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Yorodumi- PDB-1mmo: CRYSTAL STRUCTURE OF A BACTERIAL NON-HAEM IRON HYDROXYLASE THAT C... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1mmo | ||||||
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Title | CRYSTAL STRUCTURE OF A BACTERIAL NON-HAEM IRON HYDROXYLASE THAT CATALYSES THE BIOLOGICAL OXIDATION OF METHANE | ||||||
Components | (METHANE MONOOXYGENASE HYDROLASE ...) x 3 | ||||||
Keywords | OXIDOREDUCTASE (MONOOXYGENASE) | ||||||
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 / Resolution: 2.2 Å | ||||||
Authors | Rosenzweig, A.C. / Frederick, C.A. / Lippard, S.J. / Nordlund, P. | ||||||
Citation | Journal: Nature / Year: 1993 Title: Crystal structure of a bacterial non-haem iron hydroxylase that catalyses the biological oxidation of methane. Authors: Rosenzweig, A.C. / Frederick, C.A. / Lippard, S.J. / Nordlund, P. | ||||||
History |
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Remark 650 | HELIX IN *HELIX* RECORDS BELOW, HELIX IDENTIFIERS WHICH BEGIN WITH THE LETTER "D" OR "E" DENOTE THE ...HELIX IN *HELIX* RECORDS BELOW, HELIX IDENTIFIERS WHICH BEGIN WITH THE LETTER "D" OR "E" DENOTE THE A SUBUNIT. HELIX IDENTIFIERS WHICH BEGIN WITH THE LETTER "B" OR "C" DENOTE THE B SUBUNIT. HELIX IDENTIFIERS WHICH BEGIN WITH THE LETTER "G" OR "H" DENOTE THE G SUBUNIT. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1mmo.cif.gz | 565.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1mmo.ent.gz | 457 KB | Display | PDB format |
PDBx/mmJSON format | 1mmo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1mmo_validation.pdf.gz | 423.1 KB | Display | wwPDB validaton report |
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Full document | 1mmo_full_validation.pdf.gz | 510.8 KB | Display | |
Data in XML | 1mmo_validation.xml.gz | 49 KB | Display | |
Data in CIF | 1mmo_validation.cif.gz | 77 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mm/1mmo ftp://data.pdbj.org/pub/pdb/validation_reports/mm/1mmo | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Atom site foot note | 1: ALA D 19 - PRO D 20 OMEGA = 149.54 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION 2: ALA E 19 - PRO E 20 OMEGA = 146.10 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION 3: CIS PROLINE - PRO G 121 / 4: CIS PROLINE - PRO H 121 | ||||||||
Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.9999, -0.00538, -0.00427), Vector: Details | THERE IS A NON-CRYSTALLOGRAPHIC TWO-FOLD AXIS RELATING THE ABG PAIRS IN THE DIMER. THE TRANSFORMATION PRESENTED ON *MTRIX* RECORDS BELOW WILL YIELD APPROXIMATE COORDINATES FOR CHAINS C, E, AND H WHEN APPLIED TO CHAINS B, D, AND G, RESPECTIVELY. | |
-Components
-METHANE MONOOXYGENASE HYDROLASE ... , 3 types, 6 molecules BCDEGH
#1: Protein | Mass: 44452.742 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Methylococcus capsulatus (bacteria) References: UniProt: P18798, methane monooxygenase (soluble) #2: Protein | Mass: 59241.492 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Methylococcus capsulatus (bacteria) References: UniProt: P22869, methane monooxygenase (soluble) #3: Protein | Mass: 18980.639 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Methylococcus capsulatus (bacteria) References: UniProt: P11987, methane monooxygenase (soluble) |
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-Non-polymers , 3 types, 865 molecules
#4: Chemical | ChemComp-FE / #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Details
Compound details | IN *TURN* RECORDS BELOW, TURN IDENTIFIERS WHICH BEGIN WITH THE LETTER "D" OR "E" CORRESPOND TO THE ...IN *TURN* RECORDS BELOW, TURN IDENTIFIER |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.34 Å3/Da / Density % sol: 47.47 % | ||||||||||||||||||||||||||||||
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Crystal grow | *PLUS pH: 7 / Method: unknown | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Radiation | Scattering type: x-ray |
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Radiation wavelength | Relative weight: 1 |
Reflection | *PLUS Highest resolution: 2.2 Å / Num. obs: 103751 / % possible obs: 92 % / Rmerge(I) obs: 0.094 |
-Processing
Software |
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Refinement | Resolution: 2.2→5 Å / σ(F): 0 /
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Refinement step | Cycle: LAST / Resolution: 2.2→5 Å
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Refine LS restraints |
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Refinement | *PLUS Rfactor obs: 0.17 / Rfactor Rwork: 0.17 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: x_angle_d / Dev ideal: 2.9 |