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- PDB-5kst: Stationary phase Survival protein E (SurE) from Xylella fastidios... -

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Basic information

Entry
Database: PDB / ID: 5kst
TitleStationary phase Survival protein E (SurE) from Xylella fastidiosa- XfSurE-TSAmp (Tetramer Smaller - crystallization with 3'AMP).
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 / : / PHOSPHATE ION / 5'-nucleotidase SurE
Similarity search - Component
Biological speciesXylella fastidiosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.759 Å
AuthorsMachado, A.T.P. / Fonseca, E.M.B. / Dos Reis, M.A. / Saraiva, A.M. / Dos Santos, C.A. / De Toledo, M.A.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 / 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)119,32118
Polymers117,9604
Non-polymers1,36114
Water3,567198
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22140 Å2
ΔGint-171 kcal/mol
Surface area36440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)157.001, 78.209, 82.158
Angle α, β, γ (deg.)90.00, 96.74, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
12
22

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111chain A and ( ( resseq 1:129 or resseq 134:256...
211chain B and ( ( resseq 1:129 or resseq 134:256...
112chain C and ( ( resseq 1:126 or resseq 135:244...
212chain D and ( ( resseq 1:126 or resseq 135:244...

NCS ensembles :
ID
1
2

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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-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 198 / 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: 2.21 Å3/Da / Density % sol: 44.26 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.6
Details: 0.1 M bis-tris propane pH 7.6, 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: 1.428 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: 1.428 Å / Relative weight: 1
ReflectionResolution: 2.76→77.957 Å / Num. obs: 24993 / % possible obs: 97.4 % / Observed criterion σ(I): -3 / Redundancy: 5.47 % / Rsym value: 0.096 / Net I/σ(I): 16.58
Reflection shellResolution: 2.76→2.84 Å / Redundancy: 5.13 % / Rmerge(I) obs: 0.574 / Mean I/σ(I) obs: 3.4 / % possible all: 92.1

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDS30/03/2013data reduction
XSCALE30/03/2013data scaling
PHASER2.3.0phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3TY2

3ty2


Resolution: 2.759→77.957 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.42 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2483 1254 5.02 %Random selection
Rwork0.1965 ---
obs0.1991 24988 97.45 %-
Solvent computationShrinkage radii: 0.7 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.759→77.957 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7763 0 30 198 7991
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0057989
X-RAY DIFFRACTIONf_angle_d0.8210941
X-RAY DIFFRACTIONf_dihedral_angle_d11.5242875
X-RAY DIFFRACTIONf_chiral_restr0.0281289
X-RAY DIFFRACTIONf_plane_restr0.0041440
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A1819X-RAY DIFFRACTIONPOSITIONAL
12B1819X-RAY DIFFRACTIONPOSITIONAL0.053
21C1636X-RAY DIFFRACTIONPOSITIONAL
22D1636X-RAY DIFFRACTIONPOSITIONAL0.023
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.759-2.86940.33721350.26632502X-RAY DIFFRACTION94
2.8694-30.30711410.25862635X-RAY DIFFRACTION97
3-3.15820.27211400.23712615X-RAY DIFFRACTION97
3.1582-3.35610.2971390.21522617X-RAY DIFFRACTION97
3.3561-3.61520.29051370.20152610X-RAY DIFFRACTION98
3.6152-3.9790.24021400.18152667X-RAY DIFFRACTION98
3.979-4.55470.20061430.1672682X-RAY DIFFRACTION98
4.5547-5.73820.23961380.18372680X-RAY DIFFRACTION99
5.7382-77.98860.20241410.17752726X-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)
11.2340.2823-0.27521.5177-0.94171.88970.1066-0.20580.45060.215-0.00340.0912-0.23190.112-0.02920.3102-0.02440.01070.2171-0.05690.34347.644432.67122.5685
21.9484-0.24040.20321.2565-0.63972.0246-0.01860.0503-0.1981-0.18960.09510.05960.40780.0361-0.02570.4701-0.0101-0.04370.2424-0.02990.236947.56125.901520.9504
31.978-0.4295-0.37161.74680.37363.16570.0010.16280.2071-0.18320.0495-0.0215-0.2778-0.2972-0.04860.3262-0.0057-0.05860.32710.00650.263813.054132.874315.0088
41.7877-0.2524-0.26151.26420.70361.818-0.0976-0.1215-0.34780.506-0.07570.24380.7062-0.30410.08770.6062-0.09410.05270.3558-0.0240.364611.19186.871218.9063
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 1:237 ) OR ( CHAIN B AND RESID 238:259 )A1 - 237
2X-RAY DIFFRACTION1( CHAIN A AND RESID 1:237 ) OR ( CHAIN B AND RESID 238:259 )B238 - 259
3X-RAY DIFFRACTION2( CHAIN A AND RESID 238:259 ) OR ( CHAIN B AND RESID 1:237 )A238 - 259
4X-RAY DIFFRACTION2( CHAIN A AND RESID 238:259 ) OR ( CHAIN B AND RESID 1:237 )B1 - 237
5X-RAY DIFFRACTION3( CHAIN C AND RESID 1:237 ) OR ( CHAIN D AND RESID 238:259 )C1 - 237
6X-RAY DIFFRACTION3( CHAIN C AND RESID 1:237 ) OR ( CHAIN D AND RESID 238:259 )D238 - 259
7X-RAY DIFFRACTION4( CHAIN C AND RESID 238:257 ) OR ( CHAIN D AND RESID 1:237 )C238 - 257
8X-RAY DIFFRACTION4( CHAIN C AND RESID 238:257 ) OR ( CHAIN D AND RESID 1:237 )D1 - 237

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