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- PDB-3fd6: Crystal structure of human selenophosphate synthetase 1 complex w... -

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Basic information

Entry
Database: PDB / ID: 3fd6
TitleCrystal structure of human selenophosphate synthetase 1 complex with ADP and phosphate
ComponentsSelenide, water dikinase 1
KeywordsTRANSFERASE / selenophosphate synthetase 1 / selD / ATP-binding / Kinase / Nucleotide-binding / Selenium
Function / homology
Function and homology information


selenide, water dikinase / selenide, water dikinase activity / selenocysteine biosynthetic process / protein modification process / nuclear membrane / protein heterodimerization activity / phosphorylation / GTP binding / protein homodimerization activity / ATP binding ...selenide, water dikinase / selenide, water dikinase activity / selenocysteine biosynthetic process / protein modification process / nuclear membrane / protein heterodimerization activity / phosphorylation / GTP binding / protein homodimerization activity / ATP binding / identical protein binding / metal ion binding / plasma membrane / cytoplasm
Similarity search - Function
Selenophosphate synthetase / Phosphoribosyl-aminoimidazole Synthetase; Chain A, domain 2 / PurM-like C-terminal domain / PurM-like, N-terminal domain / PurM-like, N-terminal domain / AIR synthase related protein, N-terminal domain / PurM-like, C-terminal domain / PurM-like, C-terminal domain superfamily / PurM-like, N-terminal domain superfamily / AIR synthase related protein, C-terminal domain ...Selenophosphate synthetase / Phosphoribosyl-aminoimidazole Synthetase; Chain A, domain 2 / PurM-like C-terminal domain / PurM-like, N-terminal domain / PurM-like, N-terminal domain / AIR synthase related protein, N-terminal domain / PurM-like, C-terminal domain / PurM-like, C-terminal domain superfamily / PurM-like, N-terminal domain superfamily / AIR synthase related protein, C-terminal domain / 60s Ribosomal Protein L30; Chain: A; / Alpha-Beta Complex / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / PHOSPHATE ION / Selenide, water dikinase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsWang, K.T.
CitationJournal: J.Mol.Biol. / Year: 2009
Title: Crystal structures of catalytic intermediates of human selenophosphate synthetase 1.
Authors: Wang, K.T. / Wang, J. / Li, L.F. / Su, X.D.
History
DepositionNov 25, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 22, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / 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_asym_id / _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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_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.ptnr1_auth_asym_id / _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_asym_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_ref_seq_dif.details / _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: Selenide, water dikinase 1
B: Selenide, water dikinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,43114
Polymers86,1952
Non-polymers1,23612
Water9,620534
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8340 Å2
ΔGint-157 kcal/mol
Surface area24940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.618, 67.618, 182.551
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Selenide, water dikinase 1 / / Selenophosphate synthetase 1 / Selenium donor protein 1


Mass: 43097.590 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SEPHS1, SELD, SPS, SPS1 / Production host: Escherichia coli (E. coli) / References: UniProt: P49903, selenide, water dikinase

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Non-polymers , 5 types, 546 molecules

#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 534 / 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: 2.42 Å3/Da / Density % sol: 49.19 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 100mM HEPES-NaOH pH 7.0, 50mM MgCl2, 30% PEGMME550, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR
DetectorType: BRUKER SMART 6000 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection twinOperator: h,-k,-l / Fraction: 0.499
ReflectionResolution: 1.95→50 Å / Num. all: 57103 / Num. obs: 53229 / % possible obs: 93.2 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3
Reflection shellResolution: 1.95→1.98 Å / % possible all: 51.8

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Processing

Software
NameVersionClassification
PROTEUM PLUSPLUSdata collection
PHENIXmodel building
PHENIX(phenix.refine)refinement
PROTEUM PLUSPLUSdata reduction
PROTEUM PLUSPLUSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→14.96 Å / σ(F): 0.03 / Phase error: 21.13 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflectionSelection details
Rfree0.1957 2008 3.81 %RANDOM
Rwork0.1305 ---
obs0.1329 52680 88.89 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 75.621 Å2 / ksol: 0.358 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--5.045 Å20 Å20 Å2
2---5.045 Å20 Å2
3----4.37 Å2
Refinement stepCycle: LAST / Resolution: 1.95→14.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5193 0 72 534 5799
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.015350
X-RAY DIFFRACTIONf_angle_d1.3127279
X-RAY DIFFRACTIONf_chiral_restr0.078855
X-RAY DIFFRACTIONf_plane_restr0.005931
X-RAY DIFFRACTIONf_dihedral_angle_d18.161925
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-1.98360.3561420.18151060X-RAY DIFFRACTION98
1.9836-2.01950.2392520.16011453X-RAY DIFFRACTION98
2.0195-2.05830.2249660.15851781X-RAY DIFFRACTION98
2.0583-2.10020.2524730.14822093X-RAY DIFFRACTION98
2.1002-2.14570.2148860.14072338X-RAY DIFFRACTION98
2.1457-2.19550.23941050.13982763X-RAY DIFFRACTION98
2.1955-2.25020.2479980.13592679X-RAY DIFFRACTION98
2.2502-2.31090.21671060.13242705X-RAY DIFFRACTION98
2.3109-2.37860.26461060.13192775X-RAY DIFFRACTION98
2.3786-2.4550.1941050.13152777X-RAY DIFFRACTION98
2.455-2.54240.21781090.1292787X-RAY DIFFRACTION98
2.5424-2.64360.1681030.13312815X-RAY DIFFRACTION98
2.6436-2.76320.19051030.13382796X-RAY DIFFRACTION98
2.7632-2.90790.22211040.1412846X-RAY DIFFRACTION98
2.9079-3.08860.20861050.142859X-RAY DIFFRACTION98
3.0886-3.32470.2061020.1332816X-RAY DIFFRACTION98
3.3247-3.65480.1761130.1172845X-RAY DIFFRACTION98
3.6548-4.17360.17581060.10642867X-RAY DIFFRACTION98
4.1736-5.22090.13891080.10722866X-RAY DIFFRACTION98
5.2209-14.96040.15761130.152854X-RAY DIFFRACTION98
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)
10.3184-0.1635-0.26030.20920.1820.3153-0.010.0497-0.02880.0119-0.04260.034-0.0078-0.04970.04080.02670.00110.01110.0393-0.03150.047855.090740.312880.9298
20.1966-0.1964-0.19910.19480.30590.399-0.05670.0105-0.04710.0481-0.02280.04290.0751-0.0010.05920.0643-0.00390.04680.0429-0.01180.078974.060520.423362.1183
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1CHAIN AA7 - 377
2X-RAY DIFFRACTION2CHAIN BB6 - 377

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