- PDB-2oqm: Crystal structure of a dinb family member protein (sden_0562) fro... -
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Open data
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Basic information
Entry
Database: PDB / ID: 2oqm
Title
Crystal structure of a dinb family member protein (sden_0562) from shewanella denitrificans at 1.83 A resolution
Components
Hypothetical protein
Keywords
UNKNOWN FUNCTION / Structural genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homology
Protein of unknown function DUF1993 / Domain of unknown function (DUF1993) / dinb family like domain / DinB/YfiT-like putative metalloenzymes / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / Mainly Alpha / FORMIC ACID / DUF1993 domain-containing protein
Function and homology information
Biological species
Shewanella denitrificans (bacteria)
Method
X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.83 Å
Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jan 18, 2007 / Details: Flat mirror (vertical focusing)
Radiation
Monochromator: Single crystal Si(111) bent (horizontal focusing) Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
ID
Wavelength (Å)
Relative weight
1
0.91837
1
2
0.97908
1
3
0.97874
1
Reflection
Resolution: 1.83→45.22 Å / Num. obs: 68483 / % possible obs: 92.9 % / Biso Wilson estimate: 31.626 Å2 / Rmerge(I) obs: 0.065 / Net I/σ(I): 8.61
Reflection shell
Diffraction-ID: 1
Resolution (Å)
Highest resolution (Å)
Rmerge(I) obs
Mean I/σ(I) obs
Num. measured obs
Num. unique all
% possible all
1.83-1.9
0.467
2.2
14330
6155
83.2
1.9-1.97
0.373
2.7
12889
5521
87.3
1.97-2.06
0.282
3.5
14599
6244
89.5
2.06-2.17
0.211
4.6
15071
6474
92.1
2.17-2.31
0.157
5.9
15764
6766
94.8
2.31-2.48
0.122
7.2
14791
6323
95.7
2.48-2.73
0.088
9.2
15790
6770
96.9
2.73-3.13
0.066
12.1
16052
6869
97
3.13
0.042
16.7
15867
6753
97.6
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Phasing
Phasing
Method: MAD
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Processing
Software
Name
Version
Classification
NB
MolProbity
3beta29
modelbuilding
SHELX
phasing
REFMAC
5.2.0019
refinement
XSCALE
datascaling
PDB_EXTRACT
2
dataextraction
MAR345
CCD
datacollection
XDS
datareduction
SHELXD
phasing
autoSHARP
phasing
Refinement
Method to determine structure: MAD / Resolution: 1.83→45.22 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.956 / SU B: 6.306 / SU ML: 0.093 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.118 / ESU R Free: 0.115 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 3. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 3. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 4. FMT, CL AND EDO ARE MODELED BASED ON THE CRYSTALLIZATION CONDITIONS OR CRYOPROTECTANT. 5. THE REGION D115-123 HAS POORLY DEFINED ELECTRON DENSITY.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.196
3437
5 %
RANDOM
Rwork
0.157
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-
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all
0.159
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-
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obs
0.159
68463
98.4 %
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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: BABINET MODEL WITH MASK
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