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- PDB-4l7e: Three dimensional structure of mutant D78A of human HD domain-con... -

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Basic information

Entry
Database: PDB / ID: 4l7e
TitleThree dimensional structure of mutant D78A of human HD domain-containing protein 2, Genomics Consortium (NESG) Target HR6723
ComponentsHD domain-containing protein 2
KeywordsSIGNALING PROTEIN / Structural Genomics / PSI-Biology / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG / HDCC2 mutant D78A
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 / Unknown ligand / 5'-deoxynucleotidase HDDC2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.229 Å
AuthorsKuzin, A. / Su, M. / Yakunin, A. / Beloglazova, N. / Seetharaman, J. / Maglaqui, M. / Xiao, R. / Lee, D. / Brown, G. / Flick, R. ...Kuzin, A. / Su, M. / Yakunin, A. / Beloglazova, N. / 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: Northeast Structural Genomics Consortium Target HR6723
Authors: Kuzin, A. / Su, M. / Yakunin, A. / Beloglazova, N. / Seetharaman, J. / Maglaqui, M. / Xiao, R. / Lee, D. / Brown, G. / Flick, R. / Everett, J.K. / Acton, T.B. / Montelione, G.T. / Hunt, J.F. ...Authors: Kuzin, A. / Su, M. / Yakunin, A. / Beloglazova, N. / 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)
History
DepositionJun 13, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 24, 2013Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2018Group: Database references / Structure summary / Category: audit_author / citation_author / Item: _audit_author.name / _citation_author.name
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 1.4Nov 20, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,58914
Polymers47,6692
Non-polymers92012
Water1,838102
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5970 Å2
ΔGint-34 kcal/mol
Surface area17610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.762, 68.886, 106.154
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Detailsdimer,44.42 kD,92.5%

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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: 23834.652 Da / Num. of mol.: 2 / Mutation: D78A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HDDC2, C6orf74, NS5ATP2, CGI-130 / Plasmid: pET15_NESG / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+Magic / References: UniProt: Q7Z4H3
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-UNL / UNKNOWN LIGAND


Num. of mol.: 2 / Source method: obtained synthetically
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 102 / 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: 2.52 Å3/Da / Density % sol: 51.23 %
Crystal growTemperature: 277 K / Method: microbatch under oil / pH: 5
Details: Protein solution: 100mM NaCl, 5mM DTT, 0.02% NaN3, 10mM Tris-HCl (pH 7.5) . Reservoir solution:0.1M LiCl, 0.1M sodium acetate, 40% PEG1000, microbatch under oil, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 19, 2012 / Details: mirrors
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: 2.2→50 Å / Num. obs: 24213 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 7.9 % / Biso Wilson estimate: 29.15 Å2 / Rmerge(I) obs: 0.092

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Processing

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

4dmb


Resolution: 2.229→47.567 Å / Occupancy max: 1 / Occupancy min: 0.25 / SU ML: 0.24 / σ(F): 1.44 / Phase error: 21.24 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2151 1221 5.06 %
Rwork0.1736 --
obs0.1758 24153 99.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 41.102 Å2
Refinement stepCycle: LAST / Resolution: 2.229→47.567 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3079 0 61 102 3242
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073196
X-RAY DIFFRACTIONf_angle_d1.0774286
X-RAY DIFFRACTIONf_dihedral_angle_d14.3881258
X-RAY DIFFRACTIONf_chiral_restr0.064459
X-RAY DIFFRACTIONf_plane_restr0.004561
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2286-2.31780.32531300.24532468X-RAY DIFFRACTION99
2.3178-2.42330.20081410.18252501X-RAY DIFFRACTION100
2.4233-2.5510.22381270.16822525X-RAY DIFFRACTION100
2.551-2.71090.19661310.15432508X-RAY DIFFRACTION100
2.7109-2.92010.22461420.16482529X-RAY DIFFRACTION100
2.9201-3.21390.23441280.1832548X-RAY DIFFRACTION100
3.2139-3.67890.21211350.1742564X-RAY DIFFRACTION100
3.6789-4.63430.19191390.15242594X-RAY DIFFRACTION100
4.6343-47.57760.20981480.18182695X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 20.0149 Å / Origin y: 12.5146 Å / Origin z: 15.5944 Å
111213212223313233
T0.2314 Å2-0.0359 Å2-0.011 Å2-0.232 Å20.0146 Å2--0.2064 Å2
L1.3846 °2-0.3682 °20.1704 °2-0.838 °2-0.1629 °2--1.1613 °2
S0.0186 Å °0.0037 Å °-0.0574 Å °0.0326 Å °-0.0626 Å °0.0405 Å °0.0113 Å °-0.1616 Å °0.0471 Å °
Refinement TLS groupSelection details: all

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