft, P. / Dlakic, M. / Young, M.J. / Lawrence, C.M.
History
DepositionMar 3, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 31, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2May 8, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 1.3Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description / 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 / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim / 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_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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 / _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

Downloads & links

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Assembly

Deposited unit
A: B-129
B: B-129
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,9226
Polymers29,6612
Non-polymers2624
Water30617
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5460 Å2
ΔGint-41.4 kcal/mol
Surface area13140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.378, 120.464, 51.687
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Ens-ID: 1 / Refine code: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11CYSCYSCYSCYSAA7777
21CYSCYSCYSCYSBB7777
12CYSCYSCYSCYSAA8080
22CYSCYSCYSCYSBB8080
13HISHISHISHISAA9393
23HISHISHISHISBB9393
14CYSCYSCYSCYSAA103103
24CYSCYSCYSCYSBB103103
15CYSCYSCYSCYSAA106106
25CYSCYSCYSCYSBB106106
16HISHISHISHISAA119119
26HISHISHISHISBB119119
17HISHISHISHISAA124124
27HISHISHISHISBB124124

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Components

#1: Protein B-129


Mass: 14830.291 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: DISULFIDE BOND BETWEEN C 121 AND C 127 / Source: (gene. exp.) SULFOLOBUS VIRUS 1 / Plasmid: PEXP14-B129 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)RIL / References: UniProt: P20201
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 17 / 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: 2.7 Å3/Da / Density % sol: 0.55 % / Description: NONE
Crystal growMethod: vapor diffusion, sitting drop / pH: 5.3
Details: SITTING DROP VAPOR DIFFUSION, 20 MG/ML OF B129 IN 20 MM BIS-TRIS, PH 6.5, 60 MM NACL MIXED WITH 0.1 M AMMONIUM CITRATE DIBASIC, 10-14 % PEG 4000

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 1.2833, 1.2830, 1.1696
DetectorType: MARRESEARCH / Detector: CCD / Date: Mar 18, 2006
Details: FLAT COLLIMATING MIRROR, DOUBLE CRYSTAL MONOCHROMATOR, TOROID FOCUSING MIRROR
RadiationMonochromator: DOUBLE CRYSTAL MONOCHROMATOR / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.28331
21.2831
31.16961
ReflectionResolution: 2.7→50 Å / Num. obs: 8209 / % possible obs: 78.7 % / Observed criterion σ(I): 5 / Redundancy: 2.9 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 17.2
Reflection shellResolution: 2.7→2.77 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.24 / Mean I/σ(I) obs: 4.4 / % possible all: 78.8

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data reduction
DENZOdata reduction
HKL-2000data scaling
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD
Starting model: NONE

Resolution: 2.7→20 Å / Cor.coef. Fo:Fc: 0.905 / Cor.coef. Fo:Fc free: 0.874 / SU B: 28.596 / SU ML: 0.29 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.423 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.269 360 4.9 %RANDOM
Rwork0.231 ---
obs0.233 6954 78.9 %-
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: 23.08 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2--0.15 Å20 Å2
3----0.14 Å2
Refinement stepCycle: LAST / Resolution: 2.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1905 0 4 17 1926
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0340.0221967
X-RAY DIFFRACTIONr_bond_other_d0.0090.021377
X-RAY DIFFRACTIONr_angle_refined_deg1.1241.9712658
X-RAY DIFFRACTIONr_angle_other_deg1.0053.0043379
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2895238
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.64523.24777
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.51215385
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.3861510
X-RAY DIFFRACTIONr_chiral_restr0.0540.2311
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.022085
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02373
X-RAY DIFFRACTIONr_nbd_refined0.1660.2460
X-RAY DIFFRACTIONr_nbd_other0.1840.21332
X-RAY DIFFRACTIONr_nbtor_refined0.1690.2953
X-RAY DIFFRACTIONr_nbtor_other0.0830.2981
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1210.239
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.020.21
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.4260.212
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2370.246
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1510.23
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.3461.51566
X-RAY DIFFRACTIONr_mcbond_other0.0311.5469
X-RAY DIFFRACTIONr_mcangle_it0.36421965
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.3173879
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it0.5414.5692
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 / Number: 88 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Atight positional0.070.05
2Btight positional0.070.05
1Atight thermal0.30.5
2Btight thermal0.30.5
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.373 24 -
Rwork0.278 502 -
obs--81.42 %
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)
17.2818-5.12932.138210.2946-1.77130.63840.52730.45390.1648-1.0402-0.1168-1.4762-0.47780.337-0.41050.14030.00130.12130.2345-0.0040.167836.49566.0362.415
211.62034.78962.89723.54612.47621.768-0.25770.05192.53431.3582-0.4855-0.7853-0.83050.33040.74320.2898-0.0004-0.17660.3204-0.16620.471739.87457.88219.004
31.36330.5362-0.306214.5105-4.39298.52190.17460.42950.8841-0.63570.2449-1.19810.29171.2475-0.4195-0.0068-0.0161-0.13130.25080.02790.203743.42347.40611.881
41.85062.1583-2.08274.5462-3.3174.170.0353-0.20590.0491-0.3111-0.1240.11490.41230.33430.08870.02840.0299-0.00720.1639-0.0002-0.064227.79536.41215.856
51.51090.8462-1.40331.6762-2.34327.2456-0.01520.1037-0.37350.1911-0.0164-0.02380.432-0.41790.03160.0839-0.0378-0.03450.1797-0.0208-0.026519.52825.6113.149
610.3555-2.3594-2.295412.2036-0.510413.2570.10540.70910.1348-0.9877-0.1343-0.1557-0.14370.06250.0289-0.10420.03780.0240.00990.09930.323537.81855.5441.621
711.6428-3.92114.89476.4436-5.747218.5801-0.5535-1.12620.95350.37840.197-0.4884-0.4097-0.70890.3565-0.1676-0.0267-0.00210.0235-0.118-0.038631.36149.98512.581
83.928-3.5257-1.213.42682.09644.26660.21340.0274-0.0513-0.2549-0.0888-0.1959-0.1955-0.056-0.1246-0.0059-0.02310.03240.20610.0329-0.105536.74430.6564.082
918.1447-7.3666-4.824610.94482.21546.48260.64440.3265-0.8893-0.1236-0.4860.30970.54560.2859-0.15840.0288-0.0177-0.01310.09980.0397-0.077545.45819.9433.035
108.1778-0.42260.14542.9709-0.58062.88220.2103-0.3782-0.55110.21280.2189-0.0930.36860.1333-0.42920.0860.0003-0.00870.16830.0225-0.074543.16825.99716.637
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A5 - 21
2X-RAY DIFFRACTION2A22 - 37
3X-RAY DIFFRACTION3A38 - 46
4X-RAY DIFFRACTION4A47 - 88
5X-RAY DIFFRACTION5A89 - 129
6X-RAY DIFFRACTION6B18 - 33
7X-RAY DIFFRACTION7B34 - 59
8X-RAY DIFFRACTION8B60 - 89
9X-RAY DIFFRACTION9B90 - 98
10X-RAY DIFFRACTION10B99 - 128

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