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- PDB-1qik: SPECIFIC CHEMICAL AND STRUCTURAL DAMAGE AT NINE TIME POINTS (POIN... -

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Basic information

Entry
Database: PDB / ID: 1qik
TitleSPECIFIC CHEMICAL AND STRUCTURAL DAMAGE AT NINE TIME POINTS (POINT H) CAUSED BY INTENSE SYNCHROTRON RADIATION TO TORPEDO CALIFORNICA ACETYLCHOLINESTERASE
ComponentsACETYLCHOLINESTERASE
KeywordsHYDROLASE / 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 / choline metabolic process / acetylcholinesterase / acetylcholinesterase activity / synaptic cleft / side of membrane / synapse / extracellular space / plasma membrane
Similarity search - Function
Acetylcholinesterase, fish/snake / : / Cholinesterase / Carboxylesterase type B, active site / Carboxylesterases type-B serine active site. / Carboxylesterase type B, conserved site / Carboxylesterases type-B signature 2. / Carboxylesterase, type B / Carboxylesterase family / Alpha/Beta hydrolase fold, catalytic domain ...Acetylcholinesterase, fish/snake / : / Cholinesterase / Carboxylesterase type B, active site / Carboxylesterases type-B serine active site. / Carboxylesterase type B, conserved site / Carboxylesterases type-B signature 2. / Carboxylesterase, type B / Carboxylesterase family / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Acetylcholinesterase
Similarity search - Component
Biological speciesTorpedo californica (Pacific electric ray)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsKryger, G. / Weik, M. / Ravelli, R.B.G.
CitationJournal: 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
DepositionJun 14, 1999Deposition site: PDBE / Processing site: RCSB
Revision 1.0Jan 28, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Aug 16, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ACETYLCHOLINESTERASE


Theoretical massNumber of molelcules
Total (without water)60,7371
Polymers60,7371
Non-polymers00
Water5,116284
1
A: ACETYLCHOLINESTERASE

A: ACETYLCHOLINESTERASE


Theoretical massNumber of molelcules
Total (without water)121,4732
Polymers121,4732
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556y,x,-z+11
Unit cell
Length a, b, c (Å)112.203, 112.203, 138.073
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein ACETYLCHOLINESTERASE


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
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 284 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.8 Å3/Da / Density % sol: 68 %
Crystal growTemperature: 292 K / pH: 5.8 / Details: 30% PEG 200, 0.3 M MES, pH 5.8, temperature 292K
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
112 mg/mlprotein1drop
238 %PEG2001reservoir
30.1 MMES1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.932
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 1, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.932 Å / Relative weight: 1
ReflectionResolution: 2.9→36.73 Å / Num. obs: 21801 / % possible obs: 95.5 % / Observed criterion σ(I): 0 / Redundancy: 1.79 % / Biso Wilson estimate: 20.3 Å2 / Rsym value: 0.081
Reflection
*PLUS
Redundancy: 1.8 % / Rmerge(I) obs: 0.094
Reflection shell
*PLUS
% possible obs: 98.6 % / Mean I/σ(I) obs: 1.8

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Processing

Software
NameVersionClassification
CNS0.5refinement
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1VXR

1vxr


Resolution: 2.9→36.73 Å / Rfactor Rfree error: 0.007 / Data cutoff high rms absF: 1957105.54 / 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 ...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 8TH TIME POINT (8 OF 9). SEE HTTP:// SGJS3.WEIZMANN.AC.IL/~KRYGER/RADIATION_DAMAGE (LOWER CASE!)
RfactorNum. reflection% reflectionSelection details
Rfree0.226 1030 4.7 %RANDOM
Rwork0.199 ---
obs0.199 21758 95.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 36.79 Å2 / ksol: 0.326 e/Å3
Displacement parametersBiso mean: 43 Å2
Baniso -1Baniso -2Baniso -3
1-4.99 Å25.32 Å20 Å2
2--4.99 Å20 Å2
3----9.98 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.36 Å0.31 Å
Luzzati d res low-5 Å
Luzzati sigma a0.46 Å0.41 Å
Refinement stepCycle: LAST / Resolution: 2.9→36.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4238 0 0 284 4522
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.9
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.9
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it4.021.5
X-RAY DIFFRACTIONc_mcangle_it6.232
X-RAY DIFFRACTIONc_scbond_it7.512
X-RAY DIFFRACTIONc_scangle_it10.762.5
LS refinement shellResolution: 2.9→3 Å / Rfactor Rfree error: 0.03 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.3 102 4.6 %
Rwork0.295 2108 -
obs--98.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER_REP.PARAM
Software
*PLUS
Name: CNS / Version: 0.5 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.9
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.9

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