5FHK

Regulatory domain of AphB in Vibrio vulnificus

> Summary

Summary for 5FHK

DescriptorLysR family transcriptional regulator
Functional Keywordsaphb, lysr-type, transcriptional regulator, tcpph activation, transcription
Biological sourceVibrio vulnificus
Total number of polymer chains6
Total molecular weight140417.88
Authors
Song, S.,Ha, N.-C. (deposition date: 2015-12-22, release date: 2017-01-11)
Primary citation
Song, S.,Ha, N.-C.
Structure of the regulatory domain of AphB in Vibrio vulnificus at 1.9 Angstroms resolution.
To Be Published,
Experimental method
X-RAY DIFFRACTION (1.905 Å)
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Structure validation

RfreeClashscoreRamachandran outliersSidechain outliersRSRZ outliers0.250601.2%2.3%MetricValuePercentile RanksWorseBetterPercentile relative to all X-ray structuresPercentile relative to X-ray structures of similar resolution

More Asymmetric unit images

Molmil generated image of 5fhk
no rotation
Molmil generated image of 5fhk
rotated about x axis by 90°
Molmil generated image of 5fhk
rotated about y axis by 90°

> Structural details

Entity

Chain IDDescriptionTypeChain lengthFormula weightNumber of moleculesDB Name (Accession)Biological sourceDescriptive keywords
A, B, C, D, E...LysR family transcriptional regulatorpolymer20723403.06
UniProt (A0A087IWB4)
Pfam (PF03466)
Vibrio vulnificus
waterwater18.0301

Sequence viewer

Contents of the asymmetric unit

PolymersNumber of chains6
Total molecular weight140417.9
Non-Polymers*Number of molecules0
Total molecular weight0.0
All*Total molecular weight140417.9
*Water molecules are not included.

> Experimental details

Refinement Statistics

Experimental method:X-RAY DIFFRACTION (1.905 Å)

Cell axes124.965187.92657.360
Cell angles90.0090.0090.00
SpacegroupP 21 21 2
Resolution limits42.26 - 1.91
the highest resolution shell value1.927 - 1.905
R-factor0.2101
R-work0.20800
the highest resolution shell value0.407
R-free0.25070
the highest resolution shell value0.666
RMSD bond length0.010
RMSD bond angle1.021

Data Collection Statistics

Resolution limits42.26 - 1.90
the highest resolution shell value -
Number of reflections90980
Rmerge_l_obs0.111
the highest resolution shell value0.639
Completeness98.1
Redundancy8.7
the highest resolution shell value6.2

Crystallization Conditions

crystal IDmethodpHpH rangetemperatureunit
1VAPOR DIFFUSION, HANGING DROP7.0-8.0287

Crystallization Reagents

IDcrystal IDsolution IDreagent nameconcentrationdetails
Crystallization Reagents in Literatures*
IDcrystal IDsolutionreagent nameconcentration (unit)details
Annotated Information is extracted from Literature Info*

> Functional details

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Functional Information from GO Data

ChainGOidnamespacecontents
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Functional Information from PDB Data

site_idNumber of ResiduesDetails
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Functional Information from PDB atom coordinates for the "HETATM" binding sites

site_idNumber of ResiduesDetails
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Functional Information from PROSITE/UniProt

site_idNumber of ResiduesDetails
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Functional Information from SwissProt/UniProt

site_idNumber of ResiduesDetails
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Catalytic Information from CSA

site_idNumber of ResiduesDetails

> Sequence Neighbor

> Downloads

Resources

File formatFile name (file size)
PDBallpdb5fhk.ent.gz (405.9 KB)
Display
all (no-compress)pdb5fhk.ent (1.57 MB)
header onlypdb5fhk.ent.gz (11.76 KB)
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PDBx/mmCIF5fhk.cif.gz (480.61 KB)
PDBMLall5fhk.xml.gz (664.03 KB)
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no-atom5fhk-noatom.xml.gz (42.45 KB)
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ext-atom5fhk-extatom.xml.gz (221.53 KB)
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PDBMLplusall5fhk-plus.xml.gz (664.85 KB)
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no-atom5fhk-plus-noatom.xml.gz (43.27 KB)
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add only5fhk-add.xml.gz (835 B)
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RDF5fhk.rdf.gz (90.84 KB)
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Structure factorsr5fhksf.ent.gz (2.61 MB)
Biological unit (PDB format)5fhk.pdb1.gz (133.47 KB) (A,B)
*author and software defined assembly, 2 molecule(s) (dimeric)
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5fhk.pdb2.gz (134.7 KB) (C,F)
*author and software defined assembly, 2 molecule(s) (dimeric)
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5fhk.pdb3.gz (137.21 KB) (D,E)
*author and software defined assembly, 2 molecule(s) (dimeric)
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Validation reportsPDF5fhk​_validation.pdf.gz (291.17 KB)
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PDF-full5fhk​_full​_validation.pdf.gz (302.72 KB)
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XML5fhk​_validation.xml.gz (42.79 KB)
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PNG5fhk​_multipercentile​_validation.png.gz (157.03 KB)
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SVG5fhk​_multipercentile​_validation.svg.gz (931 B)
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Sequence (fasta)5fhk​_seq.txt
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