[English] 日本語
Yorodumi
- PDB-1l5x: The 2.0-Angstrom resolution crystal structure of a survival prote... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1l5x
TitleThe 2.0-Angstrom resolution crystal structure of a survival protein E (SurE) homolog from Pyrobaculum aerophilum
ComponentsSurvival protein E
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / putative acid phosphatase / mixed alpha/beta protein / N-terminal Rossmann-fold like / novel C-terminal domain with beta-hairpin extensions
Function / homology
Function and homology information


5'-deoxynucleotidase 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
ACETIC ACID / 5'-nucleotidase SurE 1
Similarity search - Component
Biological speciesPyrobaculum aerophilum (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å
AuthorsMura, C. / Katz, J.E. / Clarke, S.G. / Eisenberg, D.
Citation
Journal: J.Mol.Biol. / Year: 2003
Title: Structure and Function of an Archaeal Homolog of Survival Protein E (SurE-alpha): An Acid Phosphatase with Purine Nucleotide Specificity
Authors: Mura, C. / Katz, J.E. / Clarke, S.G. / Eisenberg, D.
#1: Journal: Nat.Struct.Biol. / Year: 2001
Title: Crystal Structure and Functional Analysis of the SurE Protein Identify a Novel Phosphatase Family
Authors: Lee, J.Y. / Kwak, J.E. / Moon, J. / Eom, S.H. / Liong, E.C. / Pedelacq, J.-D. / Berendzen, J. / Suh, S.W.
#2: Journal: Structure / Year: 2001
Title: Structure of Thermotoga maritima Stationary Phase Survival Protein SurE: A Novel Acid Phosphatase
Authors: Zhang, R.-G. / Skarina, T. / Katz, J.E. / Beasley, S. / Khachatryan, A. / Vyas, S. / Arrowsmith, C.H. / Clarke, S. / Edwards, A. / Joachimiak, A.
History
DepositionMar 8, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 25, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 400COMPOUND THE FIRST STRUCTURE OF AN ARCHAEAL SURE, WITH STRONG SIMILARITY TO THE PROKARYOTIC SURE ...COMPOUND THE FIRST STRUCTURE OF AN ARCHAEAL SURE, WITH STRONG SIMILARITY TO THE PROKARYOTIC SURE STRUCTURE FROM THERMATOGA MARITIMA (SEE RELATED ENTRIES).
Remark 999SEQUENCE THE ADDITIONAL RESIDUES FROM SER 267 ONWARDS ARE CLONING ARTIFACTS (HIS-TAG AND LINKER).

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Survival protein E
B: Survival protein E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,30111
Polymers61,5372
Non-polymers7659
Water5,170287
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7600 Å2
ΔGint-48 kcal/mol
Surface area21860 Å2
MethodPISA
2
A: Survival protein E
B: Survival protein E
hetero molecules

A: Survival protein E
B: Survival protein E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,60322
Polymers123,0734
Non-polymers1,53018
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_675x-y+1,-y+2,-z+2/31
Buried area19960 Å2
ΔGint-108 kcal/mol
Surface area38970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.500, 90.500, 129.951
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
DetailsThe biological assembly is thought to be the dimer found in the asymmetric unit of this deposition.

-
Components

#1: Protein Survival protein E / surE stationary-phase survival protein homolog


Mass: 30768.275 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrobaculum aerophilum (archaea) / Gene: PAE2908 / Plasmid: pET-22b(+) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q8ZU79
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H4O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 287 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.5 Å3/Da / Density % sol: 50.71 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.55
Details: PEG 4000, sodium acetate, glycerol, Tris buffer, pH 8.55, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Crystal grow
*PLUS
Temperature: 19.8 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
111.4 mg/mlprotein1drop
20.083 MTris1reservoirpH8.55
321.7 %(v/v)PEG40001reservoir
40.17 Msodium acetate1reservoir
515 %(v/v)glycerol1reservoir

-
Data collection

DiffractionMean temperature: 105 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.97870, 0.97860, 0.96485
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 18, 2002
RadiationMonochromator: double crystal monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97871
20.97861
30.964851
ReflectionResolution: 2→100 Å / Num. all: 42129 / Num. obs: 42129 / % possible obs: 99.9 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 7.1 % / Biso Wilson estimate: 18.1 Å2 / Rmerge(I) obs: 0.099 / Rsym value: 0.099 / Net I/σ(I): 17.4
Reflection shellResolution: 2→2.07 Å / Redundancy: 7 % / Rmerge(I) obs: 0.781 / Mean I/σ(I) obs: 2.5 / Rsym value: 0.781 / % possible all: 100
Reflection
*PLUS
Lowest resolution: 100 Å / Num. measured all: 297069
Reflection shell
*PLUS
% possible obs: 100 %

-
Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
MLPHAREphasing
CNS1.1refinement
RefinementMethod to determine structure: MAD / Resolution: 2→19.59 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 195285.23 / 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
Rfree0.223 2033 5 %RANDOM
Rwork0.185 ---
all-40410 --
obs-40410 95.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 61.4539 Å2 / ksol: 0.393386 e/Å3
Displacement parametersBiso mean: 37.3 Å2
Baniso -1Baniso -2Baniso -3
1-3.75 Å23.86 Å20 Å2
2--3.75 Å20 Å2
3----7.5 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.27 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.25 Å0.22 Å
Refinement stepCycle: LAST / Resolution: 2→19.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4230 0 50 287 4567
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.014
X-RAY DIFFRACTIONc_angle_deg1.8
X-RAY DIFFRACTIONc_dihedral_angle_d24.2
X-RAY DIFFRACTIONc_improper_angle_d1.08
X-RAY DIFFRACTIONc_mcbond_it1.681.5
X-RAY DIFFRACTIONc_mcangle_it2.662
X-RAY DIFFRACTIONc_scbond_it2.572
X-RAY DIFFRACTIONc_scangle_it3.872.5
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.279 305 4.9 %
Rwork0.269 5886 -
obs--89.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3GOL.PARAMGOL.TOP
X-RAY DIFFRACTION4ACY.PARAMACY.TOP
Refinement
*PLUS
Highest resolution: 2 Å / Lowest resolution: 20 Å / % reflection Rfree: 4.6 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.79
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24.2
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.08

+
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