[English] 日本語
Yorodumi
- PDB-4rck: Crystal Structure of Uncharacterized Membrane Spanning Protein fr... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4rck
TitleCrystal Structure of Uncharacterized Membrane Spanning Protein from Vibrio fischeri
ComponentsHypothetical membrane spanning protein
KeywordsMEMBRANE PROTEIN / Structural Genomics / PSI-Biology / Midwest Center for Structural Genomics / MCSG / alpha-beta fold / alpha-beta-alpha sandwich
Function / homology
Function and homology information


membrane => GO:0016020
Similarity search - Function
von Willebrand factor domain BatA-type / von Willebrand factor, type A domain / von Willebrand factor type A domain / von Willebrand factor (vWF) type A domain / VWFA domain profile. / von Willebrand factor, type A / von Willebrand factor A-like domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Hypothetical membrane spanning protein
Similarity search - Component
Biological speciesVibrio fischeri (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.999 Å
AuthorsKim, Y. / Tesar, C. / Bearden, J. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal Structure of Uncharacterized Membrane Spanning Protein from Vibrio fischeri
Authors: Kim, Y. / Tesar, C. / Bearden, J. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
History
DepositionSep 16, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 26, 2014Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Hypothetical membrane spanning protein
B: Hypothetical membrane spanning protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,0684
Polymers49,0192
Non-polymers492
Water1086
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7860 Å2
ΔGint-61 kcal/mol
Surface area18730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.734, 49.734, 343.880
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

-
Components

#1: Protein Hypothetical membrane spanning protein / VWA BatA type


Mass: 24509.545 Da / Num. of mol.: 2 / Fragment: VWA BatA type domain (UNP residues 68-284)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio fischeri (bacteria) / Strain: ES114 / Gene: VF_A0681 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) gold / References: UniProt: Q5DZP5
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / 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: 2.5 Å3/Da / Density % sol: 50.89 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2 M Magnesium formate, 20 %(w/v) PEG3350, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 21, 2011 / Details: mirrors
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. all: 9679 / Num. obs: 9679 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 12.5 % / Biso Wilson estimate: 83.56 Å2 / Rsym value: 0.113 / Net I/σ(I): 9.8
Reflection shellResolution: 3→3.05 Å / Redundancy: 11.8 % / Mean I/σ(I) obs: 3.7 / Num. unique all: 508 / Rsym value: 0.788 / % possible all: 100

-
Processing

Software
NameVersionClassification
SBC-Collectdata collection
HKL-3000data collection
HKL-3000phasing
SHELXSphasing
MLPHAREphasing
DMmodel building
PHENIX(phenix.refine: dev_1745)refinement
HKL-3000data reduction
HKL-3000data scaling
DMphasing
RefinementMethod to determine structure: SAD / Resolution: 2.999→38.508 Å / Isotropic thermal model: mixed / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 26.3 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflectionSelection details
Rfree0.237 461 4.81 %random
Rwork0.195 ---
all0.197 9583 --
obs0.197 9583 99.72 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 95.9 Å2
Refinement stepCycle: LAST / Resolution: 2.999→38.508 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3129 0 2 6 3137
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053207
X-RAY DIFFRACTIONf_angle_d0.8454337
X-RAY DIFFRACTIONf_dihedral_angle_d17.781194
X-RAY DIFFRACTIONf_chiral_restr0.034505
X-RAY DIFFRACTIONf_plane_restr0.004576
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / % reflection obs: 95 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs
3.0018-3.43370.29761440.271530253169
3.4337-4.31670.25661560.200330173171
4.3167-18.30980.20911610.170730323193
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)
14.2498-1.00711.07415.0408-3.28173.6752-0.35880.1829-0.3687-0.08430.0049-0.92040.41590.93660.30340.84010.3216-0.0970.7088-0.06230.8629-16.818544.5142-25.7003
24.1145-0.66541.40554.5922-1.86856.4140.3463-0.1161-0.2993-0.3611-0.06480.50440.3896-0.1393-0.38280.61890.11280.0020.47090.03490.582-0.68212.70233.189
37.4788-0.80892.48236.3961-1.74486.43380.03340.08961.1955-0.0551-0.15040.1284-0.6992-0.5920.23960.6860.19560.0540.69510.10130.5511-1.24624.72944.6936
44.28770.32470.01684.8285-1.8485.9763-0.1701-0.40450.157-0.07560.58750.30510.2171-0.3397-0.22520.6630.1793-0.1040.57960.00820.639-28.309950.8247-23.8302
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 14 through 115 )
2X-RAY DIFFRACTION2chain 'A' and (resid 116 through 217 )
3X-RAY DIFFRACTION3chain 'B' and (resid 14 through 115 )
4X-RAY DIFFRACTION4chain 'B' and (resid 116 through 217 )

+
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