[English] 日本語
Yorodumi
- PDB-4bei: V. cholera biofilm scaffolding protein RbmA in complex with 18-cr... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4bei
TitleV. cholera biofilm scaffolding protein RbmA in complex with 18-crown- 6
ComponentsRBMA
KeywordsCELL ADHESION / BACTERIAL COMMUNITY
Function / homologyImmunoglobulin-like - #3880 / Immunoglobulin-like / Sandwich / Mainly Beta / 1,4,7,10,13,16-HEXAOXACYCLOOCTADECANE / DI(HYDROXYETHYL)ETHER / :
Function and homology information
Biological speciesVIBRIO CHOLERAE MJ-1236 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsMaestre-Reyna, M. / Wang, A.H.-J.
CitationJournal: Plos One / Year: 2013
Title: Structural Insights Into Rbma, a Biofilm Scaffolding Protein of V. Cholerae.
Authors: Maestre-Reyna, M. / Wu, W. / Wang, A.H.
History
DepositionMar 11, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 18, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 25, 2013Group: Database references
Revision 1.2Jan 8, 2014Group: Database references
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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: RBMA
B: RBMA
C: RBMA
D: RBMA
E: RBMA
F: RBMA
G: RBMA
H: RBMA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)232,10820
Polymers229,5698
Non-polymers2,53912
Water5,206289
1
G: RBMA
H: RBMA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,9214
Polymers57,3922
Non-polymers5292
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5860 Å2
ΔGint-24.8 kcal/mol
Surface area19400 Å2
MethodPISA
2
C: RBMA
D: RBMA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,0275
Polymers57,3922
Non-polymers6353
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6010 Å2
ΔGint-23.1 kcal/mol
Surface area19420 Å2
MethodPISA
3
A: RBMA
B: RBMA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,0275
Polymers57,3922
Non-polymers6353
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5970 Å2
ΔGint-23.5 kcal/mol
Surface area19510 Å2
MethodPISA
4
E: RBMA
F: RBMA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,1336
Polymers57,3922
Non-polymers7414
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6230 Å2
ΔGint-21.8 kcal/mol
Surface area19480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)136.885, 136.885, 116.312
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

-
Components

#1: Protein
RBMA


Mass: 28696.119 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) VIBRIO CHOLERAE MJ-1236 (bacteria) / Variant: SEROTYPE O1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: C3NSJ9
#2: Chemical
ChemComp-O4B / 1,4,7,10,13,16-HEXAOXACYCLOOCTADECANE


Mass: 264.315 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C12H24O6
#3: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 289 / 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: 2.74 Å3/Da / Density % sol: 55.1 % / Description: NONE
Crystal growpH: 7
Details: 0.1 M HEPES PH 7 0.2 M CACL2 30 % (V/V) PEG 400 50 MM 18-CROWN-6

-
Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13C1 / Wavelength: 0.97622
DetectorType: ADSC CCD / Detector: CCD / Date: Dec 15, 2012 / Details: MIRRORS
RadiationMonochromator: HORIZONTALLY FOCUSING SINGLE CRYSTAL MONOCHROMATOR
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97622 Å / Relative weight: 1
ReflectionResolution: 2.6→22 Å / Num. obs: 75002 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 5.9 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 21.6
Reflection shellResolution: 2.6→2.9 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.93 / Mean I/σ(I) obs: 2.44 / % possible all: 100

-
Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4BE5

4be5


Resolution: 2.6→21.96 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.918 / SU B: 12.154 / SU ML: 0.253 / Cross valid method: THROUGHOUT / ESU R: 0.624 / ESU R Free: 0.312 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26087 3781 5 %RANDOM
Rwork0.22172 ---
obs0.22368 71190 99.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 53.439 Å2
Baniso -1Baniso -2Baniso -3
1-0.15 Å20.15 Å20 Å2
2--0.15 Å20 Å2
3----0.48 Å2
Refinement stepCycle: LAST / Resolution: 2.6→21.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14011 0 172 289 14472
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0214560
X-RAY DIFFRACTIONr_bond_other_d0.0050.0213597
X-RAY DIFFRACTIONr_angle_refined_deg1.311.95219771
X-RAY DIFFRACTIONr_angle_other_deg1.3393.01131182
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.13751884
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.77425.826642
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.473152238
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8521545
X-RAY DIFFRACTIONr_chiral_restr0.0710.22223
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0216959
X-RAY DIFFRACTIONr_gen_planes_other0.0040.023302
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.599→2.666 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.415 274 -
Rwork0.341 5213 -
obs--99.98 %

+
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