[English] 日本語
Yorodumi
- PDB-5ksr: Stationary phase survival protein E (SurE) from Xylella fastidios... -

+
Open data


ID or keywords:

Loading...

-
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


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: 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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.

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more