[English] 日本語
Yorodumi
- PDB-2e69: Crystal structure of the stationary phase survival protein SurE f... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2.0E+69
TitleCrystal structure of the stationary phase survival protein SurE from Thermus thermophilus HB8 in complex with sulfate
Components5'-nucleotidase surE
KeywordsHYDROLASE / SurE protein
Function / homology
Function and homology information


XMP 5'-nucleosidase activity / 5'-nucleotidase / nucleotide 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
5'-nucleotidase SurE
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsIwasaki, W. / Miki, K.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: Crystal Structure of the Stationary Phase Survival Protein SurE with Metal Ion and AMP
Authors: Iwasaki, W. / Miki, K.
History
DepositionDec 26, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 28, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Derived calculations / Source and taxonomy / Version format compliance
Revision 1.2Oct 25, 2023Group: Data collection / Database references ...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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 300BIOMOLECULE 1 This entry contains the crystallographic asymmetric unit which consists of 4 chain(s) ...BIOMOLECULE 1 This entry contains the crystallographic asymmetric unit which consists of 4 chain(s) forming a tetramer. This protein is in a dimer-tetramer equilibrium in solution. It is unknown whether this protein is functional as a dimer or a tetramer.

-
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)108,03020
Polymers106,5014
Non-polymers1,52916
Water3,909217
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19040 Å2
ΔGint-337 kcal/mol
Surface area35820 Å2
MethodPISA, PQS
2
A: 5'-nucleotidase surE
B: 5'-nucleotidase surE
C: 5'-nucleotidase surE
D: 5'-nucleotidase surE
hetero molecules

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)216,06040
Polymers213,0028
Non-polymers3,05832
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_554x-y,-y,-z-1/31
Buried area40880 Å2
ΔGint-684 kcal/mol
Surface area68840 Å2
MethodPISA
3
A: 5'-nucleotidase surE
B: 5'-nucleotidase surE
C: 5'-nucleotidase surE
D: 5'-nucleotidase surE
hetero molecules

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)216,06040
Polymers213,0028
Non-polymers3,05832
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area39610 Å2
ΔGint-680 kcal/mol
Surface area70120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)131.825, 131.825, 131.209
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Detailsprobably tetramer

-
Components

#1: Protein
5'-nucleotidase surE / Stationary Phase Survival Protein SurE / Nucleoside 5'-monophosphate phosphohydrolase


Mass: 26625.287 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Plasmid: pET11a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q53W92, 5'-nucleotidase
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 217 / 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: 3.09 Å3/Da / Density % sol: 60.16 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 8.5
Details: 0.1M Tris-HCl pH8.5, 0.75M ammonium sulhate, 10% glycerol, VAPOR DIFFUSION, temperature 293K

-
Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44B2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Apr 14, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 67207 / % possible obs: 99.9 % / Biso Wilson estimate: 24.6 Å2 / Rmerge(I) obs: 0.047 / Net I/σ(I): 16.4
Reflection shellResolution: 2.2→2.28 Å / Rmerge(I) obs: 0.302 / Mean I/σ(I) obs: 7 / % possible all: 100

-
Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1ILV

1ilv


Resolution: 2.2→43.06 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 3080294.27 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.23 3412 5.1 %RANDOM
Rwork0.195 ---
obs0.195 67111 99.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 40.9784 Å2 / ksol: 0.37035 e/Å3
Displacement parametersBiso mean: 36.8 Å2
Baniso -1Baniso -2Baniso -3
1-3.7 Å23.92 Å20 Å2
2--3.7 Å20 Å2
3----7.4 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.3 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.2 Å0.14 Å
Refinement stepCycle: LAST / Resolution: 2.2→43.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7251 0 82 217 7550
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d24.7
X-RAY DIFFRACTIONc_improper_angle_d1.02
X-RAY DIFFRACTIONc_mcbond_it3.061.5
X-RAY DIFFRACTIONc_mcangle_it4.092
X-RAY DIFFRACTIONc_scbond_it4.762
X-RAY DIFFRACTIONc_scangle_it5.992.5
LS refinement shellResolution: 2.2→2.34 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.258 568 5.1 %
Rwork0.211 10465 -
obs--100 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2cis_peptide.paramion.top
X-RAY DIFFRACTION3ion.paramwater.top
X-RAY DIFFRACTION4water_rep.paramgol.top
X-RAY DIFFRACTION5gol.param

+
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