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Open data
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Basic information
Entry | Database: PDB / ID: 3vti | ||||||
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Title | Crystal structure of HypE-HypF complex | ||||||
![]() | (Hydrogenase maturation ...) x 2 | ||||||
![]() | TRANSFERASE / carbamoyltransfer / maturation of [NiFe]-hydrogenase / nitrile synthesis / iron / ATP-dependent dehydration | ||||||
Function / homology | ![]() Ligases; Forming carbon-sulfur bonds / acylphosphatase activity / carboxyl- or carbamoyltransferase activity / ligase activity / double-stranded RNA binding / zinc ion binding / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Shomura, Y. / Higuchi, Y. | ||||||
![]() | ![]() Title: Structural basis for the reaction mechanism of S-carbamoylation of HypE by HypF in the maturation of [NiFe]-hydrogenases Authors: Shomura, Y. / Higuchi, Y. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 833 KB | Display | ![]() |
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PDB format | ![]() | 694.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3vthSC ![]() 2rb9S S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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3 | ![]()
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Unit cell |
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Components
-Hydrogenase maturation ... , 2 types, 4 molecules ABCD
#1: Protein | Mass: 86867.781 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: DSM 15242 / JCM 11007 / NBRC 100824 / MB4 / Gene: HypF, TTE0131 / Production host: ![]() ![]() References: UniProt: Q8RDB0, Transferases; Transferring one-carbon groups; Carboxy- and carbamoyltransferases #2: Protein | Mass: 33875.090 Da / Num. of mol.: 2 / Fragment: N-terminal truncated variant, UNP residues 40-351 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: DSM 15242 / JCM 11007 / NBRC 100824 / MB4 / Gene: HypE, TTE0134 / Production host: ![]() ![]() |
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-Non-polymers , 4 types, 401 molecules ![](data/chem/img/ZN.gif)
![](data/chem/img/FE.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/FE.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-ZN / #4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.56 Å3/Da / Density % sol: 51.89 % |
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Crystal grow | Temperature: 288 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.1M PIPES, 0.48M KCl, 9% PEG 3350, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 288K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX225HE / Detector: CCD / Date: Dec 21, 2011 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 2.56→20 Å / Num. all: 78733 / Num. obs: 78733 / % possible obs: 100 % / Redundancy: 7.1 % / Biso Wilson estimate: 67 Å2 / Rmerge(I) obs: 0.075 / Net I/σ(I): 12.2 |
Reflection shell | Resolution: 2.6→2.64 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.538 / Mean I/σ(I) obs: 4 / Num. unique all: 3855 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3VTH (chains A and B), 2RB9 (chains C and D) Resolution: 2.56→20 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.922 / SU B: 25.462 / SU ML: 0.248 / Cross valid method: THROUGHOUT / ESU R: 0.879 / ESU R Free: 0.314 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: 58.492 Å2
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Refinement step | Cycle: LAST / Resolution: 2.56→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.563→2.629 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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