[English] 日本語
Yorodumi
- PDB-3i71: Ethanolamine Utilization Microcompartment Shell Subunit, EutK C-t... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3i71
TitleEthanolamine Utilization Microcompartment Shell Subunit, EutK C-terminal domain
ComponentsEthanolamine utilization protein eutK
KeywordsUNKNOWN FUNCTION / helix-turn-helix
Function / homology
Function and homology information


ethanolamine degradation polyhedral organelle / ethanolamine catabolic process / response to X-ray / structural molecule activity
Similarity search - Function
EutK-Ctail domain / Ethanolamine utilization protein EutK C-terminus / Bacterial microcompartments protein, conserved site / Bacterial microcompartment (BMC) domain signature. / Bacterial microcompartment (BMC) domain profile. / BMC domain / Bacterial microcompartment domain / CcmK-like superfamily / BMC / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain ...EutK-Ctail domain / Ethanolamine utilization protein EutK C-terminus / Bacterial microcompartments protein, conserved site / Bacterial microcompartment (BMC) domain signature. / Bacterial microcompartment (BMC) domain profile. / BMC domain / Bacterial microcompartment domain / CcmK-like superfamily / BMC / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
CITRATE ANION / Ethanolamine utilization protein EutK
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 2.1 Å
AuthorsTanaka, S. / Sawaya, M.R. / Yeates, T.O.
CitationJournal: Science / Year: 2010
Title: Structure and Mechanisms of a Protein-Based Organelle in Escherichia coli.
Authors: Tanaka, S. / Sawaya, M.R. / Yeates, T.O.
History
DepositionJul 7, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 12, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_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: Ethanolamine utilization protein eutK
B: Ethanolamine utilization protein eutK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,8804
Polymers15,5022
Non-polymers3782
Water1,00956
1
A: Ethanolamine utilization protein eutK
B: Ethanolamine utilization protein eutK
hetero molecules

A: Ethanolamine utilization protein eutK
B: Ethanolamine utilization protein eutK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,7608
Polymers31,0034
Non-polymers7564
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_554-y,-x,-z-1/61
Buried area7850 Å2
ΔGint-41 kcal/mol
Surface area13180 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2900 Å2
ΔGint-8 kcal/mol
Surface area7620 Å2
MethodPISA
3
A: Ethanolamine utilization protein eutK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,1293
Polymers7,7511
Non-polymers3782
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
B: Ethanolamine utilization protein eutK

B: Ethanolamine utilization protein eutK


Theoretical massNumber of molelcules
Total (without water)15,5022
Polymers15,5022
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_554-y,-x,-z-1/61
Buried area1800 Å2
ΔGint-20 kcal/mol
Surface area9160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.345, 65.345, 146.772
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122

-
Components

#1: Protein Ethanolamine utilization protein eutK


Mass: 7750.819 Da / Num. of mol.: 2 / Fragment: residues 108-166
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K-12 / Gene: b2438, eutK, JW2431, yffI / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)Gold / References: UniProt: P76540
#2: Chemical ChemComp-FLC / CITRATE ANION / Citric acid


Mass: 189.100 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H5O7
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 56 / 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: 2.92 Å3/Da / Density % sol: 57.84 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.4
Details: 0.1M sodium citrate, 20.4% PEG4000, 16% isopropanol, pH 5.4, VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9717 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 7, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9717 Å / Relative weight: 1
ReflectionRedundancy: 20.8 % / Av σ(I) over netI: 40.55 / Number: 308327 / Rmerge(I) obs: 0.09 / Χ2: 1.03 / D res high: 2.35 Å / D res low: 80 Å / Num. obs: 14853 / % possible obs: 99.9
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
5.068099.410.0481.01721.9
4.025.0610010.0591.02222.1
3.514.0210010.0680.97921.1
3.193.5110010.0871.04420.8
2.963.1910010.121.05920.6
2.792.9610010.1571.04720.4
2.652.7910010.2221.03320.3
2.532.6510010.3091.04720.2
2.432.5310010.371.04520.1
2.352.4310010.481.02720.1
ReflectionResolution: 2.1→90 Å / Num. obs: 11489 / % possible obs: 99.9 % / Redundancy: 19.7 % / Rmerge(I) obs: 0.07 / Χ2: 1.031 / Net I/σ(I): 13.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.1-2.1820.30.32611130.9991100
2.18-2.2620.40.27411161.041100
2.26-2.3720.40.20710991.0561100
2.37-2.4920.40.16611151.0651100
2.49-2.6520.30.13311231.0371100
2.65-2.8520.20.10611371.0441100
2.85-3.14200.0911490.9921100
3.14-3.5919.60.07911481.0781100
3.59-4.5218.90.05811891.0451100
4.52-9017.40.04513000.959199.3

-
Phasing

PhasingMethod: SIRAS
Phasing MADD res high: 2.35 Å / D res low: 20 Å / FOM : 0.396 / FOM acentric: 0.376 / FOM centric: 0.455 / Reflection: 6979 / Reflection acentric: 5227 / Reflection centric: 1752
Phasing MAD setR cullis acentric: 0.88 / R cullis centric: 0.93 / Highest resolution: 2.35 Å / Lowest resolution: 20 Å / Loc acentric: 15 / Loc centric: 24.4 / Power acentric: 1.43 / Power centric: 1.17 / Reflection acentric: 5227 / Reflection centric: 1752
Phasing MAD set shell

ID: 1

Resolution (Å)R cullis acentricR cullis centricLoc acentricLoc centricPower acentricPower centricReflection acentricReflection centric
10.32-201.091.4749.864.31.981.424193
6.95-10.321.361.1537.848.32.191.47142123
5.24-6.951.130.9428.434.92.171.64298170
4.21-5.240.84120.828.61.971.2510223
3.51-4.210.760.6917.722.41.451.1793274
3.02-3.510.80.7914.317.81.150.791131316
2.64-3.020.860.8210.112.70.890.661510381
2.35-2.640.920.9810.90.690.46802172
Phasing MAD set site
IDAtom type symbolB isoFract xFract yFract zOccupancy
1I-68.080.3610.7750.0360.243
2I-66.9470.3040.9260.0480.244
3I-73.0040.5781.0190.0690.213
4I-66.670.3230.9790.0060.24
5I-76.130.3691.1720.0930.201
6I-77.2210.1930.7790.0840.203
7I-79.3550.2430.6850.0370.193
8I-77.7710.4520.8480.1620.195
9I-250.5450.3950.50
10I-91.7490.590.8920.3720.149
11I-79.410.40.5050.1180.196
Phasing MAD shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
10.32-200.4250.4980.3941344193
6.95-10.320.5180.5790.449265142123
5.24-6.950.5430.5420.545468298170
4.21-5.240.5350.5540.492733510223
3.51-4.210.4970.4730.5641067793274
3.02-3.510.4030.3890.45414471131316
2.64-3.020.3110.2910.38918911510381
2.35-2.640.2280.2070.324974802172
Phasing dmMethod: Solvent flattening and Histogram matching / Reflection: 6959
Phasing dm shell
Resolution (Å)Delta phi finalFOM Reflection
6.28-10056.10.783505
4.92-6.2849.20.886506
4.28-4.9251.40.914501
3.86-4.2843.40.926509
3.57-3.8650.60.907501
3.35-3.57540.912501
3.17-3.3550.10.79512
3.03-3.1758.70.825505
2.91-3.0351.80.847502
2.81-2.9167.30.816503
2.71-2.8167.10.793502
2.63-2.7167.50.776511
2.35-2.6367.70.697901

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MLPHAREphasing
DM6.1phasing
REFMACrefinement
PDB_EXTRACT3.005data extraction
ADSCQuantumdata collection
RefinementMethod to determine structure: SIRAS / Resolution: 2.1→44.81 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.933 / WRfactor Rfree: 0.241 / WRfactor Rwork: 0.221 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.848 / SU B: 7.588 / SU ML: 0.094 / SU R Cruickshank DPI: 0.164 / SU Rfree: 0.147 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.164 / ESU R Free: 0.146 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS; U VALUES: RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.23 546 4.8 %RANDOM
Rwork0.206 ---
obs0.207 11420 99.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 95.21 Å2 / Biso mean: 38.226 Å2 / Biso min: 15.01 Å2
Baniso -1Baniso -2Baniso -3
1-1.01 Å20.51 Å20 Å2
2--1.01 Å20 Å2
3----1.52 Å2
Refinement stepCycle: LAST / Resolution: 2.1→44.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms886 0 26 56 968
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.021924
X-RAY DIFFRACTIONr_bond_other_d0.0010.02658
X-RAY DIFFRACTIONr_angle_refined_deg1.4352.0031243
X-RAY DIFFRACTIONr_angle_other_deg0.81831582
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5675112
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.28821.28239
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.65315162
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4561512
X-RAY DIFFRACTIONr_chiral_restr0.0840.2136
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021016
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02198
X-RAY DIFFRACTIONr_mcbond_it2.1381.5568
X-RAY DIFFRACTIONr_mcbond_other0.6581.5234
X-RAY DIFFRACTIONr_mcangle_it3.9062897
X-RAY DIFFRACTIONr_scbond_it5.3213356
X-RAY DIFFRACTIONr_scangle_it8.8344.5346
LS refinement shellResolution: 2.1→2.157 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.252 41 -
Rwork0.2 768 -
all-809 -
obs--99.14 %
Refinement TLS params.Method: refined / Origin x: 27.578 Å / Origin y: -11.1134 Å / Origin z: 6.1857 Å
111213212223313233
T0.0708 Å20.0398 Å20.0065 Å2-0.0399 Å20.0168 Å2--0.03 Å2
L0.6397 °2-0.0076 °20.3893 °2-1.3146 °2-0.3057 °2--1.8672 °2
S-0.0907 Å °-0.0321 Å °-0.0668 Å °0.1518 Å °0.1845 Å °0.0274 Å °-0.0372 Å °-0.1044 Å °-0.0938 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A109 - 165
2X-RAY DIFFRACTION1B108 - 165

+
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