- PDB-3gah: Structure of a F112H variant PduO-type ATP:corrinoid adenosyltran... -
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Open data
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Basic information
Entry
Database: PDB / ID: 3gah
Title
Structure of a F112H variant PduO-type ATP:corrinoid adenosyltransferase from Lactobacillus reuteri complexed with cobalamin and ATP
Components
Cobalamin adenosyltransferase PduO-like protein
Keywords
TRANSFERASE
Function / homology
Function and homology information
corrinoid adenosyltransferase / corrinoid adenosyltransferase activity / cobalamin biosynthetic process / ATP binding / metal ion binding Similarity search - Function
Journal: Biochemistry / Year: 2009 Title: Residue Phe112 of the human-type corrinoid adenosyltransferase (PduO) enzyme of Lactobacillus reuteri is critical to the formation of the four-coordinate Co(II) corrinoid substrate and to the ...Title: Residue Phe112 of the human-type corrinoid adenosyltransferase (PduO) enzyme of Lactobacillus reuteri is critical to the formation of the four-coordinate Co(II) corrinoid substrate and to the activity of the enzyme. Authors: Mera, P.E. / St Maurice, M. / Rayment, I. / Escalante-Semerena, J.C.
Mass: 18.015 Da / Num. of mol.: 210 / 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: 2.51 Å3/Da / Density % sol: 51.07 %
Crystal grow
Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.6 Details: anoxic, 14% PEG 8000, 0.2M potassium chloride, 0.1 M HEPPS, 30 ug/mL E. coli FMN reductase, 50 mM NADH, 10 mM FMN, 10 mM hydoxycobalamin, 10 mM ATP, 10 mM magnesium chloride, 0.3 M sodium ...Details: anoxic, 14% PEG 8000, 0.2M potassium chloride, 0.1 M HEPPS, 30 ug/mL E. coli FMN reductase, 50 mM NADH, 10 mM FMN, 10 mM hydoxycobalamin, 10 mM ATP, 10 mM magnesium chloride, 0.3 M sodium chloride , pH 8.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K
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Data collection
Diffraction
Mean temperature: 298 K
Diffraction source
Source: SYNCHROTRON / Site: APS / Beamline: 19-BM
Detector
Type: SBC-3 / Detector: CCD / Date: Aug 17, 2007
Radiation
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Relative weight: 1
Reflection
Resolution: 1.17→50 Å / Num. obs: 73398 / % possible obs: 99.6 % / Redundancy: 4.4 % / Rmerge(I) obs: 0.07 / Χ2: 3.356 / Net I/σ(I): 41.478
Reflection shell
Resolution (Å)
Redundancy (%)
Rmerge(I) obs
Num. unique all
Χ2
Diffraction-ID
% possible all
1.17-1.21
2
0.179
7150
2.572
1
97.3
1.21-1.26
2.2
0.149
7391
2.524
1
99.7
1.26-1.32
2.3
0.12
7337
1.914
1
99.9
1.32-1.39
2.4
0.109
7371
2.726
1
99.9
1.39-1.47
2.9
0.108
7338
2.593
1
99.9
1.47-1.59
3.5
0.101
7387
3.449
1
99.9
1.59-1.75
4.5
0.108
7325
3.189
1
99.9
1.75-2
6.8
0.095
7386
3.158
1
100
2-2.52
9.9
0.079
7387
3.487
1
100
2.52-50
7.5
0.059
7326
4.33
1
99.8
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Phasing
Phasing
Method: molecular replacement
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Processing
Software
Name
Version
Classification
NB
DENZO
datareduction
SCALEPACK
datascaling
MOLREP
phasing
REFMAC
5.2.0005
refinement
PDB_EXTRACT
3.006
dataextraction
Refinement
Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.17→30 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.966 / Occupancy max: 1 / Occupancy min: 0 / SU B: 0.448 / SU ML: 0.021 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.034 / ESU R Free: 0.037 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.182
3689
5 %
RANDOM
Rwork
0.16
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obs
0.161
73249
99.41 %
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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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