+Open data
-Basic information
Entry | Database: PDB / ID: 7nem | ||||||
---|---|---|---|---|---|---|---|
Title | Hydrogenase-2 variant R479K - anaerobically oxidised form | ||||||
Components | (Hydrogenase-2 ...) x 2 | ||||||
Keywords | OXIDOREDUCTASE / Hydrogenase / hydrogen oxidation / proton reduction | ||||||
Function / homology | Function and homology information hydrogenase (acceptor) / [Ni-Fe] hydrogenase complex / ferredoxin hydrogenase complex / hydrogenase (acceptor) activity / ferredoxin hydrogenase activity / anaerobic respiration / 3 iron, 4 sulfur cluster binding / iron-sulfur cluster binding / nickel cation binding / 4 iron, 4 sulfur cluster binding ...hydrogenase (acceptor) / [Ni-Fe] hydrogenase complex / ferredoxin hydrogenase complex / hydrogenase (acceptor) activity / ferredoxin hydrogenase activity / anaerobic respiration / 3 iron, 4 sulfur cluster binding / iron-sulfur cluster binding / nickel cation binding / 4 iron, 4 sulfur cluster binding / periplasmic space / electron transfer activity / membrane / metal ion binding / plasma membrane Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.35 Å | ||||||
Authors | Carr, S.B. | ||||||
Funding support | United Kingdom, 1items
| ||||||
Citation | Journal: To Be Published Title: A comprehensive structural and kinetic investigation of the role of the active-site argininein bidirectional hydrogen activation by the [NiFe]-hydrogenase "Hyd-2) from Escherichia coli Authors: Evans, R.M. / Beaton, S.E. / Kertiss, L. / Myers, W.K. / Carr, S.B. / Armstrong, F.A. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 7nem.cif.gz | 364.5 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb7nem.ent.gz | 285.9 KB | Display | PDB format |
PDBx/mmJSON format | 7nem.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7nem_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 7nem_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 7nem_validation.xml.gz | 67.6 KB | Display | |
Data in CIF | 7nem_validation.cif.gz | 102.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ne/7nem ftp://data.pdbj.org/pub/pdb/validation_reports/ne/7nem | HTTPS FTP |
-Related structure data
Related structure data | 6syoS S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
-Hydrogenase-2 ... , 2 types, 4 molecules STLM
#1: Protein | Mass: 32371.498 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (strain K12) (bacteria) Strain: K12 / Gene: hybO, yghV, b2997, JW2965 / Plasmid: pOc / Details (production host): Plasmid expresses small subunit / Production host: Escherichia coli (E. coli) / References: UniProt: P69741, hydrogenase (acceptor) #2: Protein | Mass: 62529.891 Da / Num. of mol.: 2 / Mutation: R479K Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (strain K12) (bacteria) Strain: K12 / Gene: hybC, b2994, JW2962 / Plasmid: pOc / Production host: Escherichia coli (E. coli) / References: UniProt: P0ACE0, hydrogenase (acceptor) |
---|
-Non-polymers , 8 types, 1338 molecules
#3: Chemical | ChemComp-SF4 / #4: Chemical | #5: Chemical | #6: Chemical | #7: Chemical | ChemComp-MG / #8: Chemical | #9: Chemical | ChemComp-CL / | #10: Water | ChemComp-HOH / | |
---|
-Details
Has ligand of interest | Y |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.1 Å3/Da / Density % sol: 41.5 % / Description: Long rods |
---|---|
Crystal grow | Temperature: 296 K / Method: vapor diffusion, sitting drop / pH: 5.9 Details: 100 mM Bis tris pH 5.9, 200 mM MgCl2 19-21 % PEG 3350 PH range: 5.7-5.9 / Temp details: Ambient temperature inside anaerobic chamber |
-Data collection
Diffraction | Mean temperature: 100 K / Ambient temp details: cryostream - nitrogen vapour / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.7749 Å |
Detector | Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Dec 12, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.7749 Å / Relative weight: 1 |
Reflection | Resolution: 1.35→44.8 Å / Num. obs: 366877 / % possible obs: 100 % / Redundancy: 13.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.143 / Rpim(I) all: 0.059 / Rrim(I) all: 0.154 / Χ2: 0.9 / Net I/σ(I): 10.3 |
Reflection shell | Resolution: 1.35→1.37 Å / Redundancy: 12.8 % / Rmerge(I) obs: 1.8 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 18056 / CC1/2: 0.62 / Rpim(I) all: 0.77 / Rrim(I) all: 1.97 / Χ2: 0.8 / % possible all: 100 |
-Phasing
Phasing | Method: molecular replacement |
---|
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6syo Resolution: 1.35→44.8 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.972 / SU B: 0.915 / SU ML: 0.035 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.045 / ESU R Free: 0.046 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 68.29 Å2 / Biso mean: 14.875 Å2 / Biso min: 5.66 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.35→44.8 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.35→1.385 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
|