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- PDB-6sr1: X-ray pump X-ray probe on lysozyme.Gd nanocrystals: 35 fs time delay -

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Basic information

Entry
Database: PDB / ID: 6sr1
TitleX-ray pump X-ray probe on lysozyme.Gd nanocrystals: 35 fs time delay
ComponentsLysozyme C
KeywordsHYDROLASE / Radiation damage / SERIAL femtosecond CRYSTALLOGRAPHY / X-ray FREE-ELECTRON LASER / time-resolved crystallography
Function / homology
Function and homology information


Lactose synthesis / Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / defense response to Gram-negative bacterium / killing of cells of another organism / defense response to Gram-positive bacterium ...Lactose synthesis / Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / defense response to Gram-negative bacterium / killing of cells of another organism / defense response to Gram-positive bacterium / defense response to bacterium / endoplasmic reticulum / extracellular space / identical protein binding / cytoplasm
Similarity search - Function
Lysozyme - #10 / Glycoside hydrolase, family 22, lysozyme / Glycoside hydrolase family 22 domain / Glycosyl hydrolases family 22 (GH22) domain signature. / Glycoside hydrolase, family 22 / C-type lysozyme/alpha-lactalbumin family / Glycosyl hydrolases family 22 (GH22) domain profile. / Alpha-lactalbumin / lysozyme C / Lysozyme / Lysozyme-like domain superfamily ...Lysozyme - #10 / Glycoside hydrolase, family 22, lysozyme / Glycoside hydrolase family 22 domain / Glycosyl hydrolases family 22 (GH22) domain signature. / Glycoside hydrolase, family 22 / C-type lysozyme/alpha-lactalbumin family / Glycosyl hydrolases family 22 (GH22) domain profile. / Alpha-lactalbumin / lysozyme C / Lysozyme / Lysozyme-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-DO3 / GADOLINIUM ATOM / Lysozyme C
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsKloos, M. / Gorel, A. / Nass, K.
CitationJournal: Nat Commun / Year: 2020
Title: Structural dynamics in proteins induced by and probed with X-ray free-electron laser pulses.
Authors: Nass, K. / Gorel, A. / Abdullah, M.M. / V Martin, A. / Kloos, M. / Marinelli, A. / Aquila, A. / Barends, T.R.M. / Decker, F.J. / Bruce Doak, R. / Foucar, L. / Hartmann, E. / Hilpert, M. / ...Authors: Nass, K. / Gorel, A. / Abdullah, M.M. / V Martin, A. / Kloos, M. / Marinelli, A. / Aquila, A. / Barends, T.R.M. / Decker, F.J. / Bruce Doak, R. / Foucar, L. / Hartmann, E. / Hilpert, M. / Hunter, M.S. / Jurek, Z. / Koglin, J.E. / Kozlov, A. / Lutman, A.A. / Kovacs, G.N. / Roome, C.M. / Shoeman, R.L. / Santra, R. / Quiney, H.M. / Ziaja, B. / Boutet, S. / Schlichting, I.
History
DepositionSep 4, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 22, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Lysozyme C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,5109
Polymers16,2581
Non-polymers1,2538
Water46826
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1560 Å2
ΔGint-63 kcal/mol
Surface area7110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.000, 79.000, 39.500
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Lysozyme C / 1 / 4-beta-N-acetylmuramidase C / Allergen Gal d IV


Mass: 16257.660 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: Cysteine residues were modeled by alanines and a non-covalently bound sulphur during refinement
Source: (natural) Gallus gallus (chicken) / References: UniProt: P00698, lysozyme

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Non-polymers , 5 types, 34 molecules

#2: Chemical ChemComp-GD / GADOLINIUM ATOM


Mass: 157.250 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Gd
#3: Chemical ChemComp-DO3 / 10-((2R)-2-HYDROXYPROPYL)-1,4,7,10-TETRAAZACYCLODODECANE 1,4,7-TRIACETIC ACID


Mass: 404.459 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H32N4O7
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 26 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 1.9 Å3/Da / Density % sol: 35.11 % / Description: nanocrystals
Crystal growTemperature: 277 K / Method: batch mode / pH: 3
Details: 20 % NACL, 6 % PEG 6000, 0.1 M SODIUM acetate pH 3.0
Temp details: ice cold solutions

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Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: Y
Diffraction sourceSource: FREE ELECTRON LASER / Site: SLAC LCLS / Beamline: CXI / Wavelength: 1.75 Å
DetectorType: CS-PAD CXI-1 / Detector: PIXEL / Date: Feb 15, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.75 Å / Relative weight: 1
ReflectionResolution: 2.32→22.81 Å / Num. obs: 5315 / % possible obs: 100 % / Redundancy: 1 % / Biso Wilson estimate: 27.5 Å2 / CC1/2: 0.98 / R split: 0.084 / Net I/σ(I): 12
Reflection shellResolution: 2.32→2.36 Å / Mean I/σ(I) obs: 10.8 / Num. unique obs: 436 / CC1/2: 0.979 / R split: 0.085
Serial crystallography measurementFocal spot size: 0.025 µm2 / Pulse duration: 15 fsec. / Pulse energy: 500 µJ / Pulse photon energy: 7.07 keV / XFEL pulse repetition rate: 120 Hz
Serial crystallography sample deliveryDescription: GDVN injection / Method: injection
Serial crystallography data reductionFrames indexed: 16000 / Lattices indexed: 16000

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
PDB_EXTRACT3.25data extraction
CrystFELdata reduction
XSCALEdata scaling
REFMACphasing
Refinement