[English] 日本語
Yorodumi
- PDB-4lba: Crystal structure of a conjugative transposon lipoprotein (BACEGG... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4lba
TitleCrystal structure of a conjugative transposon lipoprotein (BACEGG_03088) from Bacteroides eggerthii DSM 20697 at 1.70 A resolution
Componentsconjugative transposon lipoprotein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / PF12988 family protein / DUF3872 / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY
Function / homologyUncharacterised protein PF12988, DUF3872 / Immunoglobulin-like / Sandwich / Mainly Beta / :
Function and homology information
Biological speciesBacteroides eggerthii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.7 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a conjugative transposon lipoprotein (BACEGG_03088) from Bacteroides eggerthii DSM 20697 at 1.70 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionJun 20, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 7, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.2Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.3Feb 1, 2023Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / 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_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: conjugative transposon lipoprotein
B: conjugative transposon lipoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,76410
Polymers31,9152
Non-polymers8498
Water4,414245
1
A: conjugative transposon lipoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,3825
Polymers15,9571
Non-polymers4244
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: conjugative transposon lipoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,3825
Polymers15,9571
Non-polymers4244
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)126.923, 126.923, 39.352
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number172
Space group name H-MP64
Components on special symmetry positions
IDModelComponents
11B-316-

HOH

DetailsCRYSTAL PACKING ANALYSIS SUGGESTS THE ASSIGNMENT OF A MONOMER AS THE SIGNIFICANT OLIGOMERIZATION STATE.

-
Components

#1: Protein conjugative transposon lipoprotein


Mass: 15957.280 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides eggerthii (bacteria) / Strain: DSM 20697 / Gene: BACEGG_03088, ZP_03460274.1 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): PB1 / References: UniProt: B7AKX5
#2: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 245 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHIS CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH ...THIS CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY RESIDUES 32-167 OF THE TARGET SEQUENCE.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.87 Å3/Da / Density % sol: 57.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 16.0% polyethylene glycol 3350, 0.2M magnesium chloride, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.91837, 0.97864, 0.97817
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 1, 2013
Details: Flat mirror (vertical focusing); single crystal Si(111) bent monochromator (horizontal focusing)
RadiationMonochromator: single crystal Si(111) bent / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.918371
20.978641
30.978171
ReflectionResolution: 1.7→25.217 Å / Num. all: 40202 / Num. obs: 40202 / % possible obs: 99.8 % / Redundancy: 6.2 % / Rsym value: 0.08 / Net I/σ(I): 12.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.7-1.7460.8280.91771229540.828100
1.74-1.796.40.6351.21861228930.635100
1.79-1.846.40.4961.61800928000.49699.9
1.84-1.96.20.3662.11675127030.366100
1.9-1.9660.2672.81592826410.267100
1.96-2.035.50.2063.51398325230.20699.5
2.03-2.115.90.1694.41450424780.16999.9
2.11-2.196.50.1435.21550723880.143100
2.19-2.296.50.1226.11468822650.122100
2.29-2.46.40.116.51381621750.1199.9
2.4-2.536.20.0947.51285820590.09499.8
2.53-2.695.30.0788.91051419680.07899.5
2.69-2.876.70.0719.41252118670.071100
2.87-3.16.60.0649.51135317270.064100
3.1-3.46.40.069.21020715920.06100
3.4-3.85.60.0578.6802614380.05799.1
3.8-4.3960.0598.8783612970.05999.6
4.39-5.386.40.0589.7698410880.058100
5.38-7.65.40.0667.546008570.06699.9
7.6-25.2176.40.0511.431134890.0597.4

-
Phasing

PhasingMethod: MAD

-
Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
PDB_EXTRACT3.1data extraction
SOLVEphasing
SCALA3.3.20data scaling
REFMACrefinement
MOSFLMdata reduction
RefinementMethod to determine structure: MAD / Resolution: 1.7→25.217 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.962 / Occupancy max: 1 / Occupancy min: 0.23 / SU B: 3.06 / SU ML: 0.051 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.077 / ESU R Free: 0.077
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORDS CONTAIN SUM OF TLS AND RESIDUAL B FACTORS. 3. ANISOU RECORDS CONTAIN SUM OF TLS AND RESIDUAL U FACTORS. 4. WATERS WERE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORDS CONTAIN SUM OF TLS AND RESIDUAL B FACTORS. 3. ANISOU RECORDS CONTAIN SUM OF TLS AND RESIDUAL U FACTORS. 4. WATERS WERE EXCLUDED FROM AUTOMATIC TLS ASSIGNMENT. 5. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 6. PEG3350 FRAGMENT (1PE) AND 1,2-ETHANEDIOL (EDO) MOLECULES FROM THE CRYSTALLIZATION/CRYOPROTECTION SOLUTION ARE MODELED.
RfactorNum. reflection% reflectionSelection details
Rfree0.1873 2012 5 %RANDOM
Rwork0.1651 ---
obs0.1662 40187 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 130.91 Å2 / Biso mean: 36.8299 Å2 / Biso min: 13.96 Å2
Baniso -1Baniso -2Baniso -3
1-0.08 Å20.08 Å2-0 Å2
2--0.08 Å2-0 Å2
3----0.27 Å2
Refinement stepCycle: LAST / Resolution: 1.7→25.217 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1763 0 53 245 2061
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.021971
X-RAY DIFFRACTIONr_bond_other_d0.0050.021835
X-RAY DIFFRACTIONr_angle_refined_deg1.5731.9852666
X-RAY DIFFRACTIONr_angle_other_deg1.0234252
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7545250
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.89425.185108
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.56515310
X-RAY DIFFRACTIONr_dihedral_angle_4_deg6.821158
X-RAY DIFFRACTIONr_chiral_restr0.0880.2281
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022256
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02472
X-RAY DIFFRACTIONr_mcbond_it4.1513.971907
X-RAY DIFFRACTIONr_mcbond_other4.153.959906
X-RAY DIFFRACTIONr_mcangle_it6.6377.3381140
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.328 144 -
Rwork0.271 2780 -
all-2924 -
obs--99.93 %
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)
13.15011.59490.83374.02741.50820.6878-0.0280.12540.04840.1067-0.03650.0961-0.00030.02060.06450.1526-0.1139-0.01230.0981-0.01490.072485.19630.14432.45
21.9447-0.294-0.03742.62550.75870.5531-0.06770.07070.0509-0.01610.119-0.1389-0.05660.102-0.05130.07-0.02250.00990.0541-0.01950.026676.2885.17725.43
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A41 - 146
2X-RAY DIFFRACTION2B38 - 146

+
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