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- PDB-5f81: Acoustic injectors for drop-on-demand serial femtosecond crystall... -

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Entry
Database: PDB / ID: 5f81
TitleAcoustic injectors for drop-on-demand serial femtosecond crystallography
ComponentsLysozyme C
KeywordsHYDROLASE / LYSOZYME
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
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 2.13 Å
AuthorsRoessler, C.G. / Agarwal, R. / Allaire, M. / Alonso-Mori, R. / Andi, B. / Bachega, J.F.R. / Bommer, M. / Brewster, A.S. / Browne, M.C. / Chatterjee, R. ...Roessler, C.G. / Agarwal, R. / Allaire, M. / Alonso-Mori, R. / Andi, B. / Bachega, J.F.R. / Bommer, M. / Brewster, A.S. / Browne, M.C. / Chatterjee, R. / Cho, E. / Cohen, A.E. / Cowan, M. / Datwani, S. / Davidson, V.L. / Defever, J. / Eaton, B. / Ellson, R. / Feng, Y. / Ghislain, L.P. / Glownia, J.M. / Han, G. / Hattne, J. / Hellmich, J. / Heroux, A. / Ibrahim, M. / Kern, J. / Kuczewski, A. / Lemke, H.T. / Liu, P. / Majlof, L. / McClintock, W.M. / Myers, S. / Nelsen, S. / Olechno, J. / Orville, A.M. / Sauter, N.K. / Soares, A.S. / Soltis, M.S. / Song, H. / Stearns, R.G. / Tran, R. / Tsai, Y. / Uervirojnangkoorn, M. / Wilmot, C.M. / Yachandra, V. / Yano, J. / Yukl, E.T. / Zhu, D. / Zouni, A.
Funding support United States, 3items
OrganizationGrant numberCountry
Department of Energy (DOE, United States)11-008 United States
National Institutes of Health/National Center for Research Resources (NIH/NCRR)P41 RR012408 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P41 GM103473 United States
CitationJournal: Structure / Year: 2016
Title: Acoustic Injectors for Drop-On-Demand Serial Femtosecond Crystallography.
Authors: Roessler, C.G. / Agarwal, R. / Allaire, M. / Alonso-Mori, R. / Andi, B. / Bachega, J.F. / Bommer, M. / Brewster, A.S. / Browne, M.C. / Chatterjee, R. / Cho, E. / Cohen, A.E. / Cowan, M. / ...Authors: Roessler, C.G. / Agarwal, R. / Allaire, M. / Alonso-Mori, R. / Andi, B. / Bachega, J.F. / Bommer, M. / Brewster, A.S. / Browne, M.C. / Chatterjee, R. / Cho, E. / Cohen, A.E. / Cowan, M. / Datwani, S. / Davidson, V.L. / Defever, J. / Eaton, B. / Ellson, R. / Feng, Y. / Ghislain, L.P. / Glownia, J.M. / Han, G. / Hattne, J. / Hellmich, J. / Heroux, A. / Ibrahim, M. / Kern, J. / Kuczewski, A. / Lemke, H.T. / Liu, P. / Majlof, L. / McClintock, W.M. / Myers, S. / Nelsen, S. / Olechno, J. / Orville, A.M. / Sauter, N.K. / Soares, A.S. / Soltis, S.M. / Song, H. / Stearns, R.G. / Tran, R. / Tsai, Y. / Uervirojnangkoorn, M. / Wilmot, C.M. / Yachandra, V. / Yano, J. / Yukl, E.T. / Zhu, D. / Zouni, A.
History
DepositionDec 8, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Feb 10, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 6, 2016Group: Database references
Revision 1.2Apr 20, 2016Group: Database references
Revision 1.3Nov 15, 2017Group: Data collection / Category: diffrn_source
Item: _diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.pdbx_synchrotron_site / _diffrn_source.type
Revision 1.4Nov 14, 2018Group: Data collection / Category: diffrn / Item: _diffrn.pdbx_serial_crystal_experiment
Revision 1.5Jul 21, 2021Group: Author supporting evidence / Category: pdbx_audit_support
Item: _pdbx_audit_support.funding_organization / _pdbx_audit_support.grant_number
Revision 1.6Mar 30, 2022Group: Author supporting evidence / Database references / Category: database_2 / pdbx_audit_support
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization
Revision 1.7Jan 10, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.8Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Lysozyme C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,5317
Polymers14,3311
Non-polymers2006
Water2,774154
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area720 Å2
ΔGint-57 kcal/mol
Surface area6580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.504, 78.504, 37.618
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-386-

HOH

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Components

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


Mass: 14331.160 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / References: UniProt: P00698, lysozyme
#2: Chemical ChemComp-NA / SODIUM ION


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


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 154 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.02 Å3/Da / Density % sol: 39.17 %
Crystal growTemperature: 295 K / Method: batch mode / pH: 4.6
Details: Batch crystallization 120 mg/ml dissolved in 0.1M sodium acetate (4.6), crystallized with 6% sodium chloride + 10% v/v glycerol

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Data collection

DiffractionMean temperature: 295 K
Ambient temp details: Acoustic specimen injection into xfel beam
Serial crystal experiment: Y
Diffraction sourceSource: FREE ELECTRON LASER / Site: SLAC LCLS / Beamline: XPP / Wavelength: 1.36 Å
DetectorType: CS-PAD XPP / Detector: PIXEL / Date: Jun 7, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.36 Å / Relative weight: 1
ReflectionResolution: 2.13→55.51 Å / Num. obs: 6590 / % possible obs: 99.84 % / Redundancy: 15.6 % / Net I/σ(I): 14.7
Reflection shellResolution: 2.13→2.24 Å / Redundancy: 7.5 % / Mean I/σ(I) obs: 4.5 / % possible all: 99.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
cctbx.xfeldata reduction
cctbx.xfeldata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ET8

4et8


Resolution: 2.13→55.51 Å / Cor.coef. Fo:Fc: 0.868 / Cor.coef. Fo:Fc free: 0.744 / SU B: 11.066 / SU ML: 0.283 / Cross valid method: THROUGHOUT / ESU R: 0.406 / ESU R Free: 0.303 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.33255 361 5.2 %RANDOM
Rwork0.24233 ---
obs0.24706 6590 99.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.063 Å2
Baniso -1Baniso -2Baniso -3
1--0.41 Å20 Å20 Å2
2---0.41 Å20 Å2
3---0.82 Å2
Refinement stepCycle: LAST / Resolution: 2.13→55.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1001 0 6 154 1161
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0191025
X-RAY DIFFRACTIONr_bond_other_d0.0060.02940
X-RAY DIFFRACTIONr_angle_refined_deg1.6031.9031389
X-RAY DIFFRACTIONr_angle_other_deg0.90432140
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.9985128
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.4662350
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.79515166
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.6141511
X-RAY DIFFRACTIONr_chiral_restr0.0910.2144
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021206
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02271
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9041.746515
X-RAY DIFFRACTIONr_mcbond_other0.9021.745514
X-RAY DIFFRACTIONr_mcangle_it1.5092.616642
X-RAY DIFFRACTIONr_mcangle_other1.5082.618643
X-RAY DIFFRACTIONr_scbond_it0.971.828510
X-RAY DIFFRACTIONr_scbond_other0.9661.829510
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.5652.709747
X-RAY DIFFRACTIONr_long_range_B_refined4.28314.9331489
X-RAY DIFFRACTIONr_long_range_B_other4.03514.7881438
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.13→2.185 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.448 25 -
Rwork0.323 458 -
obs--99.38 %

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