[English] 日本語
Yorodumi
- PDB-3b8m: Structure of FepE- Bacterial Polysaccharide Co-polymerase -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3b8m
TitleStructure of FepE- Bacterial Polysaccharide Co-polymerase
ComponentsFerric enterobactin (Enterochelin) transport
KeywordsBIOSYNTHETIC PROTEIN / WZZ / FepE / Bacterial Polysaccharide Co-polymerase / METAL TRANSPORT
Function / homology
Function and homology information


identical protein binding / plasma membrane
Similarity search - Function
Bacterial polysaccharide co-polymerase-like / FepE-like / Polysaccharide chain length determinant N-terminal domain / Chain length determinant protein / : / Helix Hairpins - #210 / Helix Hairpins / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Regulator of length of O-antigen component of lipopolysaccharide chains
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.7 Å
AuthorsTocilj, A. / Matte, A. / Cygler, M.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2008
Title: Bacterial polysaccharide co-polymerases share a common framework for control of polymer length
Authors: Tocilj, A. / Munger, C. / Proteau, A. / Morona, R. / Purins, L. / Ajamian, E. / Wagner, J. / Papadopoulos, M. / Van Den Bosch, L. / Rubinstein, J.L. / Fethiere, J. / Matte, A. / Cygler, M.
History
DepositionNov 1, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 22, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Ferric enterobactin (Enterochelin) transport
B: Ferric enterobactin (Enterochelin) transport
C: Ferric enterobactin (Enterochelin) transport


Theoretical massNumber of molelcules
Total (without water)95,5953
Polymers95,5953
Non-polymers00
Water50428
1
A: Ferric enterobactin (Enterochelin) transport
B: Ferric enterobactin (Enterochelin) transport
C: Ferric enterobactin (Enterochelin) transport

A: Ferric enterobactin (Enterochelin) transport
B: Ferric enterobactin (Enterochelin) transport
C: Ferric enterobactin (Enterochelin) transport

A: Ferric enterobactin (Enterochelin) transport
B: Ferric enterobactin (Enterochelin) transport
C: Ferric enterobactin (Enterochelin) transport


Theoretical massNumber of molelcules
Total (without water)286,7869
Polymers286,7869
Non-polymers00
Water1629
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Buried area33060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)139.726, 139.726, 276.654
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number182
Space group name H-MP6322
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11B
21A
12C
22A

NCS domain segments:

Component-ID: 1 / Beg auth comp-ID: LYS / Beg label comp-ID: LYS / End auth comp-ID: PRO / End label comp-ID: PRO / Refine code: 5 / Auth seq-ID: 64 - 330 / Label seq-ID: 13 - 279

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11BB
21AA
12CC
22AA

NCS ensembles :
ID
1
2

-
Components

#1: Protein Ferric enterobactin (Enterochelin) transport


Mass: 31865.092 Da / Num. of mol.: 3 / Fragment: residues 65-331
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: O157 / Gene: fepE / Plasmid: pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q8XBV8
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 28 / 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: 4.09 Å3/Da / Density % sol: 73.7 %
Crystal growTemperature: 298 K / pH: 7.5
Details: Sodium Citrate Na3C6H5O7, pH 7.5, vapor diffusion, temperature 298K, pH 7.50

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.98
DetectorType: ADSC QUANTUM 315 / Detector: CCD
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 44193 / % possible obs: 99.1 % / Redundancy: 11.8 % / Rmerge(I) obs: 0.087 / Net I/σ(I): 10.3
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.448 / % possible all: 92.2

-
Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation3.29 Å49.15 Å
Translation3.29 Å49.15 Å

-
Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
MOLREPphasing
REFMACrefmac_5.2.0019refinement
PDB_EXTRACT2data extraction
DENZOdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→46.13 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.904 / SU B: 10.213 / SU ML: 0.211 / Cross valid method: THROUGHOUT / ESU R: 0.414 / ESU R Free: 0.301 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26947 2072 5 %RANDOM
Rwork0.22577 ---
obs0.22803 39284 92.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 46.932 Å2
Baniso -1Baniso -2Baniso -3
1-0.07 Å20.03 Å20 Å2
2--0.07 Å20 Å2
3----0.1 Å2
Refinement stepCycle: LAST / Resolution: 2.7→46.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6133 0 0 28 6161
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0226250
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3671.9818459
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.755759
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.26825.655290
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.034151171
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.6941530
X-RAY DIFFRACTIONr_chiral_restr0.0890.2980
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.024619
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2250.32683
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3290.54360
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1710.5317
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1940.361
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1550.512
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.16733914
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.73666251
X-RAY DIFFRACTIONr_scbond_it3.35142577
X-RAY DIFFRACTIONr_scangle_it5.55682208
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1B1020medium positional0.240.5
2C1020medium positional0.270.5
1B1021loose positional0.515
2C1020loose positional0.485
1B1020medium thermal0.712
2C1020medium thermal0.852
1B1021loose thermal2.3810
2C1020loose thermal2.1610
LS refinement shellResolution: 2.7→2.772 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.42 115 -
Rwork0.314 2245 -
obs--73.59 %

+
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