- PDB-4cvd: Crystal structure of the central repeat of cell wall binding modu... -
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Basic information
Entry
Database: PDB / ID: 4cvd
Title
Crystal structure of the central repeat of cell wall binding module of Cpl7
Components
LYSOZYME
Keywords
HYDROLASE / STREPTOCOCCUS PNEUMONIAE
Function / homology
Function and homology information
peptidoglycan catabolic process / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / killing of cells of another organism / defense response to bacterium Similarity search - Function
Cpl-7 lysozyme, C-terminal / CW_7 repeat / Cpl-7 lysozyme C-terminal domain / Glycosyl hydrolases family 25, active site / Glycosyl hydrolases family 25 active site signature. / Glycoside hydrolase, family 25 subgroup / Glycosyl hydrolases family 25 / Glycosyl hydrolase family 25 (GH25) domain profile. / Glycoside hydrolase, family 25 / Glycosyl hydrolases family 25 / Glycoside hydrolase superfamily Similarity search - Domain/homology
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 0.9334 Å / Relative weight: 1
Reflection
Resolution: 1.67→28.54 Å / Num. obs: 4935 / % possible obs: 99.7 % / Observed criterion σ(I): 2 / Redundancy: 10.7 % / Biso Wilson estimate: 12.17 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 10.3
Reflection shell
Resolution: 1.67→1.76 Å / Redundancy: 10.4 % / Rmerge(I) obs: 0.18 / Mean I/σ(I) obs: 4.3 / % possible all: 98.7
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Processing
Software
Name
Version
Classification
PHENIX
(PHENIX.REFINE)
refinement
MOSFLM
datareduction
SCALE
CCP4
datascaling
Arcimboldo
phasing
Refinement
Method to determine structure: AB INITIO PHASING Starting model: NONE Resolution: 1.666→25.2 Å / SU ML: 0.18 / σ(F): 1.54 / Phase error: 19.78 / Stereochemistry target values: ML
Rfactor
Num. reflection
% reflection
Rfree
0.2189
230
4.7 %
Rwork
0.1699
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obs
0.1721
4927
99.68 %
Solvent computation
Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parameters
Biso mean: 11 Å2
Refinement step
Cycle: LAST / Resolution: 1.666→25.2 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
370
0
0
32
402
Refine LS restraints
Refine-ID
Type
Dev ideal
Number
X-RAY DIFFRACTION
f_bond_d
0.008
374
X-RAY DIFFRACTION
f_angle_d
1.197
509
X-RAY DIFFRACTION
f_dihedral_angle_d
13.129
135
X-RAY DIFFRACTION
f_chiral_restr
0.072
57
X-RAY DIFFRACTION
f_plane_restr
0.004
70
LS refinement shell
Resolution (Å)
Rfactor Rfree
Num. reflection Rfree
Rfactor Rwork
Num. reflection Rwork
Refine-ID
% reflection obs (%)
1.6661-2.0989
0.2314
118
0.1643
2317
X-RAY DIFFRACTION
100
2.0989-25.2028
0.2139
112
0.1723
2380
X-RAY DIFFRACTION
100
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