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Yorodumi- PDB-1qid: SPECIFIC CHEMICAL AND STRUCTURAL DAMAGE AT NINE TIME POINTS (POIN... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1qid | ||||||
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Title | SPECIFIC CHEMICAL AND STRUCTURAL DAMAGE AT NINE TIME POINTS (POINT A) CAUSED BY INTENSE SYNCHROTRON RADIATION TO TORPEDO CALIFORNICA ACETYLCHOLINESTERASE | ||||||
Components | ACETYLCHOLINESTERASE | ||||||
Keywords | HYDROLASE / RADIATION DAMAGE / TIME SERIES / DISULFIDE BOND / SERINE HYDROLASE / ALPHA/BETA HYDROLASE / NEUROTRANSMITTER CLEAVAGE / CATALYTIC TRIAD / GLYCOSYLATED PROTEIN | ||||||
Function / homology | Function and homology information acetylcholine catabolic process in synaptic cleft / acetylcholinesterase / acetylcholinesterase activity / synaptic cleft / side of membrane / synapse / plasma membrane Similarity search - Function | ||||||
Biological species | Torpedo californica (Pacific electric ray) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å | ||||||
Authors | Kryger, G. / Weik, M. / Ravelli, R.B.G. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2000 Title: Specific chemical and structural damage to proteins produced by synchrotron radiation. Authors: Weik, M. / Ravelli, R.B. / Kryger, G. / McSweeney, S. / Raves, M.L. / Harel, M. / Gros, P. / Silman, I. / Kroon, J. / Sussman, J.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1qid.cif.gz | 115.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1qid.ent.gz | 89.4 KB | Display | PDB format |
PDBx/mmJSON format | 1qid.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qi/1qid ftp://data.pdbj.org/pub/pdb/validation_reports/qi/1qid | HTTPS FTP |
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-Related structure data
Related structure data | 1qieC 1qifC 1qigC 1qihC 1qiiC 1qijC 1qikC 1qimC 1qioC 1vxrS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 60736.516 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Torpedo californica (Pacific electric ray) Organ: ELECTRIC ORGAN / Variant: G2 FORM / Tissue: ELECTROPLAQUE / References: UniProt: P04058, acetylcholinesterase |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.8 Å3/Da / Density % sol: 68 % | ||||||||||||||||||||
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Crystal grow | Temperature: 277 K / pH: 5.8 / Details: 30% PEG 200, 0.3 M MES, pH 5.8, temperature 277K | ||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / Method: vapor diffusion, hanging drop | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.932 |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 1, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.932 Å / Relative weight: 1 |
Reflection | Resolution: 2.05→35.45 Å / Num. obs: 62401 / % possible obs: 98.9 % / Observed criterion σ(I): 0 / Redundancy: 2.07 % / Biso Wilson estimate: 17.4 Å2 / Rsym value: 0.04 |
Reflection | *PLUS Lowest resolution: 40 Å / % possible obs: 99 % / Redundancy: 2.1 % / Rmerge(I) obs: 0.047 |
Reflection shell | *PLUS % possible obs: 99.3 % / Mean I/σ(I) obs: 2.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1VXR Resolution: 2.05→35.45 Å / Rfactor Rfree error: 0.004 / Data cutoff high rms absF: 1948681.27 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 Details: BULK SOLVENT MODEL USED. ONLY PARTIAL REFINEMENT DONE. ALL SIX CYSTEINE RESIDUES TAKING PART IN INTRACHAIN DISULFIDE LINKAGES,CYS 67-CYS 94, CYS 402-CYS 521 AND CYS 254-CYS 265, WERE MODELED ...Details: BULK SOLVENT MODEL USED. ONLY PARTIAL REFINEMENT DONE. ALL SIX CYSTEINE RESIDUES TAKING PART IN INTRACHAIN DISULFIDE LINKAGES,CYS 67-CYS 94, CYS 402-CYS 521 AND CYS 254-CYS 265, WERE MODELED AND REFINED AS ALANINE RESIDUES. TCACHE IS A GLYCOPROTEIN OF MR = 65,000, WHICH CONTAINS THREE INTRACHAIN DISULFIDE BONDS. IN THE COURSE OF CRYOGENIC DATA COLLECTION ON TRIGONAL CRYSTALS OF TCACHE ON THE UNDULATOR BEAMLINE, ID14-EH4, AT THE ESRF IN GRENOBLE, IN PREPARATION FOR TIME-RESOLVED STUDIES, WE COLLECTED A SERIES OF NINE HIGH-QUALITY COMPLETE DATA SETS ON THE SAME CRYSTAL. DATA COLLECTION UTILIZED THE UNATTENUATED BEAM, AND THE DURATION PER DATA SET WAS CA. 19 MIN, FOR 3 H IN TOTAL, AT 100K. ELECTRON DENSITY MAPS WERE OBTAINED FOR EACH DATA SET BY ROUTINE REFINEMENT, STARTING FROM THE SAME MODEL OF NATIVE TCACHE. FOR RESULTS, SEE: HTTP://SGJS3.WEIZMANN.AC.IL/~KRYGER/RADIATION_DAMAGE (LOWER CASE!) THIS ENTRY IS THE FIRST TIME POINT (1 OF 9). SEE HTTP:// SGJS3.WEIZMANN.AC.IL/~KRYGER/RADIATION_DAMAGE (LOWER CASE!)
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 53.7 Å2 / ksol: 0.374 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.5 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.05→35.45 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.07 Å / Rfactor Rfree error: 0.028 / Total num. of bins used: 10
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Xplor file |
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Software | *PLUS Name: CNS / Version: 0.5 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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