[English] 日本語
Yorodumi
- PDB-1v8o: Crystal Structure of PAE2754 from Pyrobaculum aerophilum -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1v8o
TitleCrystal Structure of PAE2754 from Pyrobaculum aerophilum
Componentshypothetical protein PAE2754
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / PIN-domain / SeMet substituted
Function / homology
Function and homology information


exonuclease activity / RNA nuclease activity / Hydrolases; Acting on ester bonds / magnesium ion binding
Similarity search - Function
Pae0151-like, PIN domain / : / PIN domain / VapC family / 5'-nuclease / PIN domain / PIN-like domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesPyrobaculum aerophilum (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD with data collection on Se-Met crystal at 0.97941 A / Resolution: 2.8 Å
AuthorsArcus, V.L. / Backbro, K. / Roos, A. / Daniel, E.L. / Baker, E.N.
CitationJournal: J.Biol.Chem. / Year: 2004
Title: Distant structural homology leads to the functional characterization of an archaeal PIN domain as an exonuclease
Authors: Arcus, V.L. / Backbro, K. / Roos, A. / Daniel, E.L. / Baker, E.N.
History
DepositionJan 12, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 10, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 14, 2018Group: Advisory / Database references / Category: pdbx_unobs_or_zero_occ_atoms / struct_ref_seq_dif / Item: _struct_ref_seq_dif.details
Revision 1.4Nov 10, 2021Group: Advisory / Database references / Derived calculations
Category: database_2 / pdbx_unobs_or_zero_occ_atoms ...database_2 / pdbx_unobs_or_zero_occ_atoms / 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_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_PDB_ins_code / _struct_conn.pdbx_ptnr2_PDB_ins_code / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.6Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: hypothetical protein PAE2754
B: hypothetical protein PAE2754
C: hypothetical protein PAE2754
D: hypothetical protein PAE2754
E: hypothetical protein PAE2754
F: hypothetical protein PAE2754
G: hypothetical protein PAE2754
H: hypothetical protein PAE2754
hetero molecules


Theoretical massNumber of molelcules
Total (without water)145,60812
Polymers145,4668
Non-polymers1424
Water1,18966
1
A: hypothetical protein PAE2754
B: hypothetical protein PAE2754
C: hypothetical protein PAE2754
D: hypothetical protein PAE2754
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,8046
Polymers72,7334
Non-polymers712
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8140 Å2
ΔGint-79 kcal/mol
Surface area22790 Å2
MethodPISA
2
E: hypothetical protein PAE2754
F: hypothetical protein PAE2754
G: hypothetical protein PAE2754
H: hypothetical protein PAE2754
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,8046
Polymers72,7334
Non-polymers712
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8220 Å2
ΔGint-79 kcal/mol
Surface area22670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.360, 192.780, 60.440
Angle α, β, γ (deg.)90.00, 94.68, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe biological assembly is a tetramer. There are two tetramers in the asymmetric unit.

-
Components

#1: Protein
hypothetical protein PAE2754


Mass: 18183.279 Da / Num. of mol.: 8 / Mutation: P2A, L65M, L80M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrobaculum aerophilum (archaea) / Gene: PAE2754 / Plasmid: pPROEX / Production host: Escherichia coli (E. coli) / Strain (production host): DL41(DE3) / References: UniProt: Q8ZUJ3
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 66 / 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: 2.75 Å3/Da / Density % sol: 54.96 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 9.2
Details: Tris-HCl, isopropanol, PEG 4000, trimethylamine-HCl, pH 9.2, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop / Details: Arcus, V.L., (2004) Acta Cryst., D60, 733.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
15-10 mg/mlprotein1drop
250 mMTris-HCl1droppH9.2
350 mM1dropNaCl
4100 mMTris-HCl1reservoirpH9.2
525-30 %2-propanol1reservoir
617-20 %PEG40001reservoir
710 mMtrimethylamine-HCl1reservoir

-
Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.97941, 0.83208
DetectorType: ADSC QUANTUM 4r / Detector: CCD / Date: Feb 26, 2003
RadiationMonochromator: Curved crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979411
20.832081
ReflectionResolution: 2.75→40 Å / Num. all: 62023 / Num. obs: 32550 / % possible obs: 96.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.8 % / Biso Wilson estimate: 15.8 Å2 / Rmerge(I) obs: 0.103 / Net I/σ(I): 10.7
Reflection shellResolution: 2.75→2.85 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.319 / Mean I/σ(I) obs: 1.9 / Num. unique all: 2444 / % possible all: 72.7
Reflection
*PLUS
Num. measured all: 286429
Reflection shell
*PLUS
% possible obs: 72.7 %

-
Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: SAD with data collection on Se-Met crystal at 0.97941 A
Resolution: 2.8→36.58 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 1623333.4 / 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
Rfree0.279 2853 4.8 %RANDOM
Rwork0.226 ---
all0.229 32550 --
obs0.226 32550 94.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 31.6186 Å2 / ksol: 0.34703 e/Å3
Displacement parametersBiso mean: 35.6 Å2
Baniso -1Baniso -2Baniso -3
1-3.41 Å20 Å23.06 Å2
2---2.93 Å20 Å2
3----0.48 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.47 Å0.37 Å
Luzzati d res low-5 Å
Luzzati sigma a0.56 Å0.49 Å
Refinement stepCycle: LAST / Resolution: 2.8→36.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8424 0 4 66 8494
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d20.3
X-RAY DIFFRACTIONc_improper_angle_d0.77
X-RAY DIFFRACTIONc_mcbond_it6.191.5
X-RAY DIFFRACTIONc_mcangle_it9.612
X-RAY DIFFRACTIONc_scbond_it8.972
X-RAY DIFFRACTIONc_scangle_it12.642.5
LS refinement shellResolution: 2.8→2.98 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.353 392 4.8 %
Rwork0.327 7753 -
obs-7753 78.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2ION.PARAMION.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
Refinement
*PLUS
Highest resolution: 2.8 Å / Lowest resolution: 40 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg20.3
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.77

+
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