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- PDB-4k2j: Decameric ring structure of KSHV (HHV-8) latency-associated nucle... -

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Basic information

Entry
Database: PDB / ID: 4k2j
TitleDecameric ring structure of KSHV (HHV-8) latency-associated nuclear antigen (LANA) DNA binding domain
ComponentsKSHV (HHV-8) latency-associated nuclear antigen (LANA)
KeywordsDNA BINDING PROTEIN / viral protein / DNA binding
Function / homologyEpstein Barr virus nuclear antigen-1, DNA-binding domain / Epstein Barr virus nuclear antigen-1, DNA-binding domain superfamily / Alpha-Beta Plaits / host cell nucleus / DNA binding / 2-Layer Sandwich / Alpha Beta / FORMIC ACID / Orf73
Function and homology information
Biological speciesHuman herpesvirus 8
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsDomsic, J.F. / Marmorstein, R.
CitationJournal: Plos Pathog. / Year: 2013
Title: Molecular Basis for Oligomeric-DNA Binding and Episome Maintenance by KSHV LANA.
Authors: Domsic, J.F. / Chen, H.S. / Lu, F. / Marmorstein, R. / Lieberman, P.M.
History
DepositionApr 9, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 6, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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

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Assembly

Deposited unit
A: KSHV (HHV-8) latency-associated nuclear antigen (LANA)
B: KSHV (HHV-8) latency-associated nuclear antigen (LANA)
C: KSHV (HHV-8) latency-associated nuclear antigen (LANA)
D: KSHV (HHV-8) latency-associated nuclear antigen (LANA)
E: KSHV (HHV-8) latency-associated nuclear antigen (LANA)
F: KSHV (HHV-8) latency-associated nuclear antigen (LANA)
G: KSHV (HHV-8) latency-associated nuclear antigen (LANA)
H: KSHV (HHV-8) latency-associated nuclear antigen (LANA)
I: KSHV (HHV-8) latency-associated nuclear antigen (LANA)
J: KSHV (HHV-8) latency-associated nuclear antigen (LANA)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)160,61442
Polymers159,38410
Non-polymers1,23032
Water9,044502
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area32320 Å2
ΔGint-465 kcal/mol
Surface area61140 Å2
MethodPISA
2
A: KSHV (HHV-8) latency-associated nuclear antigen (LANA)
B: KSHV (HHV-8) latency-associated nuclear antigen (LANA)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,0657
Polymers31,8772
Non-polymers1885
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5230 Å2
ΔGint-76 kcal/mol
Surface area13130 Å2
MethodPISA
3
C: KSHV (HHV-8) latency-associated nuclear antigen (LANA)
D: KSHV (HHV-8) latency-associated nuclear antigen (LANA)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,0757
Polymers31,8772
Non-polymers1985
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4980 Å2
ΔGint-68 kcal/mol
Surface area13320 Å2
MethodPISA
4
E: KSHV (HHV-8) latency-associated nuclear antigen (LANA)
F: KSHV (HHV-8) latency-associated nuclear antigen (LANA)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,21711
Polymers31,8772
Non-polymers3409
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5800 Å2
ΔGint-107 kcal/mol
Surface area13520 Å2
MethodPISA
5
G: KSHV (HHV-8) latency-associated nuclear antigen (LANA)
H: KSHV (HHV-8) latency-associated nuclear antigen (LANA)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,0657
Polymers31,8772
Non-polymers1885
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5490 Å2
ΔGint-78 kcal/mol
Surface area13000 Å2
MethodPISA
6
I: KSHV (HHV-8) latency-associated nuclear antigen (LANA)
J: KSHV (HHV-8) latency-associated nuclear antigen (LANA)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,19210
Polymers31,8772
Non-polymers3158
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6070 Å2
ΔGint-82 kcal/mol
Surface area12940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.439, 175.176, 97.065
Angle α, β, γ (deg.)90.00, 95.30, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
KSHV (HHV-8) latency-associated nuclear antigen (LANA)


Mass: 15938.413 Da / Num. of mol.: 10 / Fragment: DNA binding domain (unp residues 825-963)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human herpesvirus 8 / Gene: ORF73 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9DUN0
#2: Chemical
ChemComp-FMT / FORMIC ACID / Formic acid


Mass: 46.025 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: CH2O2
#3: Chemical...
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 23 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 502 / 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: 2.73 Å3/Da / Density % sol: 54.98 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 1M ammonium formate, 100mM HEPES pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 2, 2012
RadiationMonochromator: Rosenbaum-Rock double crystal sagittal focusing monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 2.05→50 Å / Num. all: 106003 / Num. obs: 103035 / % possible obs: 97.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.4 % / Rsym value: 0.067 / Net I/σ(I): 13.1
Reflection shellResolution: 2.05→2.12 Å / Redundancy: 3.3 % / Mean I/σ(I) obs: 2.4 / Num. unique all: 10304 / Rsym value: 0.53 / % possible all: 97.7

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Processing

Software
NameVersionClassification
CBASSdata collection
PHASERphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.05→39.89 Å / SU ML: 0.31 / σ(F): 1.37 / Phase error: 26.49 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2262 5075 4.99 %
Rwork0.1818 --
obs0.184 101723 95.31 %
all-106003 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 45.405 Å2 / ksol: 0.35 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-6.7553 Å20 Å2-11.3076 Å2
2---6.6258 Å20 Å2
3----0.1295 Å2
Refinement stepCycle: LAST / Resolution: 2.05→39.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10996 0 50 502 11548
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01411394
X-RAY DIFFRACTIONf_angle_d1.39115439
X-RAY DIFFRACTIONf_dihedral_angle_d15.0814354
X-RAY DIFFRACTIONf_chiral_restr0.0821522
X-RAY DIFFRACTIONf_plane_restr0.0082022
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0501-2.07340.31211280.29982593X-RAY DIFFRACTION77
2.0734-2.09780.36061510.2973276X-RAY DIFFRACTION98
2.0978-2.12340.33311810.27733271X-RAY DIFFRACTION97
2.1234-2.15030.28771660.25343271X-RAY DIFFRACTION96
2.1503-2.17860.30251690.25243261X-RAY DIFFRACTION98
2.1786-2.20840.30621820.24133295X-RAY DIFFRACTION97
2.2084-2.23990.33281690.23353187X-RAY DIFFRACTION95
2.2399-2.27340.2661820.22683247X-RAY DIFFRACTION98
2.2734-2.30890.31411780.21963275X-RAY DIFFRACTION96
2.3089-2.34670.30831420.21653230X-RAY DIFFRACTION94
2.3467-2.38720.27911760.21823195X-RAY DIFFRACTION97
2.3872-2.43060.28981710.22073253X-RAY DIFFRACTION95
2.4306-2.47730.26451740.2093175X-RAY DIFFRACTION95
2.4773-2.52790.27071530.21673252X-RAY DIFFRACTION96
2.5279-2.58290.28921430.22733163X-RAY DIFFRACTION93
2.5829-2.64290.31421590.22563253X-RAY DIFFRACTION96
2.6429-2.7090.26481870.20293153X-RAY DIFFRACTION93
2.709-2.78220.25221840.20553180X-RAY DIFFRACTION96
2.7822-2.86410.29451660.21263136X-RAY DIFFRACTION92
2.8641-2.95650.29481890.21163144X-RAY DIFFRACTION95
2.9565-3.06210.25231760.20413151X-RAY DIFFRACTION93
3.0621-3.18470.24881570.1943187X-RAY DIFFRACTION94
3.1847-3.32960.2151730.18893191X-RAY DIFFRACTION95
3.3296-3.5050.21261680.1823267X-RAY DIFFRACTION96
3.505-3.72450.20821540.16713269X-RAY DIFFRACTION96
3.7245-4.01180.20131730.15643276X-RAY DIFFRACTION97
4.0118-4.4150.16931690.13423360X-RAY DIFFRACTION99
4.415-5.05280.17481750.13213362X-RAY DIFFRACTION99
5.0528-6.36180.18991860.16783405X-RAY DIFFRACTION100
6.3618-39.89750.16971940.14863370X-RAY DIFFRACTION99

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