+Open data
-Basic information
Entry | Database: PDB / ID: 5och | ||||||
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Title | The crystal structure of human ABCB8 in an outward-facing state | ||||||
Components | (ATP-binding cassette sub-family B member 8, ...) x 5 | ||||||
Keywords | HYDROLASE / Membrane protein / ATP binding / ATP binding cassette / half transporter / Structural Genomics / Structural Genomics Consortium / SGC | ||||||
Function / homology | Function and homology information mitochondrial ATP-gated potassium channel complex / mitochondrial potassium ion transmembrane transport / Mitochondrial ABC transporters / cell volume homeostasis / ATPase-coupled transmembrane transporter activity / ABC-type transporter activity / potassium ion transmembrane transport / ATP-binding cassette (ABC) transporter complex / mitochondrial membrane / transmembrane transport ...mitochondrial ATP-gated potassium channel complex / mitochondrial potassium ion transmembrane transport / Mitochondrial ABC transporters / cell volume homeostasis / ATPase-coupled transmembrane transporter activity / ABC-type transporter activity / potassium ion transmembrane transport / ATP-binding cassette (ABC) transporter complex / mitochondrial membrane / transmembrane transport / mitochondrial inner membrane / nucleolus / ATP hydrolysis activity / mitochondrion / nucleoplasm / ATP binding Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.4 Å | ||||||
Authors | Faust, B. / Pike, A.C.W. / Shintre, C.A. / Quiqley, A.M. / Chu, A. / Barr, A. / Shrestha, L. / Mukhopadhyay, S. / Borkowska, O. / Chalk, R. ...Faust, B. / Pike, A.C.W. / Shintre, C.A. / Quiqley, A.M. / Chu, A. / Barr, A. / Shrestha, L. / Mukhopadhyay, S. / Borkowska, O. / Chalk, R. / Burgess-Brown, N.A. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Carpenter, E.P. / Structural Genomics Consortium (SGC) | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: To Be Published Title: The crystal structure of human ABCB8 in an outward-facing state Authors: Faust, B. / Pike, A.C.W. / Shintre, C.A. / Quiqley, A.M. / Chu, A. / Barr, A. / Shrestha, L. / Mukhopadhyay, S. / Borkowska, O. / Chalk, R. / Burgess-Brown, N.A. / Arrowsmith, C.H. / ...Authors: Faust, B. / Pike, A.C.W. / Shintre, C.A. / Quiqley, A.M. / Chu, A. / Barr, A. / Shrestha, L. / Mukhopadhyay, S. / Borkowska, O. / Chalk, R. / Burgess-Brown, N.A. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Carpenter, E.P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5och.cif.gz | 1.6 MB | Display | PDBx/mmCIF format |
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PDB format | pdb5och.ent.gz | 1.3 MB | Display | PDB format |
PDBx/mmJSON format | 5och.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oc/5och ftp://data.pdbj.org/pub/pdb/validation_reports/oc/5och | HTTPS FTP |
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-Related structure data
Related structure data | 3zdqS S: Starting model for refinement |
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Similar structure data |
-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
-ATP-binding cassette sub-family B member 8, ... , 5 types, 8 molecules ACDBEFGH
#1: Protein | Mass: 66540.805 Da / Num. of mol.: 3 / Fragment: UNP residues 111-714 Source method: isolated from a genetically manipulated source Details: Protein was alkylated with iodoacetamide prior to crystallisation Source: (gene. exp.) Homo sapiens (human) / Gene: ABCB8, MABC1 / Plasmid: pFB-CT10HF-LIC / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9NUT2 #2: Protein | | Mass: 66597.859 Da / Num. of mol.: 1 / Fragment: UNP residues 111-714 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ABCB8, MABC1 / Plasmid: pFB-CT10HF-LIC / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9NUT2 #3: Protein | | Mass: 66597.859 Da / Num. of mol.: 1 / Fragment: UNP residues 111-714 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ABCB8, MABC1 / Plasmid: pFB-CT10HF-LIC / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9NUT2 #4: Protein | Mass: 66597.859 Da / Num. of mol.: 2 / Fragment: UNP residues 111-714 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ABCB8, MABC1 / Plasmid: pFB-CT10HF-LIC / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9NUT2 #5: Protein | | Mass: 66483.750 Da / Num. of mol.: 1 / Fragment: UNP residues 111-714 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ABCB8, MABC1 / Plasmid: pFB-CT10HF-LIC / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9NUT2 |
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-Non-polymers , 3 types, 23 molecules
#6: Chemical | ChemComp-ADP / #7: Chemical | ChemComp-MG / #8: Chemical | ChemComp-Y01 / |
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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: 3.6 Å3/Da / Density % sol: 65.81 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.1M HEPES pH 7.5 -- 18% PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 27, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9686 Å / Relative weight: 1 |
Reflection | Resolution: 3.4→72.61 Å / Num. obs: 104497 / % possible obs: 99.9 % / Redundancy: 6.9 % / Biso Wilson estimate: 122.428 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.22 / Rpim(I) all: 0.09 / Net I/σ(I): 7 |
Reflection shell | Resolution: 3.4→3.46 Å / Redundancy: 6.8 % / Rmerge(I) obs: 7.3 / Mean I/σ(I) obs: 0.3 / Num. unique obs: 5020 / CC1/2: 0.078 / Rpim(I) all: 2.984 / % possible all: 98 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3ZDQ Resolution: 3.4→72.61 Å / Cor.coef. Fo:Fc: 0.8701 / Cor.coef. Fo:Fc free: 0.8638 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.667 Details: DATA WERE ANISOTROPICALLY TRUNCATED TO 3.4A PRIOR TO REFINEMENT USING STARANISO SERVER. ANISOTROPIC CUTOFFS WERE 5.14A, 5.44A and 3.4A RESPECTIVELY. DATA COMPLETENESS DROPS OFF MARKEDLY ...Details: DATA WERE ANISOTROPICALLY TRUNCATED TO 3.4A PRIOR TO REFINEMENT USING STARANISO SERVER. ANISOTROPIC CUTOFFS WERE 5.14A, 5.44A and 3.4A RESPECTIVELY. DATA COMPLETENESS DROPS OFF MARKEDLY ABOVE 4A RESOLUTION BUT THIS APPROACH RESULTED IN IMPROVED MAP QUALITY. AFTER TRUNCATION CC1/2 IN HIGH RESOLUTION SHELL WAS 0.5485. A SINGLE TLS GROUP PER PROTEIN CHAIN WAS USED. MAPS WERE SHARPENED IN COOT USING A -100A**2 FOR MODEL BUILDING. BOTH TRUNCATED AND UNTRUNCATED SF DATA ARE PRESENT IN ASSOCIATED SF FILE
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Displacement parameters | Biso mean: 137.29 Å2
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Refine analyze | Luzzati coordinate error obs: 0.604 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 3.4→72.61 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.4→3.49 Å / 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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