+Open data
-Basic information
Entry | Database: PDB / ID: 4aah | |||||||||
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Title | METHANOL DEHYDROGENASE FROM METHYLOPHILUS W3A1 | |||||||||
Components | (METHANOL DEHYDROGENASE) x 2 | |||||||||
Keywords | OXIDOREDUCTASE (PQQ(A)-CHOH(D)) | |||||||||
Function / homology | Function and homology information alcohol dehydrogenase (cytochrome c(L)) activity / methanol dehydrogenase (cytochrome c) / methanol oxidation / methanol metabolic process / alcohol dehydrogenase (NAD+) activity / outer membrane-bounded periplasmic space / calcium ion binding / plasma membrane Similarity search - Function | |||||||||
Biological species | Methylophilus methylotrophus (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / Resolution: 2.4 Å | |||||||||
Authors | Mathews, F.S. / Xia, Z.-X. | |||||||||
Citation | Journal: J.Mol.Biol. / Year: 1996 Title: Determination of the gene sequence and the three-dimensional structure at 2.4 angstroms resolution of methanol dehydrogenase from Methylophilus W3A1. Authors: Xia, Z. / Dai, W. / Zhang, Y. / White, S.A. / Boyd, G.D. / Mathews, F.S. #1: Journal: Biochemistry / Year: 1993 Title: The Active Site Structure of the Calcium-Containing Quinoprotein Methanol Dehydrogenase Authors: White, S. / Boyd, G. / Mathews, F.S. / Xia, Z.X. / Dai, W.W. / Zhang, Y.F. / Davidson, V.L. #2: Journal: J.Biol.Chem. / Year: 1992 Title: The Three-Dimensional Structures of Methanol Dehydrogenase from Two Methylotrophic Bacteria at 2.6-A Resolution Authors: Xia, Z.X. / Dai, W.W. / Xiong, J.P. / Hao, Z.P. / Davidson, V.L. / White, S. / Mathews, F.S. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4aah.cif.gz | 260.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4aah.ent.gz | 207.9 KB | Display | PDB format |
PDBx/mmJSON format | 4aah.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/aa/4aah ftp://data.pdbj.org/pub/pdb/validation_reports/aa/4aah | HTTPS FTP |
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-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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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.995206, -0.096998, 0.012534), Vector: Details | METHANOL DEHYDROGENASE IS AN A2B2 TETRAMER. THE ASYMMETRIC UNIT CONTAINS THE TETRAMER, TWO PYRROLOQUINOLINE QUINONE COFACTORS (PQQ) AND 2 CALCIUM COUNTER IONS. A NON-CRYSTALLOGRAPHIC TWO-FOLD AXIS RELATES THE TWO HALVES. | |
-Components
#1: Protein | Mass: 62500.555 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Methylophilus methylotrophus (bacteria) / Strain: W3A1 / References: UniProt: P38539, EC: 1.1.99.8 #2: Protein | Mass: 7770.640 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Methylophilus methylotrophus (bacteria) / Strain: W3A1 / References: UniProt: P38540, EC: 1.1.99.8 #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | Sequence details | THE AMINO ACID SEQUENCE OF MEDH FROM W3A1 WAS DERIVED FROM THE GENE SEQUENCES OF THE HEAVY AND ...THE AMINO ACID SEQUENCE OF MEDH FROM W3A1 WAS DERIVED FROM THE GENE SEQUENCES OF THE HEAVY AND LIGHT SUBUNITS IN THE LAB OF F.S. MATHEWS, GENBANK ACCESSION NUMBERS U41040 AND U41041, RESPECTIVE | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.36 Å3/Da / Density % sol: 47.94 % | ||||||||||||||||||||||||||||||
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Crystal grow | *PLUS pH: 6.8 / Method: macro seeding | ||||||||||||||||||||||||||||||
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 | Resolution: 2.4→50 Å / Num. obs: 51578 / % possible obs: 99.5 % / Observed criterion σ(I): 0 |
Reflection | *PLUS Rmerge(I) obs: 0.07 |
Reflection shell | *PLUS Highest resolution: 2.4 Å / Lowest resolution: 2.59 Å / Mean I/σ(I) obs: 3.4 |
-Processing
Software | Name: PROFFT / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Resolution: 2.4→10 Å / σ(F): 1 Details: THE STRUCTURE WAS SOLVED BY MULTIPLE ISOMORPHOUS REPLACEMENT USING THREE DERIVATIVES. THE STRUCTURE WAS SOLVED BY MULTIPLE ISOMORPHOUS REPLACEMENT USING THREE DERIVATIVES.
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Refinement step | Cycle: LAST / Resolution: 2.4→10 Å
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Refine LS restraints |
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