[English] 日本語
Yorodumi- PDB-1xmg: Crystal structure of apo methane monooxygenase hydroxylase from M... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1xmg | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of apo methane monooxygenase hydroxylase from M. capsulatus (Bath) | ||||||
Components |
| ||||||
Keywords | OXIDOREDUCTASE / apo protein / four-helix bundle / methane / diiron / MMOH | ||||||
Function / homology | Function and homology information methane metabolic process / methane monooxygenase (soluble) / : / : / : / one-carbon metabolic process / metal ion binding Similarity search - Function | ||||||
Biological species | Methylococcus capsulatus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Sazinsky, M.H. / Merkx, M. / Cadieux, E. / Tang, S. / Lippard, S.J. | ||||||
Citation | Journal: Biochemistry / Year: 2004 Title: Preparation and X-ray Structures of Metal-Free, Dicobalt and Dimanganese Forms of Soluble Methane Monooxygenase Hydroxylase from Methylococcus capsulatus (Bath) Authors: Sazinsky, M.H. / Merkx, M. / Cadieux, E. / Tang, S. / Lippard, S.J. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1xmg.cif.gz | 444.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1xmg.ent.gz | 360.6 KB | Display | PDB format |
PDBx/mmJSON format | 1xmg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1xmg_validation.pdf.gz | 487.6 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1xmg_full_validation.pdf.gz | 558.8 KB | Display | |
Data in XML | 1xmg_validation.xml.gz | 87.8 KB | Display | |
Data in CIF | 1xmg_validation.cif.gz | 122.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xm/1xmg ftp://data.pdbj.org/pub/pdb/validation_reports/xm/1xmg | HTTPS FTP |
-Related structure data
Related structure data | 1xmfC 1xmhC 1fz1S C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 60719.113 Da / Num. of mol.: 2 / Fragment: alpha subunit / Source method: isolated from a natural source / Details: gene MMOX / Source: (natural) Methylococcus capsulatus (bacteria) / Strain: Bath References: UniProt: P22869, methane monooxygenase (soluble) #2: Protein | Mass: 45111.504 Da / Num. of mol.: 2 / Fragment: beta subunit / Source method: isolated from a natural source / Details: gene MMOY / Source: (natural) Methylococcus capsulatus (bacteria) / Strain: Bath References: UniProt: P18798, methane monooxygenase (soluble) #3: Protein | Mass: 19748.537 Da / Num. of mol.: 2 / Fragment: gamma subunit / Source method: isolated from a natural source / Details: gene MMOZ / Source: (natural) Methylococcus capsulatus (bacteria) / Strain: Bath References: UniProt: P11987, methane monooxygenase (soluble) #4: Chemical | #5: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.6 Å3/Da / Density % sol: 52.7 % |
---|---|
Crystal grow | Temperature: 278 K / Method: vapor diffusion, hanging drop / pH: 7 Details: MOPS, PEG 8000, calcium chloride, glycerol, azide, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 278K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 10, 2003 |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→30 Å / Num. obs: 156085 / % possible obs: 92.2 % / Observed criterion σ(I): 2 / Redundancy: 3.8 % / Biso Wilson estimate: 15.5 Å2 / Rmerge(I) obs: 0.069 / Rsym value: 0.069 / Net I/σ(I): 13.6 |
Reflection shell | Resolution: 2.1→2.23 Å / Rmerge(I) obs: 0.435 / Mean I/σ(I) obs: 3.1 / Rsym value: 0.435 / % possible all: 88.3 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB 1FZ1 Resolution: 2.1→24.77 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 134957.23 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / Stereochemistry target values: Engh & Huber
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 54.1882 Å2 / ksol: 0.364143 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 39.9 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→24.77 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.1→2.23 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
|