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- PDB-4dmb: X-ray structure of human hepatitus C virus NS5A-transactivated pr... -

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Basic information

Entry
Database: PDB / ID: 4dmb
TitleX-ray structure of human hepatitus C virus NS5A-transactivated protein 2 at the resolution 1.9A, Northeast Structural Genomics Consortium (NESG) Target HR6723
ComponentsHD domain-containing protein 2
KeywordsIMMUNE SYSTEM / Structural Genomics / PSI-Biology / Protein Structure Initiative / Northeast Structural Genomics Consortium (NESG) / HD domain-containing protein 2 / hepatitus C virus NS5A-transactivated protein 2 / HCV NS5A-transactivated protein 2 / Mitochondrial Protein Partnership / MPP
Function / homology
Function and homology information


5'-deoxynucleotidase / 5'-deoxynucleotidase activity / metal ion binding / cytoplasm
Similarity search - Function
HD domain / 5'-deoxynucleotidase YfbR/HDDC2 / Hypothetical protein af1432 / Hypothetical protein af1432 / HD domain profile. / HD domain / Metal dependent phosphohydrolases with conserved 'HD' motif. / HD/PDEase domain / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
NITRATE ION / DI(HYDROXYETHYL)ETHER / PHOSPHATE ION / Unknown ligand / 5'-deoxynucleotidase HDDC2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å
AuthorsKuzin, A. / Su, M. / Seetharaman, J. / Patel, P. / Xiao, R. / Ciccosanti, C. / Lee, D. / Everett, J.K. / Acton, T.B. / Montelione, G.T. ...Kuzin, A. / Su, M. / Seetharaman, J. / Patel, P. / Xiao, R. / Ciccosanti, C. / Lee, D. / Everett, J.K. / Acton, T.B. / Montelione, G.T. / Hunt, J.F. / Tong, L. / Northeast Structural Genomics Consortium (NESG) / Mitochondrial Protein Partnership (MPP)
CitationJournal: To be Published
Title: Northeast Structural Genomics Consortium Target HR6723
Authors: Kuzin, A. / Su, M. / Seetharaman, J. / Patel, P. / Xiao, R. / Ciccosanti, C. / Lee, D. / Everett, J.K. / Acton, T.B. / Montelione, G.T. / Hunt, J.F. / Tong, L.
History
DepositionFeb 7, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 4, 2012Provider: repository / Type: Initial release
Revision 1.1Apr 11, 2012Group: Structure summary

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HD domain-containing protein 2
B: HD domain-containing protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,37515
Polymers47,5972
Non-polymers77813
Water3,099172
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4910 Å2
ΔGint-64 kcal/mol
Surface area17520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.393, 68.393, 174.452
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
DetailsDimer, or trimer,61.41 kD,74.7%, or heptamer,138.4 kD,19.4%

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein HD domain-containing protein 2 / Hepatitis C virus NS5A-transactivated protein 2 / HCV NS5A-transactivated protein 2


Mass: 23798.684 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Strain: BL21(DE3)+ Magic / Gene: HDDC2, C6orf74, NS5ATP2, CGI-130 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q7Z4H3

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Non-polymers , 7 types, 185 molecules

#2: Chemical ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: NO3
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#7: Chemical ChemComp-UNL / UNKNOWN LIGAND


Num. of mol.: 1 / Source method: obtained synthetically
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 172 / 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: 2.14 Å3/Da / Density % sol: 42.6 %
Crystal growTemperature: 293 K / pH: 6
Details: Protein solution: 100mM NaCl, 5mM DTT, 0.02% NaN3, 10mM Tris-HCl (pH 7.5) . Reservoir solution:Mg(NO3)2 0.1M, MES 0.1M, PEG4000 40% (w/v), microbatch under oil, temperature 293KK

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 0.97906 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Feb 1, 2012
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97906 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 59948 / % possible obs: 96.1 % / Redundancy: 4.7 % / Rmerge(I) obs: 0.087 / Net I/σ(I): 18.2
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 2 % / Rmerge(I) obs: 0.455 / Mean I/σ(I) obs: 1.8 / % possible all: 71.4

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Processing

Software
NameVersionClassificationNB
PHENIXdev_988refinement
PDB_EXTRACT3.1data extraction
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 1.9→42.295 Å / Occupancy max: 1 / Occupancy min: 0.65 / SU ML: 0.19 / σ(F): 1.34 / Phase error: 18.42 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2068 1673 5.08 %
Rwork0.1752 --
obs0.1768 32955 98.08 %
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 39.583 Å2 / ksol: 0.382 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.7513 Å2-0 Å20 Å2
2---0.7513 Å2-0 Å2
3---1.5027 Å2
Refinement stepCycle: LAST / Resolution: 1.9→42.295 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3064 0 50 172 3286
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073228
X-RAY DIFFRACTIONf_angle_d0.9884354
X-RAY DIFFRACTIONf_dihedral_angle_d13.3851283
X-RAY DIFFRACTIONf_chiral_restr0.069467
X-RAY DIFFRACTIONf_plane_restr0.004574
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8991-1.9550.31521190.23552132X-RAY DIFFRACTION82
1.955-2.01810.24031390.18612529X-RAY DIFFRACTION98
2.0181-2.09020.2211340.16422603X-RAY DIFFRACTION100
2.0902-2.17390.20191440.15982585X-RAY DIFFRACTION100
2.1739-2.27280.18891300.15922646X-RAY DIFFRACTION100
2.2728-2.39260.19711320.15482637X-RAY DIFFRACTION100
2.3926-2.54250.20661490.16112623X-RAY DIFFRACTION99
2.5425-2.73880.17371390.15822639X-RAY DIFFRACTION100
2.7388-3.01440.24081570.17352627X-RAY DIFFRACTION100
3.0144-3.45040.20381510.1712651X-RAY DIFFRACTION99
3.4504-4.34640.18851370.16382713X-RAY DIFFRACTION99
4.3464-42.30580.20591420.20992897X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 34.7794 Å / Origin y: 53.7885 Å / Origin z: 66.0152 Å
111213212223313233
T0.1214 Å2-0.0064 Å20.0116 Å2-0.1387 Å20.0065 Å2--0.1717 Å2
L0.4801 °2-0.1309 °2-0.1375 °2-0.5664 °20.2878 °2--0.8907 °2
S0.0115 Å °-0.0029 Å °0.0099 Å °0.0039 Å °-0.0167 Å °0.0331 Å °-0.0043 Å °-0.0391 Å °0.0052 Å °
Refinement TLS groupSelection details: all

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