+Open data
-Basic information
Entry | Database: PDB / ID: 1gq2 | ||||||
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Title | Malic Enzyme from Pigeon Liver | ||||||
Components | MALIC ENZYME | ||||||
Keywords | OXIDOREDUCTASE / MALIC ENZYME / PIGEON LIVER / NADP-DEPENDENT / NAD-NADP SELECTIVITY / DECARBOXYLASE / MALATE / MN2+ | ||||||
Function / homology | Function and homology information malate dehydrogenase (oxaloacetate-decarboxylating) (NADP+) / malate dehydrogenase (decarboxylating) (NAD+) activity / malate dehydrogenase (decarboxylating) (NADP+) activity / oxaloacetate decarboxylase activity / NAD binding / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | COLUMBA LIVIA (rock pigeon) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Yang, Z. / Zhang, H. / Liang, T. | ||||||
Citation | Journal: Protein Sci. / Year: 2002 Title: Structural Studies of the Pigeon Cytosolic Nadp+ -Dependent Malic Enzyme Authors: Yang, Z. / Zhang, H. / Huang, H.-C. / Kuo, C.-C. / Tsai, L.-C. / Yuan, H.S. / Chou, W.-Y. / Chang, G.-G. / Tong, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1gq2.cif.gz | 1.6 MB | Display | PDBx/mmCIF format |
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PDB format | pdb1gq2.ent.gz | 1.4 MB | Display | PDB format |
PDBx/mmJSON format | 1gq2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gq/1gq2 ftp://data.pdbj.org/pub/pdb/validation_reports/gq/1gq2 | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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2 |
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3 |
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4 |
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Unit cell |
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-Components
-Protein , 1 types, 16 molecules ABCDEFGHIJKLMNOP
#1: Protein | Mass: 62536.523 Da / Num. of mol.: 16 Source method: isolated from a genetically manipulated source Details: NADP+, OXALATE, MN2+ / Source: (gene. exp.) COLUMBA LIVIA (rock pigeon) / Organ: LIVER / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) References: UniProt: P40927, malate dehydrogenase (oxaloacetate-decarboxylating) (NADP+) |
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-Non-polymers , 6 types, 1166 molecules
#2: Chemical | ChemComp-NAP / #3: Chemical | ChemComp-OXL / #4: Chemical | ChemComp-MN / #5: Chemical | ChemComp-CL / #6: Chemical | ChemComp-NA / #7: Water | ChemComp-HOH / | |
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-Details
Compound details | THERE ARE 3 CIS-PRO FROM CHAIN A TO CHAIN P. THE PROLINES IN CIS CONFORMATISequence details | THE SEQUENCES WAS RENUMBERED | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.94 Å3/Da / Density % sol: 57.9 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 5.5 / Details: 100 MM SODIUM CITRATE, PH 5.5, 8% PEG6000, 1M LICL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / pH: 7.4 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 277 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 1.176 |
Detector | Type: ADSC Q-4 / Date: Feb 15, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.176 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→20 Å / Num. obs: 334606 / % possible obs: 88.2 % / Observed criterion σ(I): 2 / Redundancy: 2 % / Biso Wilson estimate: 17.4 Å2 / Rmerge(I) obs: 0.082 / Net I/σ(I): 10.6 |
Reflection shell | Resolution: 2.5→2.59 Å / Redundancy: 2 % / Rmerge(I) obs: 0.214 / Mean I/σ(I) obs: 3.6 / % possible all: 76 |
Reflection | *PLUS Lowest resolution: 20 Å / Num. obs: 314771 / % possible obs: 83 % / Num. measured all: 570674 |
Reflection shell | *PLUS Lowest resolution: 2.6 Å / % possible obs: 76 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB Resolution: 2.5→10 Å / Rfactor Rfree error: 0.002 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 36.1018 Å2 / ksol: 0.419231 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.5→10 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.52 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 50
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Xplor file |
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Refinement | *PLUS Lowest resolution: 10 Å / Rfactor obs: 0.211 / Rfactor Rfree: 0.258 / Rfactor Rwork: 0.211 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Lowest resolution: 2.6 Å / Rfactor Rfree: 0.342 / Rfactor Rwork: 0.302 / Rfactor obs: 0.302 |