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- PDB-8zn1: Structure of erythrose-4-phosphate dehydrogenase from Acinetobact... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8zn1 | |||||||||
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Title | Structure of erythrose-4-phosphate dehydrogenase from Acinetobacter baumannii at 3.00 A resolution | |||||||||
![]() | Glyceraldehyde-3-phosphate dehydrogenase | |||||||||
![]() | OXIDOREDUCTASE / Dehydrogenase | |||||||||
Function / homology | ![]() 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 | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Viswanathan, V. / Kumari, A. / Singh, A. / Kumar, A. / Sharma, P. / Chopra, S. / Sharma, S. / Raje, C.I. / Singh, T.P. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Structure of erythrose-4-phosphate dehydrogenase from Acinetobacter baumannii at 3.00 A resolution Authors: Viswanathan, V. / Kumari, A. / Singh, A. / Kumar, A. / Sharma, P. / Chopra, S. / Sharma, S. / Raje, C.I. / Singh, T.P. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 290.1 KB | Display | ![]() |
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PDB format | ![]() | 228.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 3.3 MB | Display | ![]() |
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Full document | ![]() | 3.3 MB | Display | |
Data in XML | ![]() | 52.9 KB | Display | |
Data in CIF | ![]() | 72 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3cmcS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 38062.383 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() 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: ![]() ![]() References: UniProt: A0A059ZTK9, Oxidoreductases; Acting on the aldehyde or oxo group of donors; With NAD+ or NADP+ as acceptor #2: Chemical | ChemComp-NAD / #3: Chemical | ChemComp-SO4 / #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.1 Å3/Da / Density % sol: 60.31 % |
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Crystal grow | Temperature: 298 K / Method: evaporation / pH: 7.5 Details: A reservoir solution containing 0.2 M MgCl2.6H2O, 0.1 M HEPES sodium (pH 7.5), and 30% v/v PEG 400 was prepared. |
-Data collection
Diffraction | Mean temperature: 298 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
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: 3→49.536 Å / Num. obs: 38162 / % possible obs: 100 % / Redundancy: 13.5 % / CC1/2: 0.971 / Rmerge(I) obs: 0.73 / Rpim(I) all: 0.21 / Rrim(I) all: 0.79 / Net I/σ(I): 7.3 |
Reflection shell | Resolution: 3→3.13 Å / Redundancy: 14.4 % / Rmerge(I) obs: 2.86 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 4573 / CC1/2: 0.69 / Rpim(I) all: 0.78 / Rrim(I) all: 2.98 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3CMC Resolution: 3→49.536 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.894 / SU B: 19.96 / SU ML: 0.336 / Cross valid method: FREE R-VALUE / ESU R Free: 0.4 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: 48.146 Å2
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Refinement step | Cycle: LAST / Resolution: 3→49.536 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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