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- PDB-4l1j: Three dimensional structure of mutant D143A of human HD domain-co... -

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Basic information

Entry
Database: PDB / ID: 4l1j
TitleThree dimensional structure of mutant D143A of human HD domain-containing protein 2, Northeast Structural Genomics Consortium (NESG) Target HR6723
Components
  • HD domain-containing protein 2
  • HD domain-containing protein 2 (Phosphorylate)
KeywordsHYDROLASE / Structural Genomics / PSI-Biology / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG / HDCC2 / Hepatitis C virus NS5A-transactivated protein 2 / NS5ATP2
Function / homology
Function and homology information


5'-deoxynucleotidase / 5'-deoxynucleotidase activity / metal ion binding
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
DI(HYDROXYETHYL)ETHER / 5'-deoxynucleotidase HDDC2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.824 Å
AuthorsKuzin, A. / Su, M. / Yakunin, A. / Beloglazova, O. / Seetharaman, J. / Maglaqui, M. / Xiao, R. / Lee, D. / Brown, G. / Flick, R. ...Kuzin, A. / Su, M. / Yakunin, A. / Beloglazova, O. / Seetharaman, J. / Maglaqui, M. / Xiao, R. / Lee, D. / Brown, G. / Flick, R. / Everett, J.K. / Acton, T.B. / Montelione, G.T. / Hunt, J.F. / Tong, L. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Three dimensional structure of mutant D143A of human HD domain-containing protein 2, Northeast Structural Genomics Consortium (NESG) Target HR6723
Authors: Kuzin, A. / Su, M. / Yakunin, A. / Beloglazova, O. / Seetharaman, J. / Maglaqui, M. / Xiao, R. / Lee, D. / Brown, G. / Flick, R. / Everett, J.K. / Acton, T.B. / Montelione, G.T. / Hunt, J.F. / Tong, L.
History
DepositionJun 3, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 19, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 25, 2013Group: Structure summary
Revision 1.2Sep 20, 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_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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 (Phosphorylate)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,5809
Polymers47,5892
Non-polymers9917
Water4,432246
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5450 Å2
ΔGint-12 kcal/mol
Surface area18340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.991, 69.929, 105.778
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Detailsdimer,61.27 kD,68.3%

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Components

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


Mass: 23754.674 Da / Num. of mol.: 1 / Mutation: D143A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET15_NESG / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+Magic / References: UniProt: Q7Z4H3
#2: Protein HD domain-containing protein 2 (Phosphorylate)


Mass: 23834.652 Da / Num. of mol.: 1 / Mutation: D143A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET15_NESG / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+Magic / References: UniProt: Q7Z4H3
#3: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-PE4 / 2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL / POLYETHYLENE GLYCOL PEG4000


Mass: 354.436 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H34O8 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 246 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.53 Å3/Da / Density % sol: 51.3 %
Crystal growTemperature: 277 K / Method: microbatch under oil / pH: 6
Details: Protein solution: 100mM NaCl, 5mM DTT, 0.02% NaN3, 10mM Tris-HCl (pH 7.5) . Reservoir solution:Na2H2PO4 0.1M, MES 0.1M, PEG400 40%, microbatch under oil, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 0.979 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jan 14, 2013
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.82→50 Å / Num. obs: 42001 / % possible obs: 93.6 % / Observed criterion σ(I): -3 / Redundancy: 5.7 % / Biso Wilson estimate: 26.7 Å2 / Rmerge(I) obs: 0.051 / Net I/σ(I): 47

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Processing

Software
NameVersionClassificationNB
PHENIXdev_1269refinement
PDB_EXTRACT3.1data extraction
HKL-2000data reduction
HKL-2000data scaling
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4DMB

4dmb


Resolution: 1.824→35.383 Å / Occupancy max: 1 / Occupancy min: 0 / SU ML: 0.16 / σ(F): 1.44 / Phase error: 19.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2014 1998 4.76 %
Rwork0.1756 --
obs0.1768 42001 96.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29.44 Å2
Refinement stepCycle: LAST / Resolution: 1.824→35.383 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3097 0 52 246 3395
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073242
X-RAY DIFFRACTIONf_angle_d1.0474353
X-RAY DIFFRACTIONf_dihedral_angle_d14.7631280
X-RAY DIFFRACTIONf_chiral_restr0.07466
X-RAY DIFFRACTIONf_plane_restr0.004572
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8244-1.870.2711010.2622077X-RAY DIFFRACTION71
1.87-1.92060.25331090.2252499X-RAY DIFFRACTION85
1.9206-1.97710.21591550.19742708X-RAY DIFFRACTION93
1.9771-2.04090.20761500.17212880X-RAY DIFFRACTION98
2.0409-2.11380.21211420.16862939X-RAY DIFFRACTION100
2.1138-2.19850.18331360.15532913X-RAY DIFFRACTION100
2.1985-2.29850.18651510.15572971X-RAY DIFFRACTION100
2.2985-2.41970.21321490.16192939X-RAY DIFFRACTION100
2.4197-2.57120.20531490.16972943X-RAY DIFFRACTION100
2.5712-2.76970.20061500.17222956X-RAY DIFFRACTION100
2.7697-3.04820.23891500.1912986X-RAY DIFFRACTION100
3.0482-3.4890.19741530.18892991X-RAY DIFFRACTION100
3.489-4.39450.16611470.15963037X-RAY DIFFRACTION100
4.3945-35.38980.20971560.17833164X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -20.048 Å / Origin y: -12.9506 Å / Origin z: 15.7411 Å
111213212223313233
T0.1495 Å2-0.0469 Å20.0215 Å2-0.1557 Å2-0.0257 Å2--0.1341 Å2
L1.568 °2-0.3879 °2-0.1272 °2-1.1874 °20.0094 °2--1.5908 °2
S0.0089 Å °-0.0379 Å °0.0555 Å °0.0799 Å °-0.0573 Å °-0.0174 Å °-0.0173 Å °0.1739 Å °0.0485 Å °
Refinement TLS groupSelection details: all

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