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- PDB-4d46: Crystal structure of E. coli FabI in complex with NAD and 5-bromo... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4d46 | ||||||
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Title | Crystal structure of E. coli FabI in complex with NAD and 5-bromo-2-(4-chloro-2-hydroxyphenoxy)benzonitrile | ||||||
![]() | ENOYL-[ACYL-CARRIER-PROTEIN] REDUCTASE [NADH] | ||||||
![]() | OXIDOREDUCTASE / ENOYL-ACP REDUCTASE / SHORT-CHAIN DEHYDROGENASE/REDUCTASE SUPERFAMILY / ESCHERICHIA COLI / FATTY ACID BIOSYNTHESIS / LIPID SYNTHESIS / ECFABI / FABI | ||||||
Function / homology | ![]() enoyl-[acyl-carrier-protein] reductase activity (NAD(P)H) / biotin biosynthetic process / enoyl-[acyl-carrier-protein] reductase (NADH) / enoyl-[acyl-carrier-protein] reductase (NADH) activity / fatty acid biosynthetic process / nucleotide binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Tareilus, M. / Schiebel, J. / Chang, A. / Tonge, P.J. / Sotriffer, C.A. / Kisker, C. | ||||||
![]() | ![]() Title: An Ordered Water Channel in Staphylococcus Aureus Fabi: Unraveling the Mechanism of Substrate Recognition and Reduction. Authors: Schiebel, J. / Chang, A. / Merget, B. / Bommineni, G.R. / Yu, W. / Spagnuolo, L.A. / Baxter, M.V. / Tareilus, M. / Tonge, P.J. / Kisker, C. / Sotriffer, C.A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 202.6 KB | Display | ![]() |
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PDB format | ![]() | 164.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.3 MB | Display | ![]() |
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Full document | ![]() | 1.3 MB | Display | |
Data in XML | ![]() | 22.3 KB | Display | |
Data in CIF | ![]() | 31.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4d41C ![]() 4d42C ![]() 4d43C ![]() 4d44C ![]() 4d45C ![]() 1qsgS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 28964.068 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: C6EFU4, UniProt: A0A140NA83*PLUS, enoyl-[acyl-carrier-protein] reductase (NADH) #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.52 Å3/Da / Density % sol: 51.19 % / Description: NONE |
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Crystal grow | pH: 10.5 / Details: 0.08 M NH4AC, 0.1 M CAPS PH 10.5, 20% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 10, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9184 Å / Relative weight: 1 |
Reflection | Resolution: 2→46.96 Å / Num. obs: 41818 / % possible obs: 100 % / Observed criterion σ(I): 6 / Redundancy: 19 % / Rmerge(I) obs: 0.14 / Net I/σ(I): 16.2 |
Reflection shell | Resolution: 2→2.11 Å / Redundancy: 19.2 % / Rmerge(I) obs: 1.25 / Mean I/σ(I) obs: 2.4 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1QSG Resolution: 2→68.54 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.955 / SU B: 7.733 / SU ML: 0.1 / Cross valid method: THROUGHOUT / ESU R: 0.139 / ESU R Free: 0.133 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. VERY WEAK DENSITY FOR LOOP REGION 193-210 IN SUBUNIT A, WHICH WAS NOT INTERPRETED. VERY WEAK DENSITY FOR LOOP REGION 204-209 IN SUBUNIT B, ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. VERY WEAK DENSITY FOR LOOP REGION 193-210 IN SUBUNIT A, WHICH WAS NOT INTERPRETED. VERY WEAK DENSITY FOR LOOP REGION 204-209 IN SUBUNIT B, WHICH WAS NOT INTERPRETED. INHIBITOR DENSITY BETTER FOR SUBUNIT A, BUT STILL SUFFICIENT FOR B
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 41.565 Å2
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Refinement step | Cycle: LAST / Resolution: 2→68.54 Å
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Refine LS restraints |
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