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- PDB-5ksq: Stationary phase survival protein E (SurE) from Xylella fastidiosa -

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Basic information

Entry
Database: PDB / ID: 5ksq
TitleStationary phase survival protein E (SurE) from Xylella fastidiosa
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 / : / PHOSPHATE ION / 5'-nucleotidase SurE
Similarity search - Component
Biological speciesXylella fastidiosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.63 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. / 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 / Refinement description / Category: citation / software
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _software.classification
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_struct_conn_angle / 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 / _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.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.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

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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)59,6619
Polymers58,9802
Non-polymers6817
Water2,720151
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8840 Å2
ΔGint-87 kcal/mol
Surface area23580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.984, 85.160, 76.603
Angle α, β, γ (deg.)90.00, 94.46, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-627-

HOH

21A-646-

HOH

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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-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 151 / 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: 2.63 Å3/Da / Density % sol: 53.32 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1 M Bis-tris propane pH 7.6, 0.14 M sodium iodide, 20% (W/V) PEG 3350, 5 mM dihiothreitol and 0.1 M magnesium chloride.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.437 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: 1.437 Å / Relative weight: 1
ReflectionResolution: 2.63→42.58 Å / Num. all: 17166 / Num. obs: 17166 / % possible obs: 97.4 % / Redundancy: 7.5 % / Rsym value: 0.078 / Net I/σ(I): 19.05
Reflection shellResolution: 2.63→2.71 Å / Redundancy: 7.5 % / % possible all: 96.7

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Processing

Software
NameVersionClassification
PHENIX1.8.2_1309refinement
XDS30/03/2013data scaling
XSCALE30/03/2013data scaling
PHASER2.3.0phasing
Coot0.7.1model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3TY2

3ty2


Resolution: 2.63→42.58 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.14 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.274 842 4.91 %
Rwork0.2181 --
obs0.2208 17164 97.41 %
Solvent computationShrinkage radii: 1.1 Å / VDW probe radii: 1.4 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.63→42.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3861 0 15 151 4027
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023965
X-RAY DIFFRACTIONf_angle_d0.5195434
X-RAY DIFFRACTIONf_dihedral_angle_d8.0081432
X-RAY DIFFRACTIONf_chiral_restr0.034642
X-RAY DIFFRACTIONf_plane_restr0.003716
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.63-2.79470.37141480.29722698X-RAY DIFFRACTION98
2.7947-3.01040.3561330.28192807X-RAY DIFFRACTION100
3.0104-3.31330.3331460.26992770X-RAY DIFFRACTION100
3.3133-3.79250.29321410.22592757X-RAY DIFFRACTION100
3.7925-4.77710.24751270.18812459X-RAY DIFFRACTION87
4.7771-42.58560.22261470.18582831X-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)
11.23620.19160.19241.7384-0.27282.2748-0.1035-0.2071-0.3930.0770.094-0.35780.4540.17560.00380.32450.07160.00790.2513-0.00130.340951.33067.870356.341
21.54770.5969-0.32662.0372-0.04072.30520.1227-0.02230.20510.06130.07520.0312-0.41570.1181-0.14070.28940.0150.05780.21030.0260.243948.469235.794256.4045
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 238:258 ) OR ( CHAIN B AND RESID 1:237 )A238 - 258
2X-RAY DIFFRACTION1( CHAIN A AND RESID 238:258 ) OR ( CHAIN B AND RESID 1:237 )B1 - 237
3X-RAY DIFFRACTION2( CHAIN A AND RESID 1:237 ) OR ( CHAIN B AND RESID 238:259 )A1 - 237
4X-RAY DIFFRACTION2( CHAIN A AND RESID 1:237 ) OR ( CHAIN B AND RESID 238:259 )B238 - 259

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