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- PDB-4bzc: Crystal structure of the tetrameric dGTP-bound wild type SAMHD1 c... -

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Basic information

Entry
Database: PDB / ID: 4bzc
TitleCrystal structure of the tetrameric dGTP-bound wild type SAMHD1 catalytic core
ComponentsDEOXYNUCLEOSIDE TRIPHOSPHATE TRIPHOSPHOHYDROLASE SAMHD1
KeywordsHYDROLASE / HIV RESTRICTION FACTOR / DNTPASE
Function / homology
Function and homology information


Nucleotide catabolism / Hydrolases; Acting on ester bonds; Triphosphoric-monoester hydrolases / deoxynucleoside triphosphate hydrolase activity / dGTP binding / dATP catabolic process / deoxyribonucleotide catabolic process / tetraspanin-enriched microdomain / dGTPase activity / dGTP catabolic process / DNA strand resection involved in replication fork processing ...Nucleotide catabolism / Hydrolases; Acting on ester bonds; Triphosphoric-monoester hydrolases / deoxynucleoside triphosphate hydrolase activity / dGTP binding / dATP catabolic process / deoxyribonucleotide catabolic process / tetraspanin-enriched microdomain / dGTPase activity / dGTP catabolic process / DNA strand resection involved in replication fork processing / negative regulation of type I interferon-mediated signaling pathway / regulation of innate immune response / RNA nuclease activity / somatic hypermutation of immunoglobulin genes / double-strand break repair via homologous recombination / Interferon alpha/beta signaling / single-stranded DNA binding / site of double-strand break / protein homotetramerization / defense response to virus / nucleic acid binding / immune response / innate immune response / DNA damage response / GTP binding / RNA binding / zinc ion binding / nucleoplasm / identical protein binding / nucleus / plasma membrane
Similarity search - Function
Hypothetical protein af1432 / Hypothetical protein af1432 / : / HD domain profile. / HD domain / HD domain / SAM domain (Sterile alpha motif) / SAM domain profile. / Metal dependent phosphohydrolases with conserved 'HD' motif. / Sterile alpha motif. ...Hypothetical protein af1432 / Hypothetical protein af1432 / : / HD domain profile. / HD domain / HD domain / SAM domain (Sterile alpha motif) / SAM domain profile. / Metal dependent phosphohydrolases with conserved 'HD' motif. / Sterile alpha motif. / HD/PDEase domain / Sterile alpha motif domain / Sterile alpha motif/pointed domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
: / 2'-deoxyguanosine-5'-O-(1-thiotriphosphate) / Deoxynucleoside triphosphate triphosphohydrolase SAMHD1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.88 Å
AuthorsJi, X. / Yang, H. / Wu, Y. / Yan, J. / Mehrens, J. / DeLucia, M. / Hao, C. / Gronenborn, A.M. / Skowronski, J. / Ahn, J. / Xiong, Y.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2013
Title: Mechanism of Allosteric Activation of Samhd1 by Dgtp
Authors: Ji, X. / Wu, Y. / Yan, J. / Mehrens, J. / Yang, H. / Delucia, M. / Hao, C. / Gronenborn, A.M. / Skowronski, J. / Ahn, J. / Xiong, Y.
History
DepositionJul 25, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 23, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2013Group: Database references
Revision 1.2Nov 20, 2013Group: Database references
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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_database_status.status_code_sf / _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.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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.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_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 4-STRANDED BARREL THIS IS REPRESENTED BY A 5-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "BB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 4-STRANDED BARREL THIS IS REPRESENTED BY A 5-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "CB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 4-STRANDED BARREL THIS IS REPRESENTED BY A 5-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "DB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 4-STRANDED BARREL THIS IS REPRESENTED BY A 5-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DEOXYNUCLEOSIDE TRIPHOSPHATE TRIPHOSPHOHYDROLASE SAMHD1
B: DEOXYNUCLEOSIDE TRIPHOSPHATE TRIPHOSPHOHYDROLASE SAMHD1
C: DEOXYNUCLEOSIDE TRIPHOSPHATE TRIPHOSPHOHYDROLASE SAMHD1
D: DEOXYNUCLEOSIDE TRIPHOSPHATE TRIPHOSPHOHYDROLASE SAMHD1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)260,22924
Polymers253,6334
Non-polymers6,59620
Water61334
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20650 Å2
ΔGint-49.4 kcal/mol
Surface area66930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.002, 138.727, 93.715
Angle α, β, γ (deg.)90.00, 113.56, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
DEOXYNUCLEOSIDE TRIPHOSPHATE TRIPHOSPHOHYDROLASE SAMHD1 / DNTPASE / DENDRITIC CELL-DERIVED IFNG-INDUCED PROTEIN / DCIP / MONOCYTE PROTEIN 5 / MOP-5 / SAM ...DNTPASE / DENDRITIC CELL-DERIVED IFNG-INDUCED PROTEIN / DCIP / MONOCYTE PROTEIN 5 / MOP-5 / SAM DOMAIN AND HD DOMAIN-CONTAINING PROTEIN 1 / SAMHD1


Mass: 63408.320 Da / Num. of mol.: 4 / Fragment: HD DOMAIN, RESIDUES 113-626
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA 2
References: UniProt: Q9Y3Z3, Hydrolases; Acting on ester bonds; Triphosphoric-monoester hydrolases
#2: Chemical
ChemComp-T8T / 2'-deoxyguanosine-5'-O-(1-thiotriphosphate)


Mass: 523.247 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C10H16N5O12P3S
#3: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 34 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer details2'-DEOXYGUANOSINE-5'-O-(1-THIOTRIPHOSPHATE) (DGH): DGTP NON-HYDROLYZABLE ANALOGUE

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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: 2.3 Å3/Da / Density % sol: 46 % / Description: NONE
Crystal growpH: 6.7 / Details: 100 MM BIS-TRIS PH 6.7 AND 25% (W/V) PEG1500

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.979
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.88→50 Å / Num. obs: 40369 / % possible obs: 95.6 % / Observed criterion σ(I): 1 / Redundancy: 2.9 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 8.2
Reflection shellResolution: 2.88→2.93 Å / Redundancy: 3 % / Rmerge(I) obs: 0.9 / Mean I/σ(I) obs: 1.2 / % possible all: 97.4

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3U1N

3u1n


Resolution: 2.88→49.71 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.89 / SU B: 40.606 / SU ML: 0.358 / Cross valid method: THROUGHOUT / ESU R Free: 0.559 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES 278-281, 466-471 AND 600-626 ARE DISORDERED
RfactorNum. reflection% reflectionSelection details
Rfree0.2448 1668 5.1 %RANDOM
Rwork0.19032 ---
obs0.19307 31009 77.51 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 66.501 Å2
Baniso -1Baniso -2Baniso -3
1-0.12 Å20 Å20.7 Å2
2---1.99 Å20 Å2
3---1.14 Å2
Refinement stepCycle: LAST / Resolution: 2.88→49.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15540 0 380 34 15954
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.01916304
X-RAY DIFFRACTIONr_bond_other_d0.0060.0215405
X-RAY DIFFRACTIONr_angle_refined_deg1.6731.98522102
X-RAY DIFFRACTIONr_angle_other_deg1.289335472
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.31651893
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.28824.005799
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.639152865
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.69815106
X-RAY DIFFRACTIONr_chiral_restr0.0980.22323
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02118035
X-RAY DIFFRACTIONr_gen_planes_other0.0060.023831
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.7213.4947605
X-RAY DIFFRACTIONr_mcbond_other2.7193.4947604
X-RAY DIFFRACTIONr_mcangle_it4.4625.2359487
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.0113.7378699
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.875→2.95 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3 47 -
Rwork0.208 974 -
obs--32.48 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.11930.3970.09381.60950.33340.10430.0316-0.09490.0760.1376-0.09630.2434-0.0675-0.05030.06470.33590.02130.09910.26120.00430.25516.709225.851342.4624
20.25880.1361-0.01331.0925-0.08970.587-0.17470.0495-0.0386-0.32540.10180.05090.1178-0.03550.07290.3587-0.07340.08130.27870.01540.112818.70145.51329.5076
30.2342-0.02760.06120.6271-0.03460.0560.00490.10330.1019-0.3542-0.0729-0.67340.0132-0.03360.0680.32970.02070.41260.16040.10690.757552.971915.69599.2857
40.31870.1516-0.07980.53860.21920.19160.2654-0.0486-0.22150.2416-0.1574-0.57380.0034-0.094-0.1080.2266-0.076-0.30280.07380.12610.826649.228913.207748.0208
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A114 - 599
2X-RAY DIFFRACTION2C113 - 599
3X-RAY DIFFRACTION3B113 - 599
4X-RAY DIFFRACTION4D113 - 599

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