- PDB-1tlq: Crystal structure of protein ypjQ from Bacillus subtilis, Pfam DUF64 -
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Open data
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Basic information
Entry
Database: PDB / ID: 1tlq
Title
Crystal structure of protein ypjQ from Bacillus subtilis, Pfam DUF64
Components
Hypothetical protein ypjQ
Keywords
STRUCTURAL GENOMICS / UNKNOWN FUNCTION / YPJQ / Bacillus subtilis / NYSGXRC / T1519 / PSI / Protein Structure Initiative / New York SGX Research Center for Structural Genomics
Crystal packing suggests that biological assembly is a tetramer. Other three parts can be generated with symmetry operations (Y,X, 1/3-Z), (1-Y,1-X,1/3-Z) and (1-X,1-Y,Z)
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Components
#1: Protein
HypotheticalproteinypjQ
Mass: 21565.668 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: YPJQ, BSU21830 / Plasmid: pETT7 / Production host: Escherichia coli (E. coli) / Strain (production host): B834 DE3 / References: UniProt: P54173
Resolution: 2.4→2.49 Å / Mean I/σ(I) obs: 4.45 / Num. unique all: 1998 / Rsym value: 0.456 / % possible all: 99.9
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Processing
Software
Name
Version
Classification
REFMAC
5.1.24
refinement
DENZO
datareduction
SCALEPACK
datascaling
SOLVE
phasing
Refinement
Method to determine structure: SAD Starting model: Experimental electron density from Selenium SAD experiment. Resolution: 2.4→20 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.895 / SU B: 7.609 / SU ML: 0.178 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.279 / ESU R Free: 0.252 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.29466
529
4.8 %
RANDOM
Rwork
0.23244
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obs
0.23534
10470
99.59 %
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Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parameters
Biso mean: 44.966 Å2
Baniso -1
Baniso -2
Baniso -3
1-
2.58 Å2
1.29 Å2
0 Å2
2-
-
2.58 Å2
0 Å2
3-
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-3.88 Å2
Refinement step
Cycle: LAST / Resolution: 2.4→20 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
1262
0
1
24
1287
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.046
0.022
1280
X-RAY DIFFRACTION
r_angle_refined_deg
3.232
1.985
1736
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
8.527
5
160
X-RAY DIFFRACTION
r_chiral_restr
0.238
0.2
209
X-RAY DIFFRACTION
r_gen_planes_refined
0.019
0.02
936
X-RAY DIFFRACTION
r_nbd_refined
0.312
0.2
689
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
0.187
0.2
55
X-RAY DIFFRACTION
r_metal_ion_refined
0.283
0.2
2
X-RAY DIFFRACTION
r_symmetry_vdw_refined
0.281
0.2
42
X-RAY DIFFRACTION
r_symmetry_hbond_refined
0.234
0.2
5
X-RAY DIFFRACTION
r_mcbond_it
2.034
1.5
803
X-RAY DIFFRACTION
r_mcangle_it
3.534
2
1305
X-RAY DIFFRACTION
r_scbond_it
5.288
3
477
X-RAY DIFFRACTION
r_scangle_it
7.926
4.5
431
LS refinement shell
Resolution: 2.4→2.463 Å / Total num. of bins used: 20 /
Rfactor
Num. reflection
Rfree
0.292
40
Rwork
0.247
768
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