- PDB-2c7i: Structure of protein Ta0514, putative lipoate protein ligase from... -
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ID or keywords:
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Basic information
Entry
Database: PDB / ID: 2c7i
Title
Structure of protein Ta0514, putative lipoate protein ligase from T. acidophilum.
Components
PUTATIVE LIPOATE PROTEIN LIGASE
Keywords
LIGASE / LIPOYLATION
Function / homology
Function and homology information
lipoate-protein ligase / lipoate-protein ligase activity / lipoic acid binding / protein lipoylation / protein-containing complex / ATP binding / metal ion binding / cytoplasm Similarity search - Function
Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL) catalytic domain profile. / Biotin/lipoate A/B protein ligase family / Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL), catalytic domain / Bira Bifunctional Protein; Domain 2 / BirA Bifunctional Protein; domain 2 / Class II Aminoacyl-tRNA synthetase/Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL) / 2-Layer Sandwich / Alpha Beta Similarity search - Domain/homology
Component-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: LEU / End label comp-ID: LEU / Auth seq-ID: 1 - 256 / Label seq-ID: 1 - 256
Dom-ID
Ens-ID
Refine code
Auth asym-ID
Label asym-ID
1
1
3
B
B
2
1
3
A
A
1
2
4
C
C
2
2
4
A
A
1
3
4
D
D
2
3
4
A
A
NCS ensembles :
ID
1
2
3
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Components
#1: Protein
PUTATIVELIPOATEPROTEINLIGASE / LIPOATE-PROTEIN LIGASE A
Mass: 29915.252 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) THERMOPLASMA ACIDOPHILUM (acidophilic) / Strain: DSM 1728 / Plasmid: PET 3A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9HKT1
Mass: 18.015 Da / Num. of mol.: 188 / Source method: isolated from a natural source / Formula: H2O
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Experimental details
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Experiment
Experiment
Method: X-RAY DIFFRACTION / Number of used crystals: 1
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Sample preparation
Crystal
Density Matthews: 3.11 Å3/Da / Density % sol: 60.13 % Description: A STRUCTURE OF RELATIVELY POOR QUALITY DERIVED FROM A SELENOMETHIONE CONTAINING PROTEIN CRYSTAL WAS USED AS MODEL IN CONJUNCTION WITH A GOOD QUALITY NATIVE DATA SET TO GIVE THE STRUCTURE FILES DEPOSITED.
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 1.54 Å / Relative weight: 1
Reflection
Resolution: 2.1→19.87 Å / Num. obs: 68335 / % possible obs: 95.3 % / Observed criterion σ(I): 2 / Redundancy: 10 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 22
Reflection shell
Resolution: 2.08→2.17 Å / Rmerge(I) obs: 0.23 / Mean I/σ(I) obs: 6 / % possible all: 72.3
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Processing
Software
Name
Version
Classification
REFMAC
5.2.0005
refinement
DENZO
datareduction
SCALEPACK
datascaling
PHASER
phasing
Refinement
Method to determine structure: MOLECULAR REPLACEMENT Starting model: SEE REMARK Resolution: 2.1→19.87 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.933 / SU B: 9.866 / SU ML: 0.129 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.2 / ESU R Free: 0.182 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THIS ENTRY CONTAINS ATOMS WITH ZERO OCCUPANCY FOR WHICH B-FACTORS HAVE BEEN REFINED.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.252
3634
5 %
RANDOM
Rwork
0.208
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obs
0.21
68335
94.8 %
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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: MASK