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- PDB-2z0l: Crystal structure of EBV-DNA polymerase accessory protein BMRF1 -

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Basic information

Entry
Database: PDB / ID: 2z0l
TitleCrystal structure of EBV-DNA polymerase accessory protein BMRF1
ComponentsEarly antigen protein D
KeywordsREPLICATION / alpha/beta protein / Activator / DNA-binding / Early protein / Nucleus / Transcription / Transcription regulation / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


viral tegument / bidirectional double-stranded viral DNA replication / host cell nucleus / DNA binding
Similarity search - Function
DNA polymerase processivity factor, herpesviridae / Herpes DNA replication accessory factor / Box / Proliferating Cell Nuclear Antigen / Proliferating Cell Nuclear Antigen - #10 / Alpha Beta
Similarity search - Domain/homology
DNA polymerase processivity factor BMRF1
Similarity search - Component
Biological speciesHuman herpesvirus 4 (Epstein-Barr virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.9 Å
AuthorsMurayama, K. / Kato-Murayama, M. / Terada, T. / Shirouzu, M. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: J.Biol.Chem. / Year: 2009
Title: Crystal structure of Epstein-Barr virus DNA polymerase processivity factor BMRF1
Authors: Murayama, K. / Nakayama, S. / Kato-Murayama, M. / Akasaka, R. / Ohbayashi, N. / Kamewari-Hayami, Y. / Terada, T. / Shirouzu, M. / Tsurumi, T. / Yokoyama, S.
History
DepositionMay 7, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 13, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Early antigen protein D
B: Early antigen protein D
C: Early antigen protein D
D: Early antigen protein D
E: Early antigen protein D
F: Early antigen protein D
G: Early antigen protein D
H: Early antigen protein D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)272,94917
Polymers272,6308
Non-polymers3199
Water2,180121
1
A: Early antigen protein D
B: Early antigen protein D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,2284
Polymers68,1582
Non-polymers712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2040 Å2
ΔGint-22 kcal/mol
Surface area25430 Å2
MethodPISA
2
C: Early antigen protein D
D: Early antigen protein D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,1933
Polymers68,1582
Non-polymers351
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1940 Å2
ΔGint-15 kcal/mol
Surface area24950 Å2
MethodPISA
3
E: Early antigen protein D
hetero molecules

E: Early antigen protein D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,2284
Polymers68,1582
Non-polymers712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_566x,-y+1,-z+11
Buried area2010 Å2
ΔGint-20 kcal/mol
Surface area25210 Å2
MethodPISA
4
F: Early antigen protein D
hetero molecules

F: Early antigen protein D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,2284
Polymers68,1582
Non-polymers712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556x,-y,-z+11
Buried area2160 Å2
ΔGint-20 kcal/mol
Surface area24790 Å2
MethodPISA
5
G: Early antigen protein D
H: Early antigen protein D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,2996
Polymers68,1582
Non-polymers1424
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2270 Å2
ΔGint-36 kcal/mol
Surface area25030 Å2
MethodPISA
6
A: Early antigen protein D
B: Early antigen protein D
C: Early antigen protein D
D: Early antigen protein D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)136,4217
Polymers136,3154
Non-polymers1063
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5220 Å2
ΔGint-43 kcal/mol
Surface area49140 Å2
MethodPISA
7
E: Early antigen protein D
hetero molecules

E: Early antigen protein D
hetero molecules

F: Early antigen protein D
hetero molecules

F: Early antigen protein D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)136,4578
Polymers136,3154
Non-polymers1424
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_566x,-y+1,-z+11
crystal symmetry operation5_555x+1/2,y+1/2,z1
crystal symmetry operation8_556x+1/2,-y+1/2,-z+11
Buried area5560 Å2
ΔGint-45 kcal/mol
Surface area48620 Å2
MethodPISA
8
G: Early antigen protein D
H: Early antigen protein D
hetero molecules

G: Early antigen protein D
H: Early antigen protein D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)136,59912
Polymers136,3154
Non-polymers2848
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_755-x+2,y,-z+1/21
Buried area5970 Å2
ΔGint-81 kcal/mol
Surface area48640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)125.671, 191.635, 371.720
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein
Early antigen protein D / EA-D / BMRF1


Mass: 34078.758 Da / Num. of mol.: 8 / Fragment: UNP residues 1-314
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human herpesvirus 4 (Epstein-Barr virus)
Strain: B95-8 / Description: E. coli based cell free / Plasmid: PX060518-12 / Production host: cell free protein synthesis (others) / References: UniProt: P03191
#2: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 121 / 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: 4.1 Å3/Da / Density % sol: 70.03 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 1.25M Li sulfate, 0.5M Ammonium sulfate, 8% PEG 400, 0.1M Hepes pH7.5, 27.5mM 2,6-dimethyl-4-heptyl-B-D-maltoside, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44B2 / Wavelength: 0.97907, 0.97947, 0.96400
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Sep 25, 2006
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979071
20.979471
30.9641
ReflectionResolution: 2.9→48.39 Å / Num. obs: 98550 / % possible obs: 99.6 % / Observed criterion σ(F): -3 / Redundancy: 5 % / Biso Wilson estimate: 33.8 Å2 / Rsym value: 0.092 / Net I/σ(I): 15.4
Reflection shellResolution: 2.9→3 Å / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.9→48.38 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 4893321.59 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.251 9872 10 %RANDOM
Rwork0.206 ---
obs0.206 98516 99.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 33.9643 Å2 / ksol: 0.35913 e/Å3
Displacement parametersBiso mean: 47.9 Å2
Baniso -1Baniso -2Baniso -3
1-2.16 Å20 Å20 Å2
2---0.56 Å20 Å2
3----1.6 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.4 Å0.32 Å
Luzzati d res low-5 Å
Luzzati sigma a0.5 Å0.41 Å
Refinement stepCycle: LAST / Resolution: 2.9→48.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17968 0 9 121 18098
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d25.4
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.08
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.41.5
X-RAY DIFFRACTIONc_mcangle_it2.492
X-RAY DIFFRACTIONc_scbond_it2.312
X-RAY DIFFRACTIONc_scangle_it3.432.5
LS refinement shellResolution: 2.9→3.08 Å / Rfactor Rfree error: 0.008 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.328 1583 10 %
Rwork0.288 14315 -
obs--96.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater_rep.top
X-RAY DIFFRACTION3ion.paramion.top

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