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- PDB-5kss: Stationary phase survival protein E (SurE) from Xylella fastidios... -

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Basic information

Entry
Database: PDB / ID: 5kss
TitleStationary phase survival protein E (SurE) from Xylella fastidiosa - XFSurE-Ds (Dimer Smaller)
Components5'-nucleotidase SurE
KeywordsHYDROLASE / Stationary phase survival protein E (SurE) / Xylella fastidiosa / crystallization.
Function / homology
Function and homology information


3'-nucleotidase activity / exopolyphosphatase activity / 5'-nucleotidase / 5'-nucleotidase activity / nucleotide binding / metal ion binding / identical protein binding / cytoplasm
Similarity search - Function
Stationary-phase Survival Protein Sure Homolog; Chain: A, / Survival protein SurE-like phosphatase/nucleotidase / Survival protein SurE / Survival protein SurE-like phosphatase/nucleotidase / SurE-like phosphatase/nucleotidase superfamily / Survival protein SurE / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
IODIDE ION / : / 5'-nucleotidase SurE
Similarity search - Component
Biological speciesXylella fastidiosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.82 Å
AuthorsMachado, A.T.P. / Fonseca, E.M.B. / Dos Reis, M.A. / Saraiva, A.M. / Dos Santos, C.A. / De Toledo, A.M.S. / Polikarpov, I. / De Souza, A.P. / Aparicio, R. / Iulek, J.
Funding support Brazil, 1items
OrganizationGrant numberCountry
Conselho Nacional de Desenvolvimento Cientifico e Tecnologico (CNPq)140377/2008-5 Brazil
CitationJournal: Proteins / Year: 2017
Title: Conformational variability of the stationary phase survival protein E from Xylella fastidiosa revealed by X-ray crystallography, small-angle X-ray scattering studies, and normal mode analysis.
Authors: Machado, A.T.P. / Fonseca, E.M.B. / Reis, M.A.D. / Saraiva, A.M. / Santos, C.A.D. / de Toledo, M.A.S. / Polikarpov, I. / de Souza, A.P. / Aparicio, R. / Iulek, J.
History
DepositionJul 9, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 19, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 2, 2017Group: Database references / Category: citation / Item: _citation.title
Revision 1.2Sep 20, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Oct 4, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 5'-nucleotidase SurE
B: 5'-nucleotidase SurE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,5429
Polymers58,9802
Non-polymers5617
Water32418
1
A: 5'-nucleotidase SurE
B: 5'-nucleotidase SurE
hetero molecules

A: 5'-nucleotidase SurE
B: 5'-nucleotidase SurE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,08318
Polymers117,9604
Non-polymers1,12314
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area21220 Å2
ΔGint-186 kcal/mol
Surface area37020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.941, 80.118, 71.511
Angle α, β, γ (deg.)90.00, 95.51, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-605-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111chain A and ( ( resseq 4:36 and not (...
211chain B and ( ( resseq 4:36 and not (...

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Components

#1: Protein 5'-nucleotidase SurE / Nucleoside 5'-monophosphate phosphohydrolase


Mass: 29490.037 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xylella fastidiosa (strain 9a5c) (bacteria)
Strain: 9a5c / Gene: surE, XF_0858 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9PF20, 5'-nucleotidase
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: I
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 18 / 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: 2.18 Å3/Da / Density % sol: 43.69 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1 M bis-tris propane pH 7.6, 0.13 M Sodium iodide, 16% (W/V) PEG 3350, 5 mM dithiotheitol and 0.5 manganese II chloride.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: D03B-MX1 / Wavelength: 1.437 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Aug 12, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.437 Å / Relative weight: 1
ReflectionResolution: 2.82→43.944 Å / Num. all: 9802 / Num. obs: 9802 / % possible obs: 88.5 % / Observed criterion σ(I): -3 / Redundancy: 3.73 % / Biso Wilson estimate: 70.431 Å2 / Rmerge(I) obs: 0.112 / Net I/σ(I): 8.67
Reflection shellResolution: 2.82→2.9 Å / Redundancy: 2.77 % / Rmerge(I) obs: 0.504 / Mean I/σ(I) obs: 3.25 / % possible all: 82.5

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHASER2.3.0phasing
PHENIX1.8.2_1309refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3TY2

3ty2


Resolution: 2.82→43.944 Å / SU ML: 0.54 / Cross valid method: FREE R-VALUE / Phase error: 34.4
RfactorNum. reflection% reflection
Rfree0.3286 488 4.98 %
Rwork0.2716 --
obs0.2745 9796 82.44 %
Solvent computationShrinkage radii: 1 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 83.027 Å2
Refinement stepCycle: LAST / Resolution: 2.82→43.944 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3800 0 7 18 3825
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023874
X-RAY DIFFRACTIONf_angle_d0.5195304
X-RAY DIFFRACTIONf_dihedral_angle_d8.2861392
X-RAY DIFFRACTIONf_chiral_restr0.034632
X-RAY DIFFRACTIONf_plane_restr0.003697
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A1264X-RAY DIFFRACTIONPOSITIONAL
12B1264X-RAY DIFFRACTIONPOSITIONAL0.006
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8202-3.22820.37891940.31423620X-RAY DIFFRACTION97
3.2282-4.06670.4143950.3311895X-RAY DIFFRACTION50
4.0667-43.94890.2861990.23793793X-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)
12.2382-1.1804-0.62422.48280.05253.8970.2208-0.05670.31140.00890.132-0.1576-0.6462-0.0235-0.36080.53050.0040.04790.489-0.00620.565935.403531.6518.8674
21.5548-0.5616-1.29552.7083-0.13093.7828-0.2850.0963-0.384-0.30480.22350.60970.4703-0.3080.07280.5849-0.12240.02370.64610.00530.768633.585410.681918.1917
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 1:255 )A1 - 255
2X-RAY DIFFRACTION2( CHAIN B AND RESID 1:257 )B1 - 257

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