2VH3 | pdb_00002vh3

ranasmurfin

PDB DOI: https://doi.org/10.2210/pdb2VH3/pdb

Classification: UNKNOWN FUNCTION
Organism(s): Polypedates leucomystax
Mutation(s): No

Deposited: 2007-11-17 Released: 2007-12-04
Deposition Author(s): Oke, M., Ching, R.T., Carter, L.G., Johnson, K.A., Liu, H., McMahon, S.A., Bloch Junior, C., Botting, C.H., Walsh, M.A., Latiff, A.A., Kennedy, M.W., Cooper, A., Naismith, J.H.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.16 Å
R-Value Free:
0.236 (Depositor), 0.256 (DCC)
R-Value Work:
0.214 (Depositor), 0.232 (DCC)
R-Value Observed:
0.216 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 2.0 of the entry. See complete history.

Literature

Unusual Chromophore and Cross-Links in Ranasmurfin: A Blue Protein from the Foam Nests of a Tropical Frog.

Oke, M., Ching, R.T., Carter, L.G., Johnson, K.A., Liu, H., Mcmahon, S.A., White, M.F., Bloch Jr, C., Botting, C.H., Walsh, M.A., Latiff, A.A., Kennedy, M.W., Cooper, A., Naismith, J.H.

(2008) Angew Chem Int Ed Engl 47: 7853

PubMed: 18781570 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1002/anie.200802901
Primary Citation Related Structures:
2VH3

PubMed Abstract:
Ranasmurfin is an unusual blue protein isolated from the nests of a Malaysian tree frog, Polypedates leucomystax,[1] showing the rich chemical diversity displayed by biomolecular foams. Many species of tropical frogs use foams to protect delicate eggs and developing embryos against environmental challenges. These nests act as miniature ecosystems containing a spectrum of novel proteins and other macromolecules with functions related to foam stabilization and adhesion, resistance to microbial degradation, predation, or dehydration, providing a biocompatible environment for embryonic development.Thisworkformspartofourwiderstudyofthe intriguing physical and chemical properties of biofoams as unusual examples of biological soft matter.[2]

Organizational Affiliation

Centre for Biomolecular Science and The Scottish Structural Proteomics Facility, The University, St Andrews, UK.

Macromolecule Content

Total Structure Weight: 25.94 kDa
Atom Count: 2,015
Modeled Residue Count: 225
Deposited Residue Count: 226
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RANASMURFIN	A	113	Polypedates leucomystax	Mutation(s): 0
UniProt
Find proteins for P85511 (Polypedates leucomystax) Explore P85511 Go to UniProtKB: P85511
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P85511
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
RANASMURFIN	B	113	Polypedates leucomystax	Mutation(s): 0
UniProt
Find proteins for P85511 (Polypedates leucomystax) Explore P85511 Go to UniProtKB: P85511
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P85511
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain H [auth B] SDF format, chain G [auth B] SDF format, chain F [auth B] SDF format, chain D [auth A] MOL2 format, chain H [auth B] MOL2 format, chain G [auth B] MOL2 format, chain F [auth B] MOL2 format, chain D [auth A] mmCIF format, chain H [auth B] mmCIF format, chain G [auth B] mmCIF format, chain F [auth B] mmCIF format, chain D [auth A]	D [auth A], F [auth B], G [auth B], H [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain D [auth A] Focus chain F [auth B] Focus chain G [auth B] Focus chain H [auth B] Interactions & Density Focus chain D [auth A] Focus chain F [auth B] Focus chain G [auth B] Focus chain H [auth B]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain I [auth B] SDF format, chain E [auth A] MOL2 format, chain I [auth B] MOL2 format, chain E [auth A] mmCIF format, chain I [auth B] mmCIF format, chain E [auth A]	E [auth A], I [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain I [auth B] Interactions & Density Focus chain E [auth A] Focus chain I [auth B]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Modified Residues 4 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
DAH Query on DAH	A	L-PEPTIDE LINKING	C₉ H₁₁ N O₄		TYR
TY2 Query on TY2	A	L-PEPTIDE LINKING	C₉ H₁₂ N₂ O₃		TYR
CSO Query on CSO	B	L-PEPTIDE LINKING	C₃ H₇ N O₃ S		CYS
FGL Query on FGL	B	L-PEPTIDE LINKING	C₃ H₅ N O₄		GLY

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.16 Å
R-Value Free: 0.236 (Depositor), 0.256 (DCC)
R-Value Work: 0.214 (Depositor), 0.232 (DCC)
R-Value Observed: 0.216 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 40.99	α = 90
b = 59.67	β = 93.31
c = 44.9	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2007-12-04

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2007-12-04
Type: Initial release
Version 1.1: 2011-08-31
Changes: Derived calculations, Non-polymer description, Version format compliance
Version 1.2: 2025-04-09
Changes: Data collection, Database references, Derived calculations, Other, Refinement description, Structure summary
Version 2.0: 2025-09-17
Changes: Atomic model, Data collection, Polymer sequence