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- PDB-4uzc: KSHV LANA (ORF73) C-terminal domain, spiral: hexagonal crystal form -

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Basic information

Entry
Database: PDB / ID: 4uzc
TitleKSHV LANA (ORF73) C-terminal domain, spiral: hexagonal crystal form
ComponentsORF 73
KeywordsVIRAL PROTEIN / DNA-BINDING DOMAIN / ORIGIN-BINDING DOMAIN / OLIGOMERIZATION DOMAIN / HHV-8 / GAMMAHERPESVIRUS / RHADINOVIRUS / PRIMARY EFFUSION LYMPHOMA / MULTICENTRIC CASTLEMAN'S DISEASE / TUMOR VIRUS / CANCER
Function / homology
Function and homology information


viral life cycle / : / host cell nucleus / DNA binding
Similarity search - Function
: / Protein LANA1-like, DNA-binding domain / Epstein Barr virus nuclear antigen-1, DNA-binding domain / Epstein Barr virus nuclear antigen-1, DNA-binding domain superfamily / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ORF 73 / Protein LANA1
Similarity search - Component
Biological speciesHUMAN HERPESVIRUS 8
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.7 Å
AuthorsHellert, J. / Krausze, J. / Luhrs, T.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2015
Title: The 3D Structure of Kaposi Sarcoma Herpesvirus Lana C-Terminal Domain Bound to DNA.
Authors: Hellert, J. / Weidner-Glunde, M. / Krausze, J. / Lunsdorf, H. / Ritter, C. / Schulz, T.F. / Luhrs, T.
History
DepositionSep 5, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 13, 2015Provider: repository / Type: Initial release
Revision 1.1May 20, 2015Group: Database references
Revision 1.2Jun 10, 2015Group: Database references
Revision 1.3May 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 1.4May 22, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.5Jan 10, 2024Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.
Remark 700 SHEET DETERMINATION METHOD: AUTHOR PROVIDED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ORF 73
B: ORF 73
C: ORF 73
D: ORF 73


Theoretical massNumber of molelcules
Total (without water)63,0414
Polymers63,0414
Non-polymers00
Water0
1
A: ORF 73

B: ORF 73
C: ORF 73
D: ORF 73

A: ORF 73
B: ORF 73
C: ORF 73
D: ORF 73
x 11


Theoretical massNumber of molelcules
Total (without water)756,49048
Polymers756,49048
Non-polymers00
Water0
TypeNameSymmetry operationNumber
crystal symmetry operation12_554x,x-y,-z-1/61
crystal symmetry operation12_555x,x-y,-z+5/61
identity operation1_555x,y,z1
crystal symmetry operation8_555x-y,-y,-z1
crystal symmetry operation5_555y,-x+y,z+1/61
crystal symmetry operation10_555-y,-x,-z+1/61
crystal symmetry operation3_555-x+y,-x,z+1/31
crystal symmetry operation9_555-x,-x+y,-z+1/31
crystal symmetry operation4_555-x,-y,z+1/21
crystal symmetry operation11_555-x+y,y,-z+1/21
crystal symmetry operation2_555-y,x-y,z+2/31
crystal symmetry operation7_555y,x,-z+2/31
crystal symmetry operation6_555x-y,x,z+5/61
Buried area134933.4 Å2
ΔGint-928.2 kcal/mol
Surface area281322.6 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.180, 103.180, 228.250
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.6554, 0.7544, 0.03642), (0.75525, 0.65507, 0.02197), (-0.00728, 0.0419, -0.9991)-6.85191, 3.48712, -29.04712
2given(0.31395, 0.94825, 0.04746), (-0.94944, 0.3137, 0.01271), (-0.00284, -0.04905, 0.99879)-0.66243, -7.30179, -8.91289
3given(-0.86992, -0.49185, -0.03646), (-0.49319, 0.86809, 0.05638), (0.00392, 0.06703, -0.99774)-7.86142, -4.1788, -18.95746
DetailsTHE ASSEMBLY REPRESENTED IN THIS ENTRY HAS IRREGULAR HELICAL SYMMETRY WITH THE FOLLOWING AVERAGE PARAMETERS: ROTATION PER DIMER (TWIST) = -75.00 DEGREES RISE PER DIMER (HEIGHT) = 9.51 ANGSTROMS

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Components

#1: Protein
ORF 73 / LATENCY-ASSOCIATED NUCLEAR ANTIGEN / LANA-1 / KSHV LANA


Mass: 15760.201 Da / Num. of mol.: 4 / Fragment: C-TERMINAL DOMAIN, RESIDUES 1013-1149
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HUMAN HERPESVIRUS 8 / Plasmid: PET-BASED / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q76SB0, UniProt: Q9QR71*PLUS

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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: 2.79 Å3/Da / Density % sol: 55.88 %
Description: DATA IN RESOLUTION RANGE 3.93 A - 3.87 A IS EXCLUDED DUE TO THE PRESENCE OF AN ICE RING
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.4 UL OF 31.5 MG/ML PROTEIN IN 5 MM BISTRIS-CL, 5 MM DTT, PH 6.5 WERE AS SUCH EQUILIBRATED AGAINST A RESERVOIR SOLUTION OF 170 MM LITHIUM ACETATE AND 18% (W/V) PEG3350 IN A SITTING DROP ...Details: 0.4 UL OF 31.5 MG/ML PROTEIN IN 5 MM BISTRIS-CL, 5 MM DTT, PH 6.5 WERE AS SUCH EQUILIBRATED AGAINST A RESERVOIR SOLUTION OF 170 MM LITHIUM ACETATE AND 18% (W/V) PEG3350 IN A SITTING DROP SETUP AT 20 DEGREE CENTIGRADE. AFTER TWO DAYS, CRYSTALS WERE DETACHED FROM THE CARRIER PLASTIC BY ADDING 1 UL OF 2 M AMMONIUM FORMATE.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.918409
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 19, 2014 / Details: MIRRORS
RadiationMonochromator: SI(111) DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918409 Å / Relative weight: 1
ReflectionResolution: 3.7→89.36 Å / Num. obs: 7874 / % possible obs: 95.9 % / Observed criterion σ(I): 2 / Redundancy: 29.7 % / Biso Wilson estimate: 119.8 Å2 / Rmerge(I) obs: 0.23 / Net I/σ(I): 18.53
Reflection shellResolution: 3.7→3.84 Å / Redundancy: 31.3 % / Mean I/σ(I) obs: 1.92 / % possible all: 99.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
XDSdata reduction
XDSdata scaling
PHENIXPHASER-MRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2YPY

2ypy


Resolution: 3.7→89.36 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.908 / SU B: 40.346 / SU ML: 0.553 / Cross valid method: THROUGHOUT / ESU R Free: 0.692 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.2386 389 4.9 %RANDOM
Rwork0.20078 ---
obs0.20278 7485 95.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 115.815 Å2
Baniso -1Baniso -2Baniso -3
1--2 Å2-1 Å20 Å2
2---2 Å20 Å2
3---6.49 Å2
Refinement stepCycle: LAST / Resolution: 3.7→89.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4316 0 0 0 4316
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0010.0194464
X-RAY DIFFRACTIONr_bond_other_d00.024244
X-RAY DIFFRACTIONr_angle_refined_deg0.5081.966056
X-RAY DIFFRACTIONr_angle_other_deg0.49239816
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.3325532
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.523.2200
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.49115732
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.9551528
X-RAY DIFFRACTIONr_chiral_restr0.0350.2600
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.0215024
X-RAY DIFFRACTIONr_gen_planes_other00.021076
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_it7.88811.12140
X-RAY DIFFRACTIONr_mcbond_other7.88511.0982139
X-RAY DIFFRACTIONr_mcangle_it12.58316.6362668
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it7.58811.9072324
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
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: 3.704→3.8 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.426 29 -
Rwork0.32 550 -
obs--98.81 %

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