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Yorodumi- PDB-1mio: X-RAY CRYSTAL STRUCTURE OF THE NITROGENASE MOLYBDENUM-IRON PROTEI... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1mio | ||||||
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Title | X-RAY CRYSTAL STRUCTURE OF THE NITROGENASE MOLYBDENUM-IRON PROTEIN FROM CLOSTRIDIUM PASTEURIANUM AT 3.0 ANGSTROMS RESOLUTION | ||||||
Components | (NITROGENASE MOLYBDENUM IRON PROTEIN ...) x 2 | ||||||
Keywords | MOLYBDENUM-IRON PROTEIN | ||||||
Function / homology | Function and homology information molybdenum-iron nitrogenase complex / nitrogenase / : / nitrogenase activity / nitrogen fixation / iron-sulfur cluster binding / ATP binding / metal ion binding Similarity search - Function | ||||||
Biological species | Clostridium pasteurianum (bacteria) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 3 Å | ||||||
Authors | Kim, J. / Woo, D. / Rees, D.C. | ||||||
Citation | Journal: Biochemistry / Year: 1993 Title: X-ray crystal structure of the nitrogenase molybdenum-iron protein from Clostridium pasteurianum at 3.0-A resolution. Authors: Kim, J. / Woo, D. / Rees, D.C. #1: Journal: Science / Year: 1992 Title: Structural Models for the Metal Centers in the Nitrogenase Molybdenum-Iron Protein Authors: Kim, J. / Rees, D.C. #2: Journal: Nature / Year: 1992 Title: Crystallographic Structure and Functional Implications of the Nitrogenase Molybdenum-Iron Protein from Azotobacter Vinelandii Authors: Kim, J. / Rees, D.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1mio.cif.gz | 384.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1mio.ent.gz | 304.2 KB | Display | PDB format |
PDBx/mmJSON format | 1mio.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1mio_validation.pdf.gz | 470.1 KB | Display | wwPDB validaton report |
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Full document | 1mio_full_validation.pdf.gz | 566 KB | Display | |
Data in XML | 1mio_validation.xml.gz | 49.8 KB | Display | |
Data in CIF | 1mio_validation.cif.gz | 71.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mi/1mio ftp://data.pdbj.org/pub/pdb/validation_reports/mi/1mio | 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: ILE A 14 - PRO A 15 OMEGA =215.99 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION 2: CIS PROLINE - PRO A 489 / 3: CIS PROLINE - PRO B 202 4: ILE B 337 - PRO B 338 OMEGA =142.51 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION 5: CIS PROLINE - PRO B 412 6: THR C 32 - PRO C 33 OMEGA =217.34 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION 7: CIS PROLINE - PRO C 489 8: LEU D 115 - PRO D 116 OMEGA =147.89 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION 9: CIS PROLINE - PRO D 202 / 10: CIS PROLINE - PRO D 412 |
-Components
-NITROGENASE MOLYBDENUM IRON PROTEIN ... , 2 types, 4 molecules ACBD
#1: Protein | Mass: 59071.211 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Clostridium pasteurianum (bacteria) / References: UniProt: P00467 #2: Protein | Mass: 50175.145 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Clostridium pasteurianum (bacteria) / References: UniProt: P11347 |
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-Non-polymers , 4 types, 8 molecules
#3: Chemical | #4: Chemical | #5: Chemical | #6: Chemical | |
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-Details
Nonpolymer details | Y IN THE FEMO-COFACTOR (CLM) HAS BEEN REFINED AS S. |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.77 Å3/Da / Density % sol: 55.54 % | ||||||||||||||||||||||||||||||
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Crystal grow | *PLUS pH: 8 / Method: batch methodDetails: taken from Kim, J. and Rees, D.C. (1992). Science, 257 1677-1682. | ||||||||||||||||||||||||||||||
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: 3 Å / % possible obs: 78 % / Num. measured all: 38527 / Rmerge(I) obs: 0.07 |
-Processing
Software |
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Refinement | Rfactor Rwork: 0.18 / Rfactor obs: 0.18 / Highest resolution: 3 Å Details: THERE ARE NO RELIABLE POSITIONS FROM A 527 - A 534 AND C 527 - C 534. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 3 Å
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Refine LS restraints |
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Refinement | *PLUS Highest resolution: 3 Å / Lowest resolution: 10 Å / Num. reflection obs: 37205 / Rfactor obs: 0.18 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: x_angle_d |