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

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Basic information

Entry
Database: PDB / ID: 5ksr
TitleStationary phase survival protein E (SurE) from Xylella fastidiosa - XFSurE-TB (Tetramer Bigger).
Components5'-nucleotidase SurE
KeywordsHYDROLASE / Stationary phase survival protein E (SurE) / Xylella fastidiosa / crystallization.
Function / homology
Function and homology information


XMP 5'-nucleosidase activity / 5'-nucleotidase / nucleotide binding / identical protein binding / metal ion 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: 1.96 Å
AuthorsMachado, A.T.P. / Fonseca, E.M.B. / Dos Reis, M.A. / Saraiva, A.M. / Dos Santos, C.A. / De Toledo, M.A. / Polikarpov, I. / De Souza, A.P. / De 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 / Derived calculations / 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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)119,08318
Polymers117,9604
Non-polymers1,12314
Water11,908661
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21870 Å2
ΔGint-208 kcal/mol
Surface area43980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)172.336, 84.170, 87.310
Angle α, β, γ (deg.)90.00, 96.62, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11C-638-

HOH

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Components

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


Mass: 29490.037 Da / Num. of mol.: 4
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.: 4 / Source method: obtained synthetically / Formula: Mn
#3: Chemical
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: I
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 661 / 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: 2.77 Å3/Da / Density % sol: 55.61 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1 M bis-tris propane pH 7.5, 0.14 M Sodium iodide, 20% (W/V) PEG 3350, 5 mM dithiotheitol and 0.1 manganese II chloride.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.459 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 15, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.459 Å / Relative weight: 1
ReflectionResolution: 1.96→43.248 Å / Num. all: 88536 / Num. obs: 88536 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 4.77 % / Biso Wilson estimate: 29.72 Å2 / Rmerge(I) obs: 0.049 / Net I/σ(I): 17.27
Reflection shellResolution: 1.96→2.02 Å / Redundancy: 4.34 % / Rmerge(I) obs: 0.338 / Mean I/σ(I) obs: 4.8 / % possible all: 95.7

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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: 1.96→43.248 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / Phase error: 25.07
RfactorNum. reflection% reflectionSelection details
Rfree0.2376 4431 5.01 %Random selection
Rwork0.1964 ---
obs0.1985 88529 99.48 %-
Solvent computationShrinkage radii: 1.1 Å / VDW probe radii: 1.4 Å
Displacement parametersBiso mean: 36.04 Å2
Refinement stepCycle: LAST / Resolution: 1.96→43.248 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7798 0 14 661 8473
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0188052
X-RAY DIFFRACTIONf_angle_d1.52411046
X-RAY DIFFRACTIONf_dihedral_angle_d12.6462930
X-RAY DIFFRACTIONf_chiral_restr0.1081304
X-RAY DIFFRACTIONf_plane_restr0.0061459
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.96-1.98230.30541390.26842536X-RAY DIFFRACTION91
1.9823-2.00560.2811420.2282744X-RAY DIFFRACTION98
2.0056-2.03010.29351470.22572784X-RAY DIFFRACTION100
2.0301-2.05580.24231490.22272798X-RAY DIFFRACTION100
2.0558-2.08280.28291480.22292823X-RAY DIFFRACTION100
2.0828-2.11140.29631460.21082760X-RAY DIFFRACTION100
2.1114-2.14150.261450.2052787X-RAY DIFFRACTION100
2.1415-2.17350.27161480.20812814X-RAY DIFFRACTION100
2.1735-2.20750.27281490.2032829X-RAY DIFFRACTION100
2.2075-2.24360.25171480.20972807X-RAY DIFFRACTION100
2.2436-2.28230.24491480.19412825X-RAY DIFFRACTION100
2.2823-2.32380.21841470.19282779X-RAY DIFFRACTION100
2.3238-2.36850.22681470.20042784X-RAY DIFFRACTION100
2.3685-2.41690.28111490.20572836X-RAY DIFFRACTION100
2.4169-2.46940.26761490.20752824X-RAY DIFFRACTION100
2.4694-2.52680.29071470.21382797X-RAY DIFFRACTION100
2.5268-2.590.26921490.21772810X-RAY DIFFRACTION100
2.59-2.660.24461460.21712804X-RAY DIFFRACTION100
2.66-2.73830.2691500.22532831X-RAY DIFFRACTION100
2.7383-2.82670.28111480.22192800X-RAY DIFFRACTION100
2.8267-2.92770.28251480.21832817X-RAY DIFFRACTION100
2.9277-3.04490.25551470.21652794X-RAY DIFFRACTION100
3.0449-3.18340.25511480.22122819X-RAY DIFFRACTION100
3.1834-3.35120.24841490.20712847X-RAY DIFFRACTION100
3.3512-3.56110.23681480.19372826X-RAY DIFFRACTION100
3.5611-3.83590.23951490.1832834X-RAY DIFFRACTION100
3.8359-4.22160.19651490.16682834X-RAY DIFFRACTION100
4.2216-4.83180.18191500.15822832X-RAY DIFFRACTION100
4.8318-6.08480.20361520.17072866X-RAY DIFFRACTION100
6.0848-43.25880.20471500.19012857X-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)
11.33060.3583-0.19391.5472-0.55821.47910.0122-0.10710.08490.144-0.0255-0.0385-0.15970.1777-0.02920.1358-0.03540.00380.1210.00050.126852.346431.733723.4562
21.2193-0.08070.45121.5076-0.51991.27730.05360.0723-0.1223-0.2727-0.0494-0.11980.31490.25-0.02590.23010.04150.02260.129-0.00310.135952.368710.460922.8725
31.3931-0.2125-0.10891.57290.26071.337-0.03590.09390.10640.00090.10630.0515-0.2024-0.1247-0.0770.1375-0.0231-0.01660.1750.00450.116814.063331.533516.9015
41.39380.14810.01491.72980.27351.0112-0.0342-0.0818-0.15810.18340.05810.12060.2798-0.1773-0.04480.1819-0.01090.00310.19660.00670.134813.542910.326420.4171
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 1:259 )A1 - 259
2X-RAY DIFFRACTION2( CHAIN B AND RESID 1:259 )B1 - 259
3X-RAY DIFFRACTION3( CHAIN C AND RESID 1:260 )C1 - 260
4X-RAY DIFFRACTION4( CHAIN D AND RESID 1:259 )D1 - 259

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