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- PDB-3fd5: Crystal structure of human selenophosphate synthetase 1 complex w... -

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Basic information

Entry
Database: PDB / ID: 3fd5
TitleCrystal structure of human selenophosphate synthetase 1 complex with AMPCP
ComponentsSelenide, water dikinase 1
KeywordsTRANSFERASE / selenophosphate synthetase / 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 / GTP binding / protein homodimerization activity / ATP binding / identical protein binding ...selenide, water dikinase / selenide, water dikinase activity / selenocysteine biosynthetic process / protein modification process / nuclear membrane / protein heterodimerization activity / 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
PHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER / : / PHOSPHATE ION / Selenide, water dikinase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 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_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)87,46014
Polymers86,1952
Non-polymers1,26412
Water9,260514
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8340 Å2
ΔGint-136 kcal/mol
Surface area23890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.734, 66.734, 181.168
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, 526 molecules

#2: Chemical ChemComp-AP2 / PHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER


Mass: 425.228 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H17N5O9P2
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


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-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 514 / 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: 2.34 Å3/Da / Density % sol: 47.44 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 100mM HEPES-KOH pH 7.0, 50mM MgCl2, 30% PEGMME550, 5mM K2HPO4/KH2PO4 pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection twinOperator: h,-k,-l / Fraction: 0.501
ReflectionResolution: 1.9→50 Å / Num. all: 60859 / Num. obs: 58844 / % possible obs: 96.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 1.9→1.93 Å / % possible all: 89.5

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIXmodel building
PHENIX(phenix.refine)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→14.926 Å / σ(F): 0.09 / Phase error: 20.83 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflectionSelection details
Rfree0.1954 1991 3.39 %RANDOM
Rwork0.1376 ---
obs0.1395 58701 94.79 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 67.982 Å2 / ksol: 0.371 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.3744 Å20 Å20 Å2
2---0.3744 Å20 Å2
3---0.4165 Å2
Refinement stepCycle: LAST / Resolution: 1.9→14.926 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5111 0 72 514 5697
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0095268
X-RAY DIFFRACTIONf_angle_d1.3057187
X-RAY DIFFRACTIONf_chiral_restr0.079854
X-RAY DIFFRACTIONf_plane_restr0.005922
X-RAY DIFFRACTIONf_dihedral_angle_d18.8191859
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9002-1.93290.2254870.23012398X-RAY DIFFRACTION98
1.9329-1.96790.2158850.22172545X-RAY DIFFRACTION98
1.9679-2.00570.271930.20232642X-RAY DIFFRACTION98
2.0057-2.04650.2627850.19922701X-RAY DIFFRACTION98
2.0465-2.09090.22631020.19162805X-RAY DIFFRACTION98
2.0909-2.13940.2727920.18312767X-RAY DIFFRACTION98
2.1394-2.19280.25791000.1762803X-RAY DIFFRACTION98
2.1928-2.25190.2123960.16572852X-RAY DIFFRACTION98
2.2519-2.31790.24331000.16852834X-RAY DIFFRACTION98
2.3179-2.39240.1868970.16272869X-RAY DIFFRACTION98
2.3924-2.47760.17521000.15912909X-RAY DIFFRACTION98
2.4776-2.57630.21741000.15132893X-RAY DIFFRACTION98
2.5763-2.69290.21471010.14922888X-RAY DIFFRACTION98
2.6929-2.83390.15791040.14792921X-RAY DIFFRACTION98
2.8339-3.01010.24071000.14112947X-RAY DIFFRACTION98
3.0101-3.24040.2298990.12862975X-RAY DIFFRACTION98
3.2404-3.56240.17041030.11742978X-RAY DIFFRACTION98
3.5624-4.06880.12621020.09882983X-RAY DIFFRACTION98
4.0688-5.09220.17141040.09093014X-RAY DIFFRACTION98
5.0922-14.92620.19781040.1323023X-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)
10.2577-0.1087-0.26890.17810.15230.3116-0.03810.0399-0.03160.0096-0.03030.0366-0.0029-0.04470.04280.04930.00110.00650.0736-0.0370.080854.607140.119381.237
20.2714-0.1883-0.13420.26540.27850.4274-0.03310.018-0.03390.0371-0.02590.02780.0746-0.00380.0350.0815-0.00450.03010.0558-0.01070.072473.093620.248962.3948
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain AA9 - 377
2X-RAY DIFFRACTION2chain BB6 - 377

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