- PDB-5dh2: Structure of the siderophore periplasmic binding protein from the... -
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Open data
ID or keywords:
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Basic information
Entry
Database: PDB / ID: 5dh2
Title
Structure of the siderophore periplasmic binding protein from the fuscachelin gene cluster of Thermobifida fusca in I222
Components
siderophore periplasmic binding protein
Keywords
PROTEIN BINDING / Siderophore / Periplasmic Binding Protein / fuscachelin
Function / homology
ABC transporter periplasmic binding domain / Periplasmic binding protein / Iron siderophore/cobalamin periplasmic-binding domain profile. / outer membrane-bounded periplasmic space / Similar to iron(III) dicitrate transport permease RBL00804
Function and homology information
Biological species
Thermobifida fusca (bacteria)
Method
X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.59 Å
Journal: Proteins / Year: 2016 Title: Structure and functional analysis of the siderophore periplasmic binding protein from the fuscachelin gene cluster of Thermobifida fusca. Authors: Li, K. / Bruner, S.D.
Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 24, 2014
Radiation
Monochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 0.97856 Å / Relative weight: 1
Reflection
Resolution: 2.59→37.783 Å / Num. obs: 24621 / % possible obs: 99.9 % / Redundancy: 7.5 % / Rmerge(I) obs: 0.047 / Net I/σ(I): 23.5
Reflection shell
Resolution: 2.59→2.71 Å / Redundancy: 7.7 % / Rmerge(I) obs: 0.516 / Mean I/σ(I) obs: 3.8 / % possible all: 99.9
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Processing
Software
Name
Version
Classification
PHENIX
1.9_1692
refinement
XDS
OSX10.9.5_Darwin13.4.0
datareduction
Aimless
0.5.8
datascaling
PHASER
2.5.6
phasing
ARP
3.3.1
modelbuilding
Refinement
Method to determine structure: SAD / Resolution: 2.59→37.783 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 32.39 / Stereochemistry target values: ML
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.2632
1185
4.82 %
RANDOM
Rwork
0.2295
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-
-
obs
0.2312
24566
99.67 %
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Solvent computation
Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement step
Cycle: LAST / Resolution: 2.59→37.783 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
4247
0
0
35
4282
Refine LS restraints
Refine-ID
Type
Dev ideal
Number
X-RAY DIFFRACTION
f_bond_d
0.004
4332
X-RAY DIFFRACTION
f_angle_d
0.744
5897
X-RAY DIFFRACTION
f_dihedral_angle_d
14.866
1546
X-RAY DIFFRACTION
f_chiral_restr
0.028
662
X-RAY DIFFRACTION
f_plane_restr
0.003
792
LS refinement shell
Resolution (Å)
Rfactor Rfree
Num. reflection Rfree
Rfactor Rwork
Num. reflection Rwork
Refine-ID
% reflection obs (%)
2.59-2.7079
0.3201
133
0.302
2884
X-RAY DIFFRACTION
100
2.7079-2.8506
0.3419
127
0.2989
2898
X-RAY DIFFRACTION
99
2.8506-3.0291
0.336
132
0.2917
2903
X-RAY DIFFRACTION
100
3.0291-3.2629
0.3799
152
0.285
2889
X-RAY DIFFRACTION
100
3.2629-3.591
0.2729
165
0.2458
2893
X-RAY DIFFRACTION
100
3.591-4.1101
0.258
141
0.2214
2936
X-RAY DIFFRACTION
100
4.1101-5.1762
0.2318
156
0.2008
2949
X-RAY DIFFRACTION
100
5.1762-37.7869
0.2349
179
0.2067
3029
X-RAY DIFFRACTION
99
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