[English] 日本語
Yorodumi
- PDB-3dnx: SPO1766 protein of unknown function from Silicibacter pomeroyi. -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3dnx
TitleSPO1766 protein of unknown function from Silicibacter pomeroyi.
Componentsuncharacterized protein SPO1766
Keywordsstructural genomics / unknown function / APC88088 / protein of unknown function / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homologyDNA repair protein MmcB-like / DNA repair protein MmcB-like / tRNA endonuclease-like domain superfamily / nuclease activity / Restriction endonuclease type II-like / nucleic acid binding / Uncharacterized protein
Function and homology information
Biological speciesSilicibacter pomeroyi (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.94 Å
AuthorsOsipiuk, J. / Mulligan, R. / Clancy, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: X-ray crystal structure of SPO1766 protein of unknown function from Silicibacter pomeroyi.
Authors: Osipiuk, J. / Mulligan, R. / Clancy, S. / Joachimiak, A.
History
DepositionJul 2, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 2, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: uncharacterized protein SPO1766
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,5493
Polymers17,5031
Non-polymers462
Water2,180121
1
A: uncharacterized protein SPO1766
hetero molecules

A: uncharacterized protein SPO1766
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,0996
Polymers35,0072
Non-polymers924
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_755-x+2,y,-z1
Buried area3420 Å2
ΔGint-53 kcal/mol
Surface area15350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.892, 59.892, 99.868
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number91
Space group name H-MP4122
Components on special symmetry positions
IDModelComponents
11A-246-

HOH

21A-273-

HOH

31A-292-

HOH

Detailsputative biological unit is a dimer

-
Components

#1: Protein uncharacterized protein SPO1766


Mass: 17503.332 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Silicibacter pomeroyi (bacteria) / Strain: DSS-3 / Gene: SPO1766 / Plasmid: pMCSG19b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q5LSK1
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 121 / 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: 2.56 Å3/Da / Density % sol: 51.92 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.2
Details: 2.5 M sodium chloride, 0.1 M sodium/potassium phosphate buffer, pH 6.2, VAPOR DIFFUSION, SITTING DROP, temperature 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 15, 2008
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.94→39 Å / Num. all: 14100 / Num. obs: 14100 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.8 % / Biso Wilson estimate: 39.1 Å2 / Rmerge(I) obs: 0.106 / Χ2: 1.585 / Net I/σ(I): 10.2
Reflection shellResolution: 1.94→1.97 Å / Redundancy: 11.1 % / Rmerge(I) obs: 0.82 / Mean I/σ(I) obs: 3.01 / Num. unique all: 680 / Χ2: 0.95 / % possible all: 100

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.006data extraction
SBC-Collectdata collection
HKL-3000data reduction
SHELXDphasing
MLPHAREphasing
DMphasing
SOLVEphasing
RESOLVEphasing
HKL-3000phasing
RefinementMethod to determine structure: SAD / Resolution: 1.94→39 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.941 / Occupancy max: 1 / Occupancy min: 0.27 / FOM work R set: 0.888 / SU B: 6.068 / SU ML: 0.093 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.138 / ESU R Free: 0.133 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.213 698 5 %RANDOM
Rwork0.172 ---
all0.174 14043 --
obs0.174 14043 99.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 60.85 Å2 / Biso mean: 34.766 Å2 / Biso min: 13.98 Å2
Baniso -1Baniso -2Baniso -3
1--0.73 Å20 Å20 Å2
2---0.73 Å20 Å2
3---1.46 Å2
Refinement stepCycle: LAST / Resolution: 1.94→39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1166 0 2 121 1289
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0221240
X-RAY DIFFRACTIONr_bond_other_d0.0020.02884
X-RAY DIFFRACTIONr_angle_refined_deg1.5231.9551687
X-RAY DIFFRACTIONr_angle_other_deg0.9632133
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1345158
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.35922.92365
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.65515213
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.4571514
X-RAY DIFFRACTIONr_chiral_restr0.0880.2174
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021415
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02275
X-RAY DIFFRACTIONr_nbd_refined0.2090.2241
X-RAY DIFFRACTIONr_nbd_other0.2090.2920
X-RAY DIFFRACTIONr_nbtor_refined0.1770.2569
X-RAY DIFFRACTIONr_nbtor_other0.0940.2686
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.230.283
X-RAY DIFFRACTIONr_metal_ion_refined0.1220.23
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1150.210
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3170.253
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.110.213
X-RAY DIFFRACTIONr_mcbond_it0.8921.5748
X-RAY DIFFRACTIONr_mcbond_other0.2371.5301
X-RAY DIFFRACTIONr_mcangle_it1.57221197
X-RAY DIFFRACTIONr_scbond_it2.3173514
X-RAY DIFFRACTIONr_scangle_it3.774.5483
LS refinement shellResolution: 1.941→1.991 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.254 49 -
Rwork0.221 943 -
all-992 -
obs-992 99.9 %
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)
131.3298-0.96185.259421.6327-22.552543.17880.5557-0.6166-3.8593-1.2913-0.1367-1.20693.30751.4024-0.4190.0517-0.00380.01160.14140.10330.197844.806329.90527.6245
23.9730.4478-0.69392.9847-1.19520.54640.1733-0.82160.51790.4597-0.0267-0.0702-0.11510.1884-0.1466-0.1152-0.01960.02770.0853-0.0603-0.029245.61945.89546.8117
34.935-1.9668-0.1061.17571.01332.40890.0182-0.24920.4201-0.33690.06010.0173-0.0742-0.0596-0.0783-0.1836-0.00960.03250.0119-0.0484-0.139436.491446.72733.8982
43.8905-1.8572-0.777210.48530.42620.15560.2154-0.59450.6081-0.0358-0.0579-0.03390.21820.233-0.1574-0.2198-0.04870.02860.0243-0.0861-0.043158.587550.23734.9116
56.55714.39679.19372.94816.164712.89060.1311-0.73670.45920.4537-0.33040.2778-0.8539-0.66530.19930.0693-0.00020.00160.07110.0697-0.013168.395834.80188.2345
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA5 - 128 - 15
2X-RAY DIFFRACTION2AA13 - 7516 - 78
3X-RAY DIFFRACTION3AA76 - 11779 - 120
4X-RAY DIFFRACTION4AA118 - 139121 - 142
5X-RAY DIFFRACTION5AA140 - 150143 - 153

+
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