- PDB-1rtt: Crystal structure determination of a putative NADH-dependent redu... -
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Basic information
Entry
Database: PDB / ID: 1rtt
Title
Crystal structure determination of a putative NADH-dependent reductase using sulfur anomalous signal
Components
conserved hypothetical protein
Keywords
Structural genomics / unknown function / Protein Structure Initiative / SAD with sulfur / putative reductase / PSI / New York SGX Research Center for Structural Genomics / NYSGXRC
Function / homology
Function and homology information
FMN reductase (NADPH) activity / NAD(P)H dehydrogenase (quinone) activity / Oxidoreductases / oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor / FMN binding / protein homodimerization activity / identical protein binding / cytosol Similarity search - Function
Mass: 18.015 Da / Num. of mol.: 164 / 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: 2
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Sample preparation
Crystal
Density Matthews: 2.35 Å3/Da / Density % sol: 47.63 %
Crystal grow
Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: Calcium acetate, Sodium Cacodylate, PEG 8000, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
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Data collection
Diffraction
ID
Mean temperature (K)
Crystal-ID
1
100
1
2
100
1
1,2
1
Diffraction source
Source
Site
Beamline
ID
Wavelength (Å)
SYNCHROTRON
NSLS
X12C
1
1.7
SYNCHROTRON
NSLS
X12C
2
1.1
Detector
Type
ID
Detector
Date
Details
BRANDEIS - B4
1
CCD
Nov 1, 2003
Mirrors
BRANDEIS - B4
2
CCD
Nov 1, 2003
Mirrors
Radiation
ID
Monochromator
Protocol
Monochromatic (M) / Laue (L)
Scattering type
Wavelength-ID
1
Graphite
SINGLEWAVELENGTH
M
x-ray
1
2
Graphite
SINGLEWAVELENGTH
M
x-ray
1
Radiation wavelength
ID
Wavelength (Å)
Relative weight
1
1.7
1
2
1.1
1
Reflection
Resolution: 1.28→33.04 Å / Num. all: 44069 / Num. obs: 44069 / % possible obs: 85.3 % / Observed criterion σ(F): 0 / Redundancy: 6.9 % / Biso Wilson estimate: 10 Å2 / Rmerge(I) obs: 0.036 / Net I/σ(I): 21.2
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Processing
Software
Name
Version
Classification
CNS
1.1
refinement
CBASS
datacollection
HKL-2000
datascaling
PHASES
phasing
SOLVE
phasing
SHARP
phasing
ARP/wARP
modelbuilding
Refinement
Method to determine structure: SAD / Resolution: 1.28→33.04 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 495941.69 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber Details: Though this is a hypothetical flavin mononucleotide reductase protein, FMN is not seen in the structure.
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