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- PDB-5ao0: Crystal structure of human SAMHD1 (amino acid residues 41-583) bo... -

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Basic information

Entry
Database: PDB / ID: 5ao0
TitleCrystal structure of human SAMHD1 (amino acid residues 41-583) bound to ddGTP
ComponentsDEOXYNUCLEOSIDE TRIPHOSPHATE TRIPHOSPHOHYDROLASE SAMHD1
KeywordsHYDROLASE / DEOXYNUCLEOSIDE / DEOXYNUCLEOSIDE TRIPHOSPHATE TRIPHOSPHOHYDROLASE / HIV RESTRICTION FACTOR
Function / homology
Function and homology information


Nucleotide catabolism / Hydrolases; Acting on ester bonds; Triphosphoric-monoester hydrolases / deoxynucleoside triphosphate hydrolase activity / dGTP binding / triphosphoric monoester hydrolase activity / dATP catabolic process / dGTPase activity / tetraspanin-enriched microdomain / 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 / triphosphoric monoester hydrolase activity / dATP catabolic process / dGTPase activity / tetraspanin-enriched microdomain / dGTP catabolic process / DNA strand resection involved in replication fork processing / deoxyribonucleotide catabolic process / regulation of innate immune response / negative regulation of type I interferon-mediated signaling pathway / somatic hypermutation of immunoglobulin genes / RNA nuclease activity / 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. / HD/PDEase domain ...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'-3'-DIDEOXYGUANOSINE-5'-TRIPHOSPHATE / : / Deoxynucleoside triphosphate triphosphohydrolase SAMHD1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.731 Å
AuthorsSchwefel, D. / Taylor, I.A.
CitationJournal: Plos Pathog. / Year: 2015
Title: Phospho-Dependent Regulation of Samhd1 Oligomerisation Couples Catalysis and Restriction.
Authors: Arnold, L.H. / Groom, H.C. / Kunzelmann, S. / Schwefel, D. / Caswell, S.J. / Ordonez, P. / Mann, M.C. / Rueschenbaum, S. / Goldstone, D.C. / Pennell, S. / Howell, S.A. / Stoye, J.P. / Webb, ...Authors: Arnold, L.H. / Groom, H.C. / Kunzelmann, S. / Schwefel, D. / Caswell, S.J. / Ordonez, P. / Mann, M.C. / Rueschenbaum, S. / Goldstone, D.C. / Pennell, S. / Howell, S.A. / Stoye, J.P. / Webb, M. / Taylor, I.A. / Bishop, K.N.
History
DepositionSep 9, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 14, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: 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_asym_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_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.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

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)132,89310
Polymers130,7682
Non-polymers2,1258
Water543
1
A: DEOXYNUCLEOSIDE TRIPHOSPHATE TRIPHOSPHOHYDROLASE SAMHD1
B: DEOXYNUCLEOSIDE TRIPHOSPHATE TRIPHOSPHOHYDROLASE SAMHD1
hetero molecules

A: DEOXYNUCLEOSIDE TRIPHOSPHATE TRIPHOSPHOHYDROLASE SAMHD1
B: DEOXYNUCLEOSIDE TRIPHOSPHATE TRIPHOSPHOHYDROLASE SAMHD1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)265,78520
Polymers261,5354
Non-polymers4,25016
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_555-x+2/3,-x+y+1/3,-z+1/31
Buried area7380 Å2
ΔGint-58.4 kcal/mol
Surface area34160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)163.173, 163.173, 260.716
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

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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: 65383.801 Da / Num. of mol.: 2 / Fragment: RESIDUES 41-583
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 PLYSS / References: UniProt: Q9Y3Z3
#2: Chemical ChemComp-FE / FE (III) ION / Iron


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#3: Chemical
ChemComp-DG3 / 2'-3'-DIDEOXYGUANOSINE-5'-TRIPHOSPHATE


Mass: 491.182 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H16N5O12P3
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 3 / 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: 2.66 Å3/Da / Density % sol: 53.71 % / Description: NONE
Crystal growDetails: 160 MM SUCCINIC ACID, 11% PEG 3350, PH 7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 3.73→50 Å / Num. obs: 14005 / % possible obs: 98.7 % / Observed criterion σ(I): -3 / Redundancy: 9.67 % / Biso Wilson estimate: 96.38 Å2 / Rmerge(I) obs: 0.17 / Net I/σ(I): 12.23
Reflection shellResolution: 3.73→3.96 Å / Redundancy: 8.26 % / Rmerge(I) obs: 0.59 / Mean I/σ(I) obs: 4.37 / % possible all: 92.5

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3U1N

3u1n


Resolution: 3.731→49.423 Å / SU ML: 0.38 / σ(F): 2.02 / Phase error: 27.52 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2677 703 5 %
Rwork0.2188 --
obs0.2212 13996 98.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 93.4 Å2
Refinement stepCycle: LAST / Resolution: 3.731→49.423 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6779 0 124 3 6906
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0067082
X-RAY DIFFRACTIONf_angle_d1.0569656
X-RAY DIFFRACTIONf_dihedral_angle_d15.0382516
X-RAY DIFFRACTIONf_chiral_restr0.0441049
X-RAY DIFFRACTIONf_plane_restr0.0061240
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.7311-4.01910.33271550.24942465X-RAY DIFFRACTION94
4.0191-4.42330.23881380.20662679X-RAY DIFFRACTION100
4.4233-5.06290.24781300.19242675X-RAY DIFFRACTION100
5.0629-6.37650.26391390.22562687X-RAY DIFFRACTION100
6.3765-49.42760.26871410.2262787X-RAY DIFFRACTION100
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)
10.02950.0089-0.01550.01370.01060.0261-0.1546-0.00140.13880.11220.0461-0.00540.17680.09770.00030.4302-0.0775-0.02620.35290.17560.468726.494438.445127.9149
20.00920.00330.00410.00060.00310.0145-0.04120.26820.2133-0.02620.3952-0.01850.1985-0.0583-0.00010.6730.0168-0.05770.63780.06030.449542.281328.802619.574
30.05990.02570.04990.00960.00510.02260.01020.06950.50480.06150.21850.077-0.1919-0.25620.00020.39510.04440.0630.49120.06420.518234.014547.851231.4225
40.0465-0.05010.00230.05240.00410.00910.0001-0.01970.1494-0.21080.0801-0.4194-0.1620.16790.00350.521-0.20320.06130.94170.07930.444451.367838.825912.1295
5-0.01480.0035-0.0032-0.0002-0.00480.02160.08840.2270.2767-0.1583-0.19550.194-0.1152-0.129700.5233-0.1295-0.01420.64810.27170.891535.377552.519318.0855
6-0.0022-0.01420.01150.01450.0078-0.01750.04940.2278-0.1850.0310.1844-0.01870.03050.27220.00020.5775-0.09070.02650.63320.04540.481644.499143.770831.5191
7-0.0102-0.01540.0721-0.01530.03450.0093-0.2464-0.13010.23210.16090.21710.11410.23930.0372-00.4993-0.0949-0.02370.513-0.06120.721947.710543.531941.0244
80.12580.06260.01520.12150.07130.0425-0.19690.45060.3012-0.2410.43920.04580.0285-0.12020.01260.598-0.15050.04510.8798-0.09030.403548.260230.81016.6429
90.0193-0.02910.02470.0171-0.04070.0250.11650.16690.33880.0866-0.1588-0.3454-0.2660.0050.00030.7196-0.08680.08921.0561-0.27130.814760.954924.880511.9098
100.00630.01040.00760.0050.01090.0051-0.16580.0250.15090.0529-0.14420.0164-0.09740.0006-0.00190.7693-0.22410.63840.7769-0.17150.900174.669630.93328.6097
110.27350.0450.05960.00010.01620.0212-0.0853-0.1141-0.09740.34990.0348-0.2149-0.3526-0.2657-0.0072-0.2124-0.29940.11860.6343-0.17830.950359.506639.117827.4701
120.021-0.0087-0.00170.0075-0.0115-0.00160.14820.0170.18650.03650.0916-0.0524-0.060.09020.00091.0069-0.4340.24852.1692-0.69332.1977.248528.96616.3601
130.16850.1420.06190.04670.01440.13040.29250.0049-0.6088-0.09870.58-0.2287-0.35790.45150.62170.07110.0349-0.35990.4458-0.34970.472146.05538.247427.2324
14-0.00140.0344-0.06180.3976-0.04730.1890.3670.5677-0.4172-0.3214-0.2288-0.34860.58760.14330.50540.4227-0.118-0.65310.3375-0.7869-0.233238.2824-1.131919.4093
150.5562-0.07030.4940.1963-0.3510.65330.12880.235-0.321-0.05680.13810.04540.11970.06480.80240.4078-0.0437-0.09890.4321-0.01110.408729.839813.787221.8245
160.0386-0.01490.0325-0.0155-0.03360.04390.07480.0835-0.11520.15120.2983-0.0073-0.2838-0.030.00690.7106-0.4192-0.42420.4060.27720.80475.765115.068810.8905
170.13090.0643-0.1684-0.0119-0.17680.0040.2485-0.05770.22870.1662-0.03490.26820.0965-0.13020.0010.7614-0.0899-0.19840.76560.17150.979313.054813.224123.9453
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 110 THROUGH 138 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 139 THROUGH 163 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 164 THROUGH 205 )
4X-RAY DIFFRACTION4CHAIN 'A' AND (RESID 206 THROUGH 232 )
5X-RAY DIFFRACTION5CHAIN 'A' AND (RESID 233 THROUGH 291 )
6X-RAY DIFFRACTION6CHAIN 'A' AND (RESID 292 THROUGH 323 )
7X-RAY DIFFRACTION7CHAIN 'A' AND (RESID 324 THROUGH 372 )
8X-RAY DIFFRACTION8CHAIN 'A' AND (RESID 373 THROUGH 435 )
9X-RAY DIFFRACTION9CHAIN 'A' AND (RESID 436 THROUGH 469 )
10X-RAY DIFFRACTION10CHAIN 'A' AND (RESID 470 THROUGH 494 )
11X-RAY DIFFRACTION11CHAIN 'A' AND (RESID 495 THROUGH 558 )
12X-RAY DIFFRACTION12CHAIN 'A' AND (RESID 559 THROUGH 582 )
13X-RAY DIFFRACTION13CHAIN 'B' AND (RESID 113 THROUGH 205 )
14X-RAY DIFFRACTION14CHAIN 'B' AND (RESID 206 THROUGH 309 )
15X-RAY DIFFRACTION15CHAIN 'B' AND (RESID 310 THROUGH 469 )
16X-RAY DIFFRACTION16CHAIN 'B' AND (RESID 470 THROUGH 494 )
17X-RAY DIFFRACTION17CHAIN 'B' AND (RESID 495 THROUGH 583 )

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