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Yorodumi- PDB-3oz2: Crystal structure of a geranylgeranyl bacteriochlorophyll reducta... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3oz2 | |||||||||
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Title | Crystal structure of a geranylgeranyl bacteriochlorophyll reductase-like (Ta0516) from Thermoplasma acidophilum at 1.60 A resolution | |||||||||
Components | Digeranylgeranylglycerophospholipid reductase | |||||||||
Keywords | Flavoprotein / oxidoreductase / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI-BIOLOGY | |||||||||
Function / homology | Function and homology information 2,3-bis-O-geranylgeranyl-sn-glycerol 1-phosphate reductase [NAD(P)H] / membrane lipid biosynthetic process / glycerophospholipid metabolic process / oxidoreductase activity, acting on the CH-CH group of donors, NAD or NADP as acceptor / geranylgeranyl reductase activity / phospholipid biosynthetic process / FAD binding / NAD binding / NADP binding / plasma membrane Similarity search - Function | |||||||||
Biological species | Thermoplasma acidophilum (acidophilic) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.6 Å | |||||||||
Authors | Joint Center for Structural Genomics (JCSG) | |||||||||
Citation | Journal: J.Mol.Biol. / Year: 2010 Title: Insights into substrate specificity of geranylgeranyl reductases revealed by the structure of digeranylgeranylglycerophospholipid reductase, an essential enzyme in the biosynthesis of archaeal membrane lipids. Authors: Xu, Q. / Eguchi, T. / Mathews, I.I. / Rife, C.L. / Chiu, H.J. / Farr, C.L. / Feuerhelm, J. / Jaroszewski, L. / Klock, H.E. / Knuth, M.W. / Miller, M.D. / Weekes, D. / Elsliger, M.A. / ...Authors: Xu, Q. / Eguchi, T. / Mathews, I.I. / Rife, C.L. / Chiu, H.J. / Farr, C.L. / Feuerhelm, J. / Jaroszewski, L. / Klock, H.E. / Knuth, M.W. / Miller, M.D. / Weekes, D. / Elsliger, M.A. / Deacon, A.M. / Godzik, A. / Lesley, S.A. / Wilson, I.A. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3oz2.cif.gz | 184.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3oz2.ent.gz | 150 KB | Display | PDB format |
PDBx/mmJSON format | 3oz2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3oz2_validation.pdf.gz | 960.3 KB | Display | wwPDB validaton report |
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Full document | 3oz2_full_validation.pdf.gz | 966.4 KB | Display | |
Data in XML | 3oz2_validation.xml.gz | 21.7 KB | Display | |
Data in CIF | 3oz2_validation.cif.gz | 32.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oz/3oz2 ftp://data.pdbj.org/pub/pdb/validation_reports/oz/3oz2 | HTTPS FTP |
-Related structure data
Similar structure data | |
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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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 44029.816 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermoplasma acidophilum (acidophilic) / Gene: Ta0516 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 References: UniProt: Q9HKS9, Oxidoreductases; Acting on the CH-CH group of donors; With NAD+ or NADP+ as acceptor |
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-Non-polymers , 5 types, 347 molecules
#2: Chemical | ChemComp-FAD / | ||||
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#3: Chemical | ChemComp-OZ2 / ( | ||||
#4: Chemical | ChemComp-EDO / #5: Chemical | #6: Water | ChemComp-HOH / | |
-Details
Sequence details | THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH ...THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATI |
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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: 2.35 Å3/Da / Density % sol: 47.55 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 15.00% Glycerol, 8.50% iso-Propanol, 17.00% PEG-4000, 0.1M HEPES pH 7.5, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.91837,0.97920,0.97862 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Feb 1, 2008 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1.6→45.257 Å / Num. obs: 55071 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 20.479 Å2 / Rmerge(I) obs: 0.052 / Net I/σ(I): 13.16 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: MAD |
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-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.6→45.257 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.968 / Occupancy max: 1 / Occupancy min: 0.37 / SU B: 2.679 / SU ML: 0.046 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.079 / ESU R Free: 0.074 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 3. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 4. WATERS WERE EXCLUDED FROM AUTOMATIC TLS ASSIGNMENT. 5. FAD IS MODELED BASED ON DENSITY AND FUNCTION. 6. A BACTERIAL LIPID FOUND IN THE ACTIVE SITE WAS TENTATIVELY ASSIGNED AS A PHOSPHATIDYLGYLCEROL (OZ2) BASED ON DENSITY AND FUNCTION. THE DENSITY FOR THE HEAD GROUP AND LIPID TAILS ARE POORLY DEFINED. 7. ETHYLENE GLYCOL (EDO) AND GLYCEROL (GOL) WERE MODELED BASED ON CRYSTALLIZATION/CYRO CONDITIONS.
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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: 101.48 Å2 / Biso mean: 29.0611 Å2 / Biso min: 9.41 Å2
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Refinement step | Cycle: LAST / Resolution: 1.6→45.257 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.6→1.642 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 13.7612 Å / Origin y: 50.0025 Å / Origin z: 25.9353 Å
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Refinement TLS group |
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