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- PDB-4l7w: Crystal structure mutant H77A of human HD domain-containing prote... -

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Basic information

Entry
Database: PDB / ID: 4l7w
TitleCrystal structure mutant H77A 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
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
5'-deoxynucleotidase HDDC2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.305 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 14, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 3, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 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 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)23,9336
Polymers23,8121
Non-polymers1225
Water79344
1
A: HD domain-containing protein 2
hetero molecules

A: HD domain-containing protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,86612
Polymers47,6232
Non-polymers24310
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_455-x-1,-y,z1
Buried area5900 Å2
ΔGint-118 kcal/mol
Surface area16580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.380, 71.380, 199.308
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122
Components on special symmetry positions
IDModelComponents
11A-402-

HOH

Detailsdimer,43.66 kD,73.0%|dimer,40.35 kD,20.3%

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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: 23811.594 Da / Num. of mol.: 1 / Mutation: H77A
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-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 44 / 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: 2.67 Å3/Da / Density % sol: 53.85 %
Crystal growTemperature: 277 K / Method: microbatch under oil / pH: 8
Details: Protein solution: 100mM NaCl, 5mM DTT, 0.02% NaN3, 10mM Tris-HCl (pH 7.5) . Reservoir solution: 0.1M Mg(NO3)2, 0.1M Tris, 12% PEG 20000, 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 6, 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: 2.3→50 Å / Num. obs: 11866 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 8.9 % / Biso Wilson estimate: 42.21 Å2 / Rmerge(I) obs: 0.096 / Net I/σ(I): 40.9

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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: 2.305→35.69 Å / Occupancy max: 1 / Occupancy min: 0.5 / SU ML: 0.2 / σ(F): 1.33 / Phase error: 20.96 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2281 562 4.75 %
Rwork0.1739 --
obs0.1763 11843 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 57.794 Å2
Refinement stepCycle: LAST / Resolution: 2.305→35.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1520 0 5 44 1569
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081544
X-RAY DIFFRACTIONf_angle_d1.1012080
X-RAY DIFFRACTIONf_dihedral_angle_d15.087604
X-RAY DIFFRACTIONf_chiral_restr0.073227
X-RAY DIFFRACTIONf_plane_restr0.004275
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3045-2.53640.24121350.18572760X-RAY DIFFRACTION100
2.5364-2.90320.2451440.18732745X-RAY DIFFRACTION100
2.9032-3.65720.26431530.1892799X-RAY DIFFRACTION100
3.6572-35.69430.1981300.16072977X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -37.926 Å / Origin y: 10.2734 Å / Origin z: 8.7663 Å
111213212223313233
T0.5261 Å20.0441 Å20.0175 Å2-0.3129 Å20.0622 Å2--0.3179 Å2
L1.9497 °2-1.103 °2-0.5679 °2-3.6743 °20.333 °2--2.3721 °2
S0.3158 Å °0.4414 Å °0.2334 Å °-0.8404 Å °-0.2865 Å °-0.1672 Å °-0.3439 Å °0.0302 Å °-0.0059 Å °
Refinement TLS groupSelection details: all

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