[English] 日本語
Yorodumi
- PDB-3rob: The crystal structure of a conserved protein from Planctomyces li... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3rob
TitleThe crystal structure of a conserved protein from Planctomyces limnophilus DSM 3776
Componentsuncharacterized conserved protein
KeywordsStructural Genomics / unknown function / PSI-Biology / protein structure initiative / midwest center for structural genomics / MCSG
Function / homologyDomain of unknown function DUF4440 / Domain of unknown function (DUF4440) / Steroid delta5-4-isomerase / Nuclear Transport Factor 2; Chain: A, - #50 / NTF2-like domain superfamily / Nuclear Transport Factor 2; Chain: A, / Roll / Alpha Beta / DUF4440 domain-containing protein
Function and homology information
Biological speciesPlanctomyces limnophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.48 Å
AuthorsTan, K. / Li, H. / Bearden, J. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The crystal structure of a conserved protein from Planctomyces limnophilus DSM 3776
Authors: Tan, K. / Li, H. / Bearden, J. / Joachimiak, A.
History
DepositionApr 25, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 11, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: uncharacterized conserved protein
B: uncharacterized conserved protein
C: uncharacterized conserved protein
D: uncharacterized conserved protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,7388
Polymers63,3694
Non-polymers3684
Water12,250680
1
A: uncharacterized conserved protein
B: uncharacterized conserved protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,8694
Polymers31,6852
Non-polymers1842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2620 Å2
ΔGint-24 kcal/mol
Surface area13590 Å2
MethodPISA
2
C: uncharacterized conserved protein
D: uncharacterized conserved protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,8694
Polymers31,6852
Non-polymers1842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2740 Å2
ΔGint-25 kcal/mol
Surface area13260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.098, 68.098, 124.520
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31
DetailsExperimentally unknown. The chains A and B, C and D are predicted to form dimers, respectively.

-
Components

#1: Protein
uncharacterized conserved protein


Mass: 15842.309 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Planctomyces limnophilus (bacteria) / Strain: DSM 3776 / Gene: Plim_4131 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: D5SZ41
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 680 / 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: 2.63 Å3/Da / Density % sol: 53.24 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1M Tris:HCl, 15% (v/v) Ethanol, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97923 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 22, 2011 / Details: Mirror
RadiationMonochromator: Si 111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97923 Å / Relative weight: 1
ReflectionResolution: 1.48→30 Å / Num. all: 107855 / Num. obs: 107855 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.9 % / Rmerge(I) obs: 0.084 / Net I/σ(I): 38
Reflection shellResolution: 1.48→1.52 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.565 / Mean I/σ(I) obs: 2.8 / Num. unique all: 5291 / % possible all: 99.9

-
Processing

Software
NameVersionClassification
SBC-Collectdata collection
SHELXDphasing
MLPHAREphasing
DMmodel building
ARPmodel building
WARPmodel building
HKL-3000phasing
PHENIX(phenix.refine: 1.6.4_486)refinement
HKL-3000data reduction
HKL-3000data scaling
DMphasing
RefinementMethod to determine structure: SAD / Resolution: 1.48→29.487 Å / SU ML: 0.17 / σ(F): 0.01 / Phase error: 18.71 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1937 5254 5 %random
Rwork0.1722 ---
all0.1733 105018 --
obs0.1733 105018 97.29 %-
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 52.011 Å2 / ksol: 0.381 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.3448 Å2-0 Å2-0 Å2
2--0.3448 Å20 Å2
3----0.6896 Å2
Refinement stepCycle: LAST / Resolution: 1.48→29.487 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4154 0 24 680 4858
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074356
X-RAY DIFFRACTIONf_angle_d1.0765910
X-RAY DIFFRACTIONf_dihedral_angle_d14.4071637
X-RAY DIFFRACTIONf_chiral_restr0.068663
X-RAY DIFFRACTIONf_plane_restr0.005770
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4784-1.53130.24044290.23989222X-RAY DIFFRACTION90
1.5313-1.59260.24164840.20859657X-RAY DIFFRACTION94
1.5926-1.66510.22264810.19319850X-RAY DIFFRACTION96
1.6651-1.75280.20275320.17959950X-RAY DIFFRACTION97
1.7528-1.86270.18875700.169510011X-RAY DIFFRACTION98
1.8627-2.00640.19635480.171310228X-RAY DIFFRACTION99
2.0064-2.20830.1975460.170110213X-RAY DIFFRACTION100
2.2083-2.52770.20285650.171310264X-RAY DIFFRACTION100
2.5277-3.1840.20015590.177210221X-RAY DIFFRACTION100
3.184-29.49320.16955400.156310148X-RAY DIFFRACTION99
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)
11.20990.6669-0.09950.9777-0.45480.76230.0469-0.0750.16820.04590.00570.0971-0.0594-0.0376-0.04860.06250.00340.01630.0766-0.00960.07692.642252.957837.1694
20.85390.2161-0.10091.3881-0.36010.5519-0.00140.0287-0.1347-0.06250.0216-0.11570.127-0.0146-0.00930.09980.0049-0.01230.0694-0.01640.0929-7.986430.968640.5844
30.8796-0.57620.04830.9568-0.72340.94910.03690.0837-0.1552-0.09220.0446-0.00270.1098-0.0885-0.0650.0764-0.014-0.02160.09-0.02380.087536.594443.088536.5452
40.539-0.28580.53071.328-0.42250.5064-0.06830.02880.08290.05550.0065-0.1435-0.14470.00920.05680.108-0.01810.0030.0823-0.00390.083325.953464.875432.1311
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B
3X-RAY DIFFRACTION3chain C
4X-RAY DIFFRACTION4chain D

+
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://pdbjlvh1.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