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- PDB-7s4w: Serial Macromolecular Crystallography at ALBA Synchrotron Light S... -

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Basic information

Entry
Database: PDB / ID: 7s4w
TitleSerial Macromolecular Crystallography at ALBA Synchrotron Light Source - Lysozyme
ComponentsLysozyme C
KeywordsHYDROLASE / Serial Crystallography
Function / homology
Function and homology information


Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / killing of cells of another organism / defense response to Gram-negative bacterium / defense response to Gram-positive bacterium / defense response to bacterium ...Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / killing of cells of another organism / defense response to Gram-negative bacterium / defense response to Gram-positive bacterium / defense response to bacterium / endoplasmic reticulum / extracellular space / identical protein binding / cytoplasm
Similarity search - Function
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-like domain superfamily
Similarity search - Domain/homology
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsMartin-Garcia, J.M. / Botha, S. / Hu, H. / Jernigan, R. / Castellvi, A. / Lisova, S. / Gil, F. / Calisto, B. / Crespo, I. / Roy-Chowdbury, S. ...Martin-Garcia, J.M. / Botha, S. / Hu, H. / Jernigan, R. / Castellvi, A. / Lisova, S. / Gil, F. / Calisto, B. / Crespo, I. / Roy-Chowdbury, S. / Grieco, A. / Ketawala, G. / Weierstall, U. / Spence, J. / Fromme, P. / Zatsepin, N. / Boer, R. / Carpena, X.
Funding support2items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)1231306
Other government2019-T1BMD-15552
CitationJournal: J.Synchrotron Radiat. / Year: 2022
Title: Serial macromolecular crystallography at ALBA Synchrotron Light Source.
Authors: Martin-Garcia, J.M. / Botha, S. / Hu, H. / Jernigan, R. / Castellvi, A. / Lisova, S. / Gil, F. / Calisto, B. / Crespo, I. / Roy-Chowdhury, S. / Grieco, A. / Ketawala, G. / Weierstall, U. / ...Authors: Martin-Garcia, J.M. / Botha, S. / Hu, H. / Jernigan, R. / Castellvi, A. / Lisova, S. / Gil, F. / Calisto, B. / Crespo, I. / Roy-Chowdhury, S. / Grieco, A. / Ketawala, G. / Weierstall, U. / Spence, J. / Fromme, P. / Zatsepin, N. / Boer, D.R. / Carpena, X.
History
DepositionSep 9, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 27, 2021Provider: repository / Type: Initial release
Revision 1.1May 18, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)14,3672
Polymers14,3311
Non-polymers351
Water30617
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)79.000, 79.000, 38.200
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-304-

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 genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Gene: LYZ / Production host: Escherichia coli (E. coli) / References: UniProt: P00698, lysozyme
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 17 / Source method: isolated from a natural source / Formula: H2O
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: 2.08 Å3/Da / Density % sol: 40.85 %
Crystal growTemperature: 298 K / Method: batch mode
Details: 0.1 M sodium acetate pH 3.0, 18 % (w/v) sodium chloride, 6% PEG 400

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Data collection

DiffractionMean temperature: 298 K / Serial crystal experiment: Y
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97918 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 8, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.1→38.2 Å / Num. obs: 7498 / % possible obs: 100 % / Redundancy: 679 % / Biso Wilson estimate: 37.4 Å2 / CC1/2: 0.996 / CC star: 0.999 / Net I/σ(I): 9.8
Reflection shellResolution: 2.1→2.17 Å / Redundancy: 161 % / Mean I/σ(I) obs: 0.5 / Num. unique obs: 716 / CC1/2: 0.207 / CC star: 0.5855
Serial crystallography sample deliveryDescription: LCP Injection / Method: injection
Serial crystallography sample delivery injectionInjector diameter: 5.0E-5 µm
Serial crystallography data reductionFrames total: 114080 / Lattices indexed: 23733

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
CrystFELv0.10.0data reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1VDS

1vds


Resolution: 2.1→35.35 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.945 / SU B: 14.523 / SU ML: 0.165 / Cross valid method: THROUGHOUT / ESU R: 0.241 / ESU R Free: 0.197 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.23225 741 9.9 %RANDOM
Rwork0.17847 ---
obs0.18359 6723 99.97 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.1 Å / Solvent model: MASK
Displacement parametersBiso mean: 47.711 Å2
Baniso -1Baniso -2Baniso -3
1--0.64 Å20 Å20 Å2
2---0.64 Å20 Å2
3---1.28 Å2
Refinement stepCycle: LAST / Resolution: 2.1→35.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1001 0 1 17 1019
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0181025
X-RAY DIFFRACTIONr_bond_other_d0.0010.02938
X-RAY DIFFRACTIONr_angle_refined_deg1.3891.8251389
X-RAY DIFFRACTIONr_angle_other_deg1.1422.6812136
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5425128
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.6920.65661
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.00415166
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.7471511
X-RAY DIFFRACTIONr_chiral_restr0.0810.2144
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021206
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02280
X-RAY DIFFRACTIONr_mcbond_it2.4823.568515
X-RAY DIFFRACTIONr_mcbond_other2.4783.564514
X-RAY DIFFRACTIONr_mcangle_it3.265.347642
X-RAY DIFFRACTIONr_mcangle_other3.2615.352643
X-RAY DIFFRACTIONr_scbond_it3.5634.055510
X-RAY DIFFRACTIONr_scbond_other3.564.055510
X-RAY DIFFRACTIONr_scangle_other5.3985.908747
X-RAY DIFFRACTIONr_long_range_B_refined6.71341.471178
X-RAY DIFFRACTIONr_long_range_B_other6.71141.5041179
LS refinement shellResolution: 2.1→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.363 59 -
Rwork0.376 479 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: 0.912 Å / Origin y: 20.447 Å / Origin z: 9.511 Å
111213212223313233
T0.0187 Å20.0033 Å20.0027 Å2-0.0374 Å20.0149 Å2--0.0182 Å2
L2.3224 °21.1706 °20.0884 °2-3.0534 °20.365 °2--1.9543 °2
S0.001 Å °0.0155 Å °-0.0253 Å °-0.0361 Å °-0.0062 Å °-0.1879 Å °0.0062 Å °0.1033 Å °0.0052 Å °

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