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Yorodumi- PDB-7sua: Crystal Structure of the Hypothetical Protein (ACX60_00475) from ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7sua | ||||||
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Title | Crystal Structure of the Hypothetical Protein (ACX60_00475) from Acinetobacter baumannii | ||||||
Components | DUF4175 domain-containing protein | ||||||
Keywords | UNKNOWN FUNCTION / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / Center for Structural Biology of Infectious Diseases / CSBID | ||||||
Function / homology | membrane => GO:0016020 / DI(HYDROXYETHYL)ETHER / DUF4175 domain-containing protein Function and homology information | ||||||
Biological species | Acinetobacter baumannii (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.65 Å | ||||||
Authors | Minasov, G. / Shuvalova, L. / Dubrovska, I. / Kiryukhina, O. / Satchell, K.J.F. / Center for Structural Biology of Infectious Diseases (CSBID) | ||||||
Funding support | United States, 1items
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Citation | Journal: To be Published Title: Crystal Structure of the Hypothetical Protein (ACX60_00475) from Acinetobacter baumannii Authors: Minasov, G. / Shuvalova, L. / Dubrovska, I. / Kiryukhina, O. / Satchell, K.J.F. / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7sua.cif.gz | 101.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7sua.ent.gz | 78.9 KB | Display | PDB format |
PDBx/mmJSON format | 7sua.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/su/7sua ftp://data.pdbj.org/pub/pdb/validation_reports/su/7sua | HTTPS FTP |
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-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 31845.115 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Acinetobacter baumannii (bacteria) Gene: C2U32_13765, C5H40_02315, CPI82_04650, CTZ19_00475, D8O08_001740, DLI71_12185, DLI72_04775, E1A87_06460, E2535_11650, E2539_19140, EA706_08735, EA720_011135, EA722_13985, EKS29_19110, EP550_ ...Gene: C2U32_13765, C5H40_02315, CPI82_04650, CTZ19_00475, D8O08_001740, DLI71_12185, DLI72_04775, E1A87_06460, E2535_11650, E2539_19140, EA706_08735, EA720_011135, EA722_13985, EKS29_19110, EP550_00510, EP560_17500, F2P40_11735, F4T85_08810, F4T91_09080, FE003_00465, FJU36_16290, FJU42_18320, FR761_00435, GSE42_19580, H0529_16845, HBK86_17525, IMO23_17555 Plasmid: pMCSG53 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): magic / References: UniProt: A0A237U7Y1 |
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#2: Chemical | ChemComp-PEG / |
#3: Chemical | ChemComp-EDO / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.8 Å3/Da / Density % sol: 31.72 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: Protein: 8.8 mg/ml, 0.01M Tris HCl (pH 8.3); Screen: Classics II (D10), 0.1M Bis-Tris (pH 6.5), 20% (w/v) PEG5000 MME |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-E / Wavelength: 0.97872 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 22, 2019 / Details: Be |
Radiation | Monochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97872 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→30 Å / Num. obs: 27958 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 4.3 % / Biso Wilson estimate: 22.7 Å2 / Rmerge(I) obs: 0.069 / Rpim(I) all: 0.037 / Rrim(I) all: 0.079 / Rsym value: 0.069 / Χ2: 1.572 / Net I/σ(I): 24.3 |
Reflection shell | Resolution: 1.65→1.68 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.687 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 1354 / CC1/2: 0.71 / CC star: 0.911 / Rpim(I) all: 0.379 / Rrim(I) all: 0.787 / Rsym value: 0.687 / Χ2: 1 / % possible all: 99 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.65→27.06 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.945 / SU B: 3.616 / SU ML: 0.061 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.095 / ESU R Free: 0.095 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
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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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 98.08 Å2 / Biso mean: 25.796 Å2 / Biso min: 13.01 Å2
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Refinement step | Cycle: final / Resolution: 1.65→27.06 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.655→1.697 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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