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- PDB-4z98: Crystal Structure of Hen Egg White Lysozyme using Serial X-ray Di... -

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Basic information

Entry
Database: PDB / ID: 4z98
TitleCrystal Structure of Hen Egg White Lysozyme using Serial X-ray Diffraction Data Collection
ComponentsLysozyme C
KeywordsHYDROLASE
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
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
ACETATE ION / Lysozyme C
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsMurray, T.D. / Lyubimov, A.Y. / Ogata, C.M. / Uervirojnangkoorn, M. / Brunger, A.T. / Berger, J.M.
Funding support United States, 1items
OrganizationGrant numberCountry
HCIA United States
CitationJournal: Acta Crystallogr. D Biol. Crystallogr. / Year: 2015
Title: A high-transparency, micro-patternable chip for X-ray diffraction analysis of microcrystals under native growth conditions.
Authors: Murray, T.D. / Lyubimov, A.Y. / Ogata, C.M. / Vo, H. / Uervirojnangkoorn, M. / Brunger, A.T. / Berger, J.M.
History
DepositionApr 10, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 14, 2015Provider: repository / Type: Initial release
Revision 1.1May 16, 2018Group: Data collection / Database references / Derived calculations
Category: citation / pdbx_struct_oper_list
Item: _citation.journal_abbrev / _citation.page_first ..._citation.journal_abbrev / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Sep 27, 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

Downloads & links

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Assembly

Deposited unit
A: Lysozyme C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,3902
Polymers14,3311
Non-polymers591
Water1,44180
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)79.144, 79.144, 38.111
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-334-

HOH

21A-365-

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 / Fragment: residues 19-147 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Tissue: egg white / References: UniProt: P00698, lysozyme
#2: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 80 / 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: 2.08 Å3/Da / Density % sol: 40.93 % / Description: Tetragonal microcrystals
Crystal growTemperature: 277 K / Method: small tubes / pH: 3.5
Details: 20% w/v NaCl, 8% w/v PEG 8000, 0.5 M Sodium acetate

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Data collection

DiffractionMean temperature: 293 K / Ambient temp details: Room temperature
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.03318 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 8, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03318 Å / Relative weight: 1
ReflectionResolution: 1.55→39.59 Å / Num. obs: 17566 / % possible obs: 96.9 % / Redundancy: 7.9 % / Net I/σ(I): 14.58
Reflection shellResolution: 1.55→1.58 Å / Redundancy: 3.44 % / Mean I/σ(I) obs: 3.68 / % possible all: 91.6

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Processing

Software
NameVersionClassification
PHENIX1.9refinement
PDB_EXTRACT3.15data extraction
cctbx.xfeldata reduction
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1VDP

1vdp


Resolution: 1.55→27.981 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.85 / Phase error: 27.18 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2458 1757 10.01 %
Rwork0.2051 15795 -
obs0.2089 17552 96.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 83.46 Å2 / Biso mean: 30.5192 Å2 / Biso min: 11.65 Å2
Refinement stepCycle: final / Resolution: 1.55→27.981 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1001 0 7 80 1088
Biso mean--54.49 41.76 -
Num. residues----129
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081147
X-RAY DIFFRACTIONf_angle_d1.0781560
X-RAY DIFFRACTIONf_chiral_restr0.044156
X-RAY DIFFRACTIONf_plane_restr0.004210
X-RAY DIFFRACTIONf_dihedral_angle_d14.48443
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.55-1.59220.37871260.3481134126092
1.5922-1.6390.34391270.34051138126594
1.639-1.69190.36451310.33531176130795
1.6919-1.75240.34951300.28641163129395
1.7524-1.82250.32891320.26061190132297
1.8225-1.90540.27741360.23281233136998
1.9054-2.00590.25461340.20941199133398
2.0059-2.13150.25061360.19071220135699
2.1315-2.2960.22461370.1761233137099
2.296-2.52690.21511380.16591241137999
2.5269-2.89230.23141390.17561255139499
2.8923-3.64270.19091420.18061277141999
3.6427-27.9860.24261490.2011336148597
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.52320.5634-0.06961.25540.80781.22880.4957-0.2023-0.33290.2722-0.4799-0.07480.5937-0.32570.00280.26690.0157-0.06040.25540.05650.22137.330195.026256.4923
21.56821.17410.8622.9819-0.00930.9363-0.00050.0041-0.1735-0.0837-0.0361-0.2940.180.04650.00140.1375-0.02-0.00310.15640.02470.16294.7873102.010350.3978
31.65523.33931.22286.7532.57251.4669-0.1217-0.0430.2146-0.29850.04880.6197-0.29280.2416-0.25520.1723-0.00960.00660.31250.04680.1861-15.232799.308942.745
40.13340.0199-0.10150.1232-0.05650.332-0.0246-0.1260.2231-0.0473-0.08840.0801-0.45170.1134-0.00010.1902-0.0346-0.02140.24040.01110.1649-5.780496.966746.0904
51.93430.0981-0.69321.3260.94640.9897-0.44181.17120.6548-0.33770.2490.7446-0.7162-0.2739-0.09290.2631-0.0637-0.05470.26180.04810.2755-9.063695.57736.8033
62.18823.0581-0.34244.2861-0.47960.0651-0.22840.5328-0.5837-0.93730.4997-0.19640.4317-0.4108-0.08580.2798-0.10650.01430.3757-0.03440.1789-5.056393.726333.4298
71.08390.01380.46151.16250.69750.60340.0028-0.1008-0.32050.28590.0726-0.26340.07860.0681-0.00050.1884-0.02740.00360.19610.0030.22651.938593.022244.3112
81.55980.52920.56322.2645-0.22030.4569-0.23620.30710.1268-0.40.12510.4751-0.0601-0.3385-0.00270.18980.0061-0.00740.20710.04180.2299-0.2476109.311944.5358
90.8949-0.530.41390.3258-0.24651.4817-0.09510.0270.21920.5289-0.1146-0.9813-0.46090.69070.04460.2532-0.0467-0.12450.30610.01830.40349.1234106.870359.0364
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 14 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 15 through 42 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 43 through 50 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 51 through 58 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 59 through 68 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 69 through 78 )A0
7X-RAY DIFFRACTION7chain 'A' and (resid 79 through 99 )A0
8X-RAY DIFFRACTION8chain 'A' and (resid 100 through 114 )A0
9X-RAY DIFFRACTION9chain 'A' and (resid 115 through 129 )A0

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