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Open data
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Basic information
Entry | Database: PDB / ID: 2vh3 | ||||||
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Title | ranasmurfin | ||||||
![]() | (RANASMURFIN) x 2 | ||||||
![]() | UNKNOWN FUNCTION / LTQ / BISLTQ | ||||||
Function / homology | Four Helix Bundle (Hemerythrin (Met), subunit A) - #1410 / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / extracellular region / Mainly Alpha / metal ion binding / Ranasmurfin![]() | ||||||
Biological species | POLYPEDATES LEUCOMYSTAX (Java whipping frog) | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | 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. ...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. | ||||||
![]() | ![]() Title: Unusual Chromophore and Cross-Links in Ranasmurfin: A Blue Protein from the Foam Nests of a Tropical Frog. Authors: 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. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 104.9 KB | Display | ![]() |
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PDB format | ![]() | 87.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 454.6 KB | Display | ![]() |
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Full document | ![]() | 457.5 KB | Display | |
Data in XML | ![]() | 13.3 KB | Display | |
Data in CIF | ![]() | 18.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS ensembles :
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Components
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 12646.316 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: FROM FROG NESTS Source: (natural) POLYPEDATES LEUCOMYSTAX (Java whipping frog) References: UniProt: P85511 |
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#2: Protein | Mass: 12661.286 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: FROM FROG NESTS Source: (natural) POLYPEDATES LEUCOMYSTAX (Java whipping frog) References: UniProt: P85511 |
-Non-polymers , 4 types, 191 molecules ![](data/chem/img/ZN.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-ZN / | ||||
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#4: Chemical | ChemComp-SO4 / #5: Chemical | #6: Water | ChemComp-HOH / | |
-Details
Nonpolymer details | THE CHROMOPHORE IN THIS ENTRY IS FORMED BY 4 RESIDUES ACROSS CHAINS A AND B. LYS (A30)-TY2 (A108)- ...THE CHROMOPHOR |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.95 Å3/Da / Density % sol: 44.52 % / Description: NONE |
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Crystal grow | pH: 6 / Details: pH 6 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.976 Å / Relative weight: 1 |
Reflection | Resolution: 1.16→44 Å / Num. obs: 65500 / % possible obs: 93 % / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 12 |
Reflection shell | Resolution: 1.16→1.22 Å / Redundancy: 80 % / Rmerge(I) obs: 0.63 / Mean I/σ(I) obs: 1.8 / % possible all: 70 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: NONE Resolution: 1.16→44.81 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.945 / SU B: 2.254 / SU ML: 0.044 / Cross valid method: THROUGHOUT / ESU R: 0.054 / ESU R Free: 0.05 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.THE SEQUENCE IS FROM X-RAY STRUCTURE.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 13.9 Å2
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Refinement step | Cycle: LAST / Resolution: 1.16→44.81 Å
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Refine LS restraints |
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