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- PDB-6xam: Crystal structure of NzeB in complex with cyclo-(L-Trp-L-homoalanine) -
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Open data
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Basic information
Entry | Database: PDB / ID: 6xam | |||||||||
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Title | Crystal structure of NzeB in complex with cyclo-(L-Trp-L-homoalanine) | |||||||||
![]() | NzeB | |||||||||
![]() | OXIDOREDUCTASE / monooxygenase / dimerase / P450 | |||||||||
Function / homology | PROTOPORPHYRIN IX CONTAINING FE / Chem-WMA![]() | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Shende, V.V. / Khatri, Y. / Newmister, S.A. / Sanders, J.N. / Lindovska, P. / Yu, F. / Doyon, T.J. / Kim, J. / Movassaghi, M. / Houk, K.N. / Sherman, D.H. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Structure and Function of NzeB, a Versatile C-C and C-N Bond-Forming Diketopiperazine Dimerase. Authors: Shende, V.V. / Khatri, Y. / Newmister, S.A. / Sanders, J.N. / Lindovska, P. / Yu, F. / Doyon, T.J. / Kim, J. / Houk, K.N. / Movassaghi, M. / Sherman, D.H. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 104.9 KB | Display | ![]() |
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PDB format | ![]() | 75.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.4 MB | Display | ![]() |
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Full document | ![]() | 1.4 MB | Display | |
Data in XML | ![]() | 20.3 KB | Display | |
Data in CIF | ![]() | 30.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6xaiSC ![]() 6xajC ![]() 6xakC ![]() 6xalC 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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Unit cell |
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Components
#1: Protein | Mass: 43804.465 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Production host: ![]() ![]() | ||||||
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#2: Chemical | ChemComp-HEM / | ||||||
#3: Chemical | #4: Chemical | ChemComp-EDO / | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.96 Å3/Da / Density % sol: 37.16 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 23% PEG 3350, 100 mM DL-malic acid, 2.5% ethylene glycol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 15, 2018 |
Radiation | Monochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.03 Å / Relative weight: 1 |
Reflection | Resolution: 1.481→39.261 Å / Num. obs: 50302 / % possible obs: 89.27 % / Redundancy: 6.2 % / Biso Wilson estimate: 19.9 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.02968 / Rrim(I) all: 0.0322 / Net I/σ(I): 31.27 |
Reflection shell | Resolution: 1.481→1.534 Å / Redundancy: 2 % / Rmerge(I) obs: 0.3031 / Mean I/σ(I) obs: 2.31 / Num. unique obs: 2484 / CC1/2: 0.834 / Rrim(I) all: 0.3933 / % possible all: 44.42 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6xai Resolution: 1.481→39.261 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26.31 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 70.87 Å2 / Biso mean: 26.2657 Å2 / Biso min: 11.55 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.481→39.261 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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