- PDB-5v1v: TbiB1 in Complex with the TbiA(alpha) Leader Peptide -
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Open data
ID or keywords:
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Basic information
Entry
Database: PDB / ID: 5v1v
Title
TbiB1 in Complex with the TbiA(alpha) Leader Peptide
Components
TbiA(alpha) Leader Peptide
TbiB1
Keywords
PROTEIN BINDING / Lasso Peptide / RiPP / Peptide Binding
Function / homology
Coenzyme PQQ synthesis protein D / Coenzyme PQQ synthesis protein D superfamily / Coenzyme PQQ synthesis protein D (PqqD) / Uncharacterized protein / PqqD family protein
Function and homology information
Biological species
Thermobaculum terrenum (bacteria)
Method
X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.35 Å
Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 7, 2015
Radiation
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 0.97872 Å / Relative weight: 1
Reflection
Resolution: 1.35→48.1 Å / Num. obs: 40418 / % possible obs: 99.8 % / Redundancy: 6.8 % / Rsym value: 0.061 / Net I/σ(I): 19.7
Reflection shell
Resolution: 1.351→1.355 Å / Redundancy: 6.7 % / Mean I/σ(I) obs: 2.3 / Num. unique obs: 409 / Rsym value: 0.85 / % possible all: 95.1
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Processing
Software
Name
Version
Classification
REFMAC
5.7.0029
refinement
XDS
datareduction
XDS
datascaling
PHASER
phasing
Refinement
Method to determine structure: SAD / Resolution: 1.35→25 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.95 / SU B: 2.08 / SU ML: 0.045 / Cross valid method: THROUGHOUT / ESU R: 0.076 / ESU R Free: 0.069 / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.22684
2027
5 %
RANDOM
Rwork
0.19212
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obs
0.19391
38331
99.63 %
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Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å