[English] 日本語
Yorodumi
- PDB-9i2l: BtuJ2 - DUF4465 domain containing protein -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9i2l
TitleBtuJ2 - DUF4465 domain containing protein
ComponentsDUF4465 domain-containing protein
KeywordsMEMBRANE PROTEIN / Outer membrane / B12 binding / Lipoprotein
Function / homologyProtein of unknown function DUF4465 / Domain of unknown function (DUF4465) / Prokaryotic membrane lipoprotein lipid attachment site profile. / CYANOCOBALAMIN / DUF4465 domain-containing protein
Function and homology information
Biological speciesBacteroides thetaiotaomicron VPI-5482 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.73 Å
AuthorsClarke, C. / Banasik, M. / Pickersgill, R.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/X001946/1 United Kingdom
CitationJournal: To Be Published
Title: To be released (2024).
Authors: Juodeikis, R. / Ulrich, R. / Clarke, C. / Banasik, M. / Warren, M. / Pickersgill, R.
History
DepositionJan 21, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 5, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
B: DUF4465 domain-containing protein
A: DUF4465 domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,4136
Polymers67,6202
Non-polymers2,7934
Water95553
1
B: DUF4465 domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,2073
Polymers33,8101
Non-polymers1,3962
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: DUF4465 domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,2073
Polymers33,8101
Non-polymers1,3962
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)83.746, 97.98, 70.472
Angle α, β, γ (deg.)90, 90, 90
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11B
21A

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: THR / Beg label comp-ID: THR / End auth comp-ID: ILE / End label comp-ID: ILE / Auth seq-ID: 49 - 303 / Label seq-ID: 50 - 304

Dom-IDAuth asym-IDLabel asym-ID
1BA
2AB

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

-
Components

#1: Protein DUF4465 domain-containing protein


Mass: 33810.090 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Lipoprotein export sequence removed, His-tagged
Source: (gene. exp.) Bacteroides thetaiotaomicron VPI-5482 (bacteria)
Gene: BT_1957 / Plasmid: pET14b / Details (production host): Ampicillin resistance / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pLysS / References: UniProt: Q8A6C7
#2: Chemical ChemComp-CNC / CYANOCOBALAMIN


Mass: 1356.373 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C63H89CoN14O14P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 53 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.69 Å3/Da / Density % sol: 54.4 % / Description: Shards with a distinctly red color
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 3.5 / Details: 29% w/v PEG, 0.2M sodium citrate pH 3.5 / PH range: 3-4

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Feb 5, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873 Å / Relative weight: 1
ReflectionResolution: 1.6→81.09 Å / Num. obs: 66258 / % possible obs: 82 % / Redundancy: 4.4 % / Biso Wilson estimate: 13.12 Å2 / CC1/2: 0.968 / Rmerge(I) obs: 0.2 / Rpim(I) all: 0.1 / Rrim(I) all: 0.2 / Net I/σ(I): 1.7
Reflection shellResolution: 1.6→1.7 Å / Num. unique obs: 66258 / CC1/2: 0.381

-
Processing

Software
NameVersionClassification
REFMAC5.8.0430 (refmacat 0.4.88)refinement
autoPROC1.1.7data reduction
STARANISO2.3.94data scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.73→70.472 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.856 / WRfactor Rfree: 0.228 / WRfactor Rwork: 0.161 / SU B: 16.605 / SU ML: 0.317 / Average fsc free: 0.9457 / Average fsc work: 0.9685 / Cross valid method: THROUGHOUT / ESU R Free: 0.392
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2609 754 4.823 %
Rwork0.1849 14881 -
all0.188 --
obs-15635 97.89 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 38.391 Å2
Baniso -1Baniso -2Baniso -3
1--0.42 Å20 Å20 Å2
2--0.951 Å2-0 Å2
3----0.531 Å2
Refinement stepCycle: LAST / Resolution: 2.73→70.472 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4069 0 188 53 4310
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0124388
X-RAY DIFFRACTIONr_bond_other_d0.0030.0153786
X-RAY DIFFRACTIONr_angle_refined_deg2.5061.8466047
X-RAY DIFFRACTIONr_angle_other_deg1.0241.7798678
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.6335512
X-RAY DIFFRACTIONr_dihedral_angle_2_deg11.282510
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.95210598
X-RAY DIFFRACTIONr_dihedral_angle_6_deg13.82910216
X-RAY DIFFRACTIONr_chiral_restr0.1160.2617
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.025317
X-RAY DIFFRACTIONr_gen_planes_other0.0040.021127
X-RAY DIFFRACTIONr_nbd_refined0.2030.2827
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1780.23732
X-RAY DIFFRACTIONr_nbtor_refined0.1830.22168
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0830.22262
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1470.2110
X-RAY DIFFRACTIONr_metal_ion_refined0.3150.27
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1680.215
X-RAY DIFFRACTIONr_nbd_other0.1730.235
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1080.26
X-RAY DIFFRACTIONr_mcbond_it4.7513.7092060
X-RAY DIFFRACTIONr_mcbond_other4.7513.712060
X-RAY DIFFRACTIONr_mcangle_it6.9176.6592568
X-RAY DIFFRACTIONr_mcangle_other6.9186.662569
X-RAY DIFFRACTIONr_scbond_it5.3113.9792328
X-RAY DIFFRACTIONr_scbond_other5.313.9782329
X-RAY DIFFRACTIONr_scangle_it7.8067.1613479
X-RAY DIFFRACTIONr_scangle_other7.8057.163480
X-RAY DIFFRACTIONr_lrange_it9.55537.1774875
X-RAY DIFFRACTIONr_lrange_other9.55537.1774875
X-RAY DIFFRACTIONr_ncsr_local_group_10.1060.058253
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11BX-RAY DIFFRACTIONLocal ncs0.106220.05009
12AX-RAY DIFFRACTIONLocal ncs0.106220.05009
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.73-2.8010.374490.32710890.32911590.910.91398.18810.306
2.801-2.8770.372370.28710960.28911370.9110.9499.64820.266
2.877-2.9610.398460.26810310.27310770.9170.9481000.234
2.961-3.0520.305530.23610060.23910600.9360.95999.90570.205
3.052-3.1520.293500.2149810.21810310.9330.9671000.188
3.152-3.2620.285490.1979710.20110200.9440.9721000.168
3.262-3.3850.255600.1929060.1959660.9520.9751000.166
3.385-3.5230.237430.1857660.1889400.9620.97786.06380.157
3.523-3.6790.23480.1487320.1529070.9660.98685.99780.131
3.679-3.8580.185410.1478100.1498510.9850.9871000.13
3.858-4.0660.317410.1667380.1748290.8710.98193.96860.151
4.066-4.3120.192440.1757390.1767830.9750.9781000.158
4.312-4.6080.264300.1317030.1367350.9590.98899.72790.124
4.608-4.9760.203340.1356640.1396980.9760.9881000.125
4.976-5.4480.268270.1436200.1476470.9620.9881000.132
5.448-6.0860.205230.1655560.1675790.9730.9861000.154
6.086-7.0190.224260.1464890.1495150.9680.9881000.139
7.019-8.5750.299230.174290.1764520.9480.981000.165
8.575-12.0390.237170.1693440.1723610.9620.9821000.173
12.039-70.4720.289130.2662110.2682250.9640.95799.55560.268

+
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