4BEI | pdb_00004bei

V. cholera biofilm scaffolding protein RbmA in complex with 18-crown- 6

PDB DOI: https://doi.org/10.2210/pdb4BEI/pdb

Classification: CELL ADHESION
Organism(s): Vibrio cholerae MJ-1236
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2013-03-11 Released: 2013-12-18
Deposition Author(s): Maestre-Reyna, M., Wang, A.H.-J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free:
0.261 (Depositor), 0.260 (DCC)
R-Value Work:
0.222 (Depositor), 0.220 (DCC)
R-Value Observed:
0.224 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Structural Insights Into Rbma, a Biofilm Scaffolding Protein of V. Cholerae.

Maestre-Reyna, M., Wu, W., Wang, A.H.

(2013) PLoS One 8: 82458

PubMed: 24340031 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1371/journal.pone.0082458
Primary Citation of Related Structures:
4BE5, 4BE6, 4BEI

PubMed Abstract:
V. cholerae can form sessile biofilms associated with abiotic surfaces, cyanobacteria, zoo-plankton, mollusks, or crustaceans. Along with the vibrio polysaccharide, secreted proteins of the rbm gene cluster are key to the biofilm ultrastructure. Here we provide a thorough structural characterization of RbmA, a protein involved in mediating cell-cell and cell-biofilm contacts. We correlate our structural findings with initial ligand specificity screening results, NMR protein-ligand interaction analysis, and complement our results with a full biocomputational study.

Organizational Affiliation

Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan.

Macromolecule Content

Total Structure Weight: 232.11 kDa
Atom Count: 14,574
Modelled Residue Count: 1,866
Deposited Residue Count: 2,096
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RBMA	A, B, C, D, E A, B, C, D, E, F, G, H	262	Vibrio cholerae MJ-1236	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
O4B Query on O4B Download Ideal Coordinates CCD File SDF format, chain O [auth E] SDF format, chain Q [auth F] SDF format, chain S [auth G] SDF format, chain I [auth A] SDF format, chain K [auth B] SDF format, chain L [auth C] SDF format, chain M [auth D] SDF format, chain T [auth H] MOL2 format, chain O [auth E] MOL2 format, chain Q [auth F] MOL2 format, chain S [auth G] MOL2 format, chain I [auth A] MOL2 format, chain K [auth B] MOL2 format, chain L [auth C] MOL2 format, chain M [auth D] MOL2 format, chain T [auth H] mmCIF format, chain O [auth E] mmCIF format, chain Q [auth F] mmCIF format, chain S [auth G] mmCIF format, chain I [auth A] mmCIF format, chain K [auth B] mmCIF format, chain L [auth C] mmCIF format, chain M [auth D] mmCIF format, chain T [auth H]	I [auth A] K [auth B] L [auth C] M [auth D] O [auth E] I [auth A], K [auth B], L [auth C], M [auth D], O [auth E], Q [auth F], S [auth G], T [auth H]	1,4,7,10,13,16-HEXAOXACYCLOOCTADECANE C₁₂ H₂₄ O₆ XEZNGIUYQVAUSS-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain K [auth B] Focus chain L [auth C] Focus chain M [auth D] Focus chain O [auth E] Focus chain Q [auth F] Focus chain S [auth G] Focus chain T [auth H] Interactions & Density Focus chain I [auth A] Focus chain K [auth B] Focus chain L [auth C] Focus chain M [auth D] Focus chain O [auth E] Focus chain Q [auth F] Focus chain S [auth G] Focus chain T [auth H]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain P [auth E] SDF format, chain R [auth F] SDF format, chain J [auth A] SDF format, chain N [auth D] MOL2 format, chain P [auth E] MOL2 format, chain R [auth F] MOL2 format, chain J [auth A] MOL2 format, chain N [auth D] mmCIF format, chain P [auth E] mmCIF format, chain R [auth F] mmCIF format, chain J [auth A] mmCIF format, chain N [auth D]	J [auth A], N [auth D], P [auth E], R [auth F]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Focus chain N [auth D] Focus chain P [auth E] Focus chain R [auth F] Interactions & Density Focus chain J [auth A] Focus chain N [auth D] Focus chain P [auth E] Focus chain R [auth F]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free: 0.261 (Depositor), 0.260 (DCC)
R-Value Work: 0.222 (Depositor), 0.220 (DCC)
R-Value Observed: 0.224 (Depositor)

Space Group: P 3₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 136.885	α = 90
b = 136.885	β = 90
c = 116.312	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2013-12-18

Deposition Author(s):

Maestre-Reyna, M.

Wang, A.H.-J.

Revision History (Full details and data files)

Version 1.0: 2013-12-18
Type: Initial release
Version 1.1: 2013-12-25
Changes: Database references
Version 1.2: 2014-01-08
Changes: Database references
Version 1.3: 2023-12-20
Changes: Data collection, Database references, Derived calculations, Other, Refinement description

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V. cholera biofilm scaffolding protein RbmA in complex with 18-crown- 6

Structural Insights Into Rbma, a Biofilm Scaffolding Protein of V. Cholerae.

Entity ID: 1

Entity Groups

Sequence Annotations

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