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- PDB-4hob: The crystal structure of the Zalpha domain from Cyprinid Herpes v... -

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Basic information

Entry
Database: PDB / ID: 4hob
TitleThe crystal structure of the Zalpha domain from Cyprinid Herpes virus 3
ComponentsPutative uncharacterized protein
KeywordsDNA BINDING PROTEIN / Domain Swapping / Z-DNA binding domain / DNA and RNA binding
Function / homology
Function and homology information


double-stranded RNA adenosine deaminase activity / RNA binding
Similarity search - Function
Z-binding domain profile. / Z-binding domain / Adenosine deaminase z-alpha domain / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Uncharacterized protein
Similarity search - Component
Biological speciesCyprinid herpesvirus 3
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.76 Å
AuthorsTome, A.R. / Kus, K. / de Rosa, M. / Paulo, L.M. / Figueiredo, D. / Athanasiadis, A.
CitationJournal: J.Virol. / Year: 2013
Title: Crystal structure of a poxvirus-like zalpha domain from cyprinid herpesvirus 3
Authors: Tome, A.R. / Kus, K. / Correia, S. / Paulo, L.M. / Zacarias, S. / de Rosa, M. / Figueiredo, D. / Parkhouse, R.M. / Athanasiadis, A.
History
DepositionOct 22, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 11, 2013Provider: repository / Type: Initial release
Revision 1.1Mar 4, 2015Group: Other
Revision 1.2Dec 4, 2019Group: Data collection / Database references / Category: reflns / reflns_shell / struct_ref_seq_dif
Item: _reflns.pdbx_Rsym_value / _reflns_shell.pdbx_Rsym_value / _struct_ref_seq_dif.details
Revision 1.3Dec 18, 2019Group: Data collection / Category: reflns_shell / Item: _reflns_shell.Rmerge_I_obs
Revision 1.4Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Putative uncharacterized protein
B: Putative uncharacterized protein
C: Putative uncharacterized protein
D: Putative uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,97213
Polymers31,1084
Non-polymers8659
Water3,675204
1
A: Putative uncharacterized protein
B: Putative uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,9386
Polymers15,5542
Non-polymers3844
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3520 Å2
ΔGint-69 kcal/mol
Surface area7870 Å2
MethodPISA
2
C: Putative uncharacterized protein
D: Putative uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,0347
Polymers15,5542
Non-polymers4805
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3360 Å2
ΔGint-93 kcal/mol
Surface area7980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.736, 54.584, 86.642
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
Putative uncharacterized protein


Mass: 7776.898 Da / Num. of mol.: 4 / Fragment: Zalpha domain, UNP residues 216-278
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cyprinid herpesvirus 3 / Gene: KHVJ122, ORF112 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A4FTK7
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 204 / Source method: isolated from a natural source / Formula: H2O

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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: 1.97 Å3/Da / Density % sol: 37.45 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.2M NaCl, 0.1M Cacodylate, 2M Ammonium Sulfate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9763 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 16, 2011
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.76→46.183 Å / Num. all: 25156 / Num. obs: 23721 / % possible obs: 94.8 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 4.2 % / Biso Wilson estimate: 31.1 Å2 / Rmerge(I) obs: 0.036 / Net I/σ(I): 13.1
Reflection shell
Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. unique allDiffraction-ID% possible all
1.76-1.833.748.6423187.7
1.77-1.833.72.31769176.4

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Processing

Software
NameVersionClassification
DNAdata collection
PHASERphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1QBJ

1qbj


Resolution: 1.76→46.183 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 2.02 / Phase error: 25.94 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2466 1174 4.96 %RANDOM
Rwork0.2013 ---
obs0.2036 23670 94.21 %-
all-24844 --
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 59.36 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 38.93 Å2
Baniso -1Baniso -2Baniso -3
1-5.7736 Å2-0 Å2-0 Å2
2---6.1618 Å2-0 Å2
3---0.3882 Å2
Refinement stepCycle: LAST / Resolution: 1.76→46.183 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1995 0 45 204 2244
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032093
X-RAY DIFFRACTIONf_angle_d0.6772833
X-RAY DIFFRACTIONf_dihedral_angle_d12.633782
X-RAY DIFFRACTIONf_chiral_restr0.047293
X-RAY DIFFRACTIONf_plane_restr0.002359
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.76-1.8370.41821090.3208208271
1.837-1.93380.33121390.2886278595
1.9338-2.0550.34071500.2519287498
2.055-2.21360.27991540.2177288898
2.2136-2.43640.26271470.2212292598
2.4364-2.78890.2531560.2007292398
2.7889-3.51350.23741580.1927296299
3.5135-46.19910.20991610.1757305797
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)
16.7508-0.2345-0.95910.3384-1.55218.45240.1705-0.1695-0.5685-0.132-0.0879-0.26020.7580.077-0.08510.2690.0074-0.01040.1828-0.00180.150912.9645-12.40540.3379
26.1311-6.5719-6.47197.21096.63577.3783-0.0608-0.70840.04490.2697-0.1392-0.7870.351.7516-0.2220.26090.12750.0730.28990.11870.345621.8612-12.349-3.2388
32.4530.5655-2.14581.48071.14245.242-0.5770.4514-0.203-1.10390.17140.01111.4282-0.09420.22960.7616-0.0303-0.09360.26440.02510.351911.5906-15.2258-8.8156
40.6963-0.40031.03473.1652-4.58798.62140.61280.02170.12270.15790.36071.37690.2025-0.6011-0.68750.2399-0.0928-0.04820.35010.12670.35225.602-5.5743-8.4046
54.45252.4456-0.09192.2869-1.68892.88030.2542-0.0676-0.6803-0.1179-0.0636-0.80020.314-0.29670.06170.24880.0001-0.05880.112-0.01340.298514.8374-4.6929-24.8274
62.675-2.8091-2.04973.91192.51631.7093-0.4992-1.4329-0.84551.9461-1.1770.25752.54010.3570.54860.8029-0.17080.05720.43540.08030.29026.8724-24.1926-22.1551
73.8482-3.523-0.68188.7536-3.036.64120.1069-0.0048-0.151-0.1675-0.2040.02190.2522-0.26250.08350.2619-0.0257-0.04780.1795-0.03070.23689.106-12.9173-31.2477
85.10195.4196-4.05828.3356-4.40556.41480.0772-0.40320.5961-0.2123-0.16820.5267-0.2209-0.23610.10090.26120.0237-0.07780.2352-0.00840.25123.225-6.1421-26.824
93.7615-1.98783.67992.4365-2.09948.0517-0.4179-0.64160.50680.8740.3953-0.80680.2754-0.50910.02060.46630.0046-0.14330.2184-0.04640.31749.2597-14.4806-20.4349
100.31540.2561-0.74143.54593.86966.34790.22620.0176-0.1639-0.2510.2168-0.2058-0.00340.1555-0.56280.22110.0505-0.05390.19820.00160.244914.8339-6.067-14.7325
113.1006-2.55720.54412.46280.67724.79030.04860.15350.2737-0.1105-0.0704-0.4451-0.4426-0.0025-0.05170.1799-0.0234-0.03520.1484-0.01490.150117.261617.4633-29.9803
124.22081.83331.81364.51.0285.54830.2052-0.28640.80320.1418-0.0738-0.4915-0.30280.08190.01460.1358-0.027-0.03260.1711-0.02150.21317.528916.6969-24.536
131.6172-0.7336-1.88696.77851.82782.2865-0.0648-0.0244-0.2772-0.19440.157-0.1113-0.4147-0.59220.08290.1241-0.0044-0.00270.18020.02490.195812.64947.3051-10.1603
149.19356.4372.37474.54132.11244.7332-0.0114-0.40220.9570.0166-0.20520.6166-0.7724-0.15040.23410.3896-0.01140.03110.2273-0.01460.26713.658916.18773.9175
152.7813-1.08160.93753.6987-4.56896.8296-0.3839-0.39060.13440.35330.32670.25770.0478-1.0814-0.04230.22170.08990.00280.32490.0010.29965.944612.7505-1.8554
168.1084-3.53772.09433.144-1.34068.78010.27790.161.13160.1835-0.0755-0.405-1.82940.6609-0.17560.4418-0.10460.03210.26470.04210.302416.696717.6015-5.4331
174.2401-0.593-0.97051.9775-0.26380.31790.091-0.1794-0.3112-0.1020.24260.6360.16610.0646-0.13890.2173-0.0468-0.06050.22390.02150.238314.29567.3591-20.0786
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and (resseq 217:237)
2X-RAY DIFFRACTION2chain A and (resseq 238:248)
3X-RAY DIFFRACTION3chain A and (resseq 249:261)
4X-RAY DIFFRACTION4chain A and (resseq 262:271)
5X-RAY DIFFRACTION5chain A and (resseq 272:278)
6X-RAY DIFFRACTION6chain B and (resseq 215:219)
7X-RAY DIFFRACTION7chain B and (resseq 220:232)
8X-RAY DIFFRACTION8chain B and (resseq 233:248)
9X-RAY DIFFRACTION9chain B and (resseq 249:261)
10X-RAY DIFFRACTION10chain B and (resseq 262:277)
11X-RAY DIFFRACTION11chain C and (resseq 212:237)
12X-RAY DIFFRACTION12chain C and (resseq 238:266)
13X-RAY DIFFRACTION13chain C and (resseq 267:278)
14X-RAY DIFFRACTION14chain D and (resseq 219:232)
15X-RAY DIFFRACTION15chain D and (resseq 233:248)
16X-RAY DIFFRACTION16chain D and (resseq 249:266)
17X-RAY DIFFRACTION17chain D and (resseq 267:278)

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