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Yorodumi- PDB-9iil: Structure of the complex of erythrose-4-phosphate dehydrogenase f... -
+Open data
-Basic information
Entry | Database: PDB / ID: 9iil | |||||||||
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Title | Structure of the complex of erythrose-4-phosphate dehydrogenase from Acinetobacter baumannii with nicotinamide adenine dinucleotide in the presence of poly(ethylene glycol) at 2.20 A resolution | |||||||||
Components | Glyceraldehyde-3-phosphate dehydrogenase | |||||||||
Keywords | OXIDOREDUCTASE / Dehydrogenase | |||||||||
Function / homology | Function and homology information Oxidoreductases; Acting on the aldehyde or oxo group of donors; With NAD+ or NADP+ as acceptor / glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity / glucose metabolic process / NAD binding / NADP binding / cytosol Similarity search - Function | |||||||||
Biological species | Acinetobacter baumannii (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | |||||||||
Authors | Viswanathan, V. / Kumari, A. / Singh, A. / Kumar, A. / Sharma, P. / Chopra, S. / Jeyakanthan, J. / Sharma, S. / Raje, C.I. / Singh, T.P. | |||||||||
Funding support | India, 2items
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Citation | Journal: To Be Published Title: Structure of the complex of erythrose-4-phosphate dehydrogenase from Acinetobacter baumannii with nicotinamide adenine dinucleotide in the presence of poly(ethylene glycol) at 2.20 A resolution Authors: Viswanathan, V. / Kumari, A. / Singh, A. / Kumar, A. / Sharma, P. / Chopra, S. / Jeyakanthan, J. / Sharma, S. / Raje, C.I. / Singh, T.P. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 9iil.cif.gz | 308.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb9iil.ent.gz | 243 KB | Display | PDB format |
PDBx/mmJSON format | 9iil.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 9iil_validation.pdf.gz | 9 MB | Display | wwPDB validaton report |
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Full document | 9iil_full_validation.pdf.gz | 9.1 MB | Display | |
Data in XML | 9iil_validation.xml.gz | 59.4 KB | Display | |
Data in CIF | 9iil_validation.cif.gz | 82.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ii/9iil ftp://data.pdbj.org/pub/pdb/validation_reports/ii/9iil | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 38062.383 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Acinetobacter baumannii (bacteria) Gene: epd, gap, A7M90_08740, Aba7835_13565, ABCAM1_1226, ABR2091_1144, APD17_19525, AYR68_05750, B7L45_13105, B9W25_17760, C2U32_02225, CAS83_00220, CBL15_12235, CTZ19_12640, D8O08_008145, DLI71_ ...Gene: epd, gap, A7M90_08740, Aba7835_13565, ABCAM1_1226, ABR2091_1144, APD17_19525, AYR68_05750, B7L45_13105, B9W25_17760, C2U32_02225, CAS83_00220, CBL15_12235, CTZ19_12640, D8O08_008145, DLI71_18430, EA706_09520, EA720_004470, EGM95_14355, F4T85_07645, FDN00_13975, FE003_13215, FJU42_18405, FJV09_11310, GSE42_06795, HBK86_03865, IAG11_16195, SAMEA4394745_03679 Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: A0A059ZTK9, Oxidoreductases; Acting on the aldehyde or oxo group of donors; With NAD+ or NADP+ as acceptor |
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-Non-polymers , 10 types, 661 molecules
#2: Chemical | ChemComp-NAD / #3: Chemical | ChemComp-PEG / #4: Chemical | ChemComp-PG4 / #5: Chemical | ChemComp-EDO / #6: Chemical | ChemComp-PO4 / | #7: Chemical | ChemComp-PGE / #8: Chemical | #9: Chemical | #10: Chemical | ChemComp-GOL / | #11: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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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: 2.98 Å3/Da / Density % sol: 58.78 % |
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Crystal grow | Temperature: 298 K / Method: evaporation / pH: 7.5 Details: 0.2 M MgCl2.6H2O, 0.1M HEPES sodium (pH 7.5), 30% v/v PEG 400 |
-Data collection
Diffraction | Mean temperature: 298 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.87313 Å |
Detector | Type: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Jul 28, 2023 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.87313 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→88.454 Å / Num. obs: 91060 / % possible obs: 98.9 % / Redundancy: 13.9 % / CC1/2: 0.997 / Rmerge(I) obs: 0.23 / Rpim(I) all: 0.064 / Rrim(I) all: 0.23 / Net I/σ(I): 9.3 |
Reflection shell | Resolution: 2.2→2.24 Å / Redundancy: 14.4 % / Rmerge(I) obs: 2.38 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 4425 / CC1/2: 0.725 / Rpim(I) all: 0.64 / Rrim(I) all: 2.46 / % possible all: 98.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→88.454 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.948 / WRfactor Rfree: 0.202 / WRfactor Rwork: 0.152 / SU B: 6.775 / SU ML: 0.159 / Average fsc free: 0.9572 / Average fsc work: 0.9694 / Cross valid method: FREE R-VALUE / ESU R: 0.197 / ESU R Free: 0.175 Details: Hydrogens have been added in their riding positions
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 45.029 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→88.454 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20
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