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- PDB-5l16: Crystal Structure of N-terminus truncated selenophosphate synthet... -

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Basic information

Entry
Database: PDB / ID: 5l16
TitleCrystal Structure of N-terminus truncated selenophosphate synthetase from Leishmania major
ComponentsPutative selenophosphate synthetase
KeywordsTRANSFERASE / Enzyme
Function / homology
Function and homology information


selenide, water dikinase / selenide, water dikinase activity / selenocysteine biosynthetic process / ATP binding / metal ion binding / cytoplasm
Similarity search - Function
Selenophosphate synthetase / 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; / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Selenide, water dikinase
Similarity search - Component
Biological speciesLeishmania major (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.882 Å
AuthorsFaim, L.M. / Silva, I.R. / Pereira, H.M. / Dias, M.B. / Silva, M.T.A. / Brandao-Neto, J. / Thiemann, O.H.
Funding support Brazil, 1items
OrganizationGrant numberCountry
Sao Paulo Research Foundation (FAPESP)2007/06591-0 Brazil
CitationJournal: Plos Negl Trop Dis / Year: 2020
Title: Trypanosomatid selenophosphate synthetase structure, function and interaction with selenocysteine lyase.
Authors: da Silva, M.T.A. / Silva, I.R.E. / Faim, L.M. / Bellini, N.K. / Pereira, M.L. / Lima, A.L. / de Jesus, T.C.L. / Costa, F.C. / Watanabe, T.F. / Pereira, H.D. / Valentini, S.R. / Zanelli, C.F. ...Authors: da Silva, M.T.A. / Silva, I.R.E. / Faim, L.M. / Bellini, N.K. / Pereira, M.L. / Lima, A.L. / de Jesus, T.C.L. / Costa, F.C. / Watanabe, T.F. / Pereira, H.D. / Valentini, S.R. / Zanelli, C.F. / Borges, J.C. / Dias, M.V.B. / da Cunha, J.P.C. / Mittra, B. / Andrews, N.W. / Thiemann, O.H.
History
DepositionJul 28, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 9, 2017Provider: repository / Type: Initial release
Revision 1.1Apr 17, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Dec 2, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.4Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative selenophosphate synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,8262
Polymers42,7301
Non-polymers961
Water5,278293
1
A: Putative selenophosphate synthetase
hetero molecules

A: Putative selenophosphate synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,6524
Polymers85,4602
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_455-x-1,-y+1/2,z1
Buried area3230 Å2
ΔGint-63 kcal/mol
Surface area25920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.950, 81.690, 177.920
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number24
Space group name H-MI212121
Components on special symmetry positions
IDModelComponents
11A-693-

HOH

21A-698-

HOH

31A-741-

HOH

41A-749-

HOH

51A-774-

HOH

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Components

#1: Protein Putative selenophosphate synthetase


Mass: 42729.871 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leishmania major (eukaryote) / Gene: LMJF_36_5410 / Production host: Escherichia coli (E. coli) / References: UniProt: Q4Q0M0, selenide, water dikinase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 293 / 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: 2.38 Å3/Da / Density % sol: 48.29 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.2
Details: 100mM tri-sodium ciitrate pH 5.2, 200mM ammonium sulphate, 21% PEG4000.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: May 24, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 1.882→88.96 Å / Num. obs: 33416 / % possible obs: 99.7 % / Redundancy: 5 % / Biso Wilson estimate: 19.52 Å2 / Rsym value: 0.108 / Net I/av σ(I): 6.6 / Net I/σ(I): 11.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
1.882-1.985.20.6871199.9
1.98-2.14.70.4561.6199.8
2.1-2.254.80.3242.2199.7
2.25-2.435.40.243199.8
2.43-2.665.20.1624.5199.9
2.66-2.984.80.116.6199.8
2.98-3.444.70.079.9199.3
3.44-4.215.40.04614.7199.6
4.21-5.954.60.03618.2198.4
5.95-40.9735.30.03218.1198.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
SCALA3.3.16data scaling
PHASERphasing
PHENIX1.7.2_869refinement
PDB_EXTRACT3.2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3FD5

3fd5


Resolution: 1.882→40.845 Å / SU ML: 0.47 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.63
RfactorNum. reflection% reflectionSelection details
Rfree0.2131 1692 5.06 %Random selection
Rwork0.1732 ---
obs0.1753 33411 99.5 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Bsol: 39.215 Å2 / ksol: 0.344 e/Å3
Displacement parametersBiso max: 81.04 Å2 / Biso mean: 27.33 Å2 / Biso min: 7.34 Å2
Baniso -1Baniso -2Baniso -3
1--0.636 Å20 Å2-0 Å2
2--6.8868 Å2-0 Å2
3----6.2507 Å2
Refinement stepCycle: final / Resolution: 1.882→40.845 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2399 0 5 293 2697
Biso mean--46.51 37.74 -
Num. residues----323
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062495
X-RAY DIFFRACTIONf_angle_d1.0183401
X-RAY DIFFRACTIONf_chiral_restr0.072397
X-RAY DIFFRACTIONf_plane_restr0.005441
X-RAY DIFFRACTIONf_dihedral_angle_d12.031908
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.882-1.93740.30331420.251126252767100
1.9374-1.99990.2911450.220126232768100
1.9999-2.07140.25421340.205226062740100
2.0714-2.15430.2581570.19122593275099
2.1543-2.25240.23511280.178126302758100
2.2524-2.37110.2621390.161926302769100
2.3711-2.51960.21131330.172826282761100
2.5196-2.71410.21481170.168226602777100
2.7141-2.98720.21711270.170626742801100
2.9872-3.41930.20531500.16912635278599
3.4193-4.30720.16991620.14832666282899
4.3072-40.85460.18711580.16662749290798
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)
12.07420.54051.4441.31790.7653.60790.4215-0.32940.0387-0.0552-0.1558-0.02990.2334-0.1993-0.12150.07210.05990.00420.1904-0.08070.1117-24.334515.6785-32.3584
21.9291-0.8744-0.82971.83430.31811.77360.1184-0.42340.31690.0924-0.03220.0222-0.3171-0.0755-0.10390.0894-0.0220.02880.1609-0.07520.1198-17.111924.5024-20.1769
31.8429-0.07990.01491.2035-0.15250.86420.2372-0.3564-0.02580.0553-0.2712-0.2763-0.00630.1006-0.0140.0064-0.1023-0.08490.0917-0.08430.0159-9.18219.4025-21.6384
41.92930.0220.17351.06010.30561.87790.2718-0.3098-0.40660.2541-0.1836-0.11220.23880.0003-0.07430.1196-0.0357-0.08750.07880.01120.1597-10.1388-2.0921-23.9228
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resseq 6:37)A6 - 37
2X-RAY DIFFRACTION2chain 'A' and (resseq 38:112)A38 - 112
3X-RAY DIFFRACTION3chain 'A' and (resseq 113:214)A113 - 214
4X-RAY DIFFRACTION4chain 'A' and (resseq 215:330)A215 - 330

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