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- PDB-6apm: Hen egg-white lysozyme (WT), solved with serial millisecond cryst... -

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Basic information

Entry
Database: PDB / ID: 6apm
TitleHen egg-white lysozyme (WT), solved with serial millisecond crystallography using synchrotron radiation
ComponentsLysozyme C
KeywordsHYDROLASE / HEWL / lysozyme / XFEL crystal structure / serial millisecond 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
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.05 Å
AuthorsLyubimov, A.Y. / Mathews, I.I. / Uervivojnangkoorn, M. / Soltis, S.M. / Cohen, A.E.
CitationJournal: Biochemistry / Year: 2017
Title: The Conformational Flexibility of the Acyltransferase from the Disorazole Polyketide Synthase Is Revealed by an X-ray Free-Electron Laser Using a Room-Temperature Sample Delivery Method for Serial Crystallography.
Authors: Mathews, I.I. / Allison, K. / Robbins, T. / Lyubimov, A.Y. / Uervirojnangkoorn, M. / Brunger, A.T. / Khosla, C. / DeMirci, H. / McPhillips, S.E. / Hollenbeck, M. / Soltis, M. / Cohen, A.E.
History
DepositionAug 17, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 4, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 4, 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: Lysozyme C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,3542
Polymers14,3311
Non-polymers231
Water1,874104
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)79.035, 79.035, 38.245
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-375-

HOH

21A-402-

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-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 104 / 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: 40.97 %
Crystal growTemperature: 298 K / Method: small tubes / pH: 4.5
Details: 2.5 M NaCl, 6% PEG 6K, 0.15 M sodium acetate (pH 4.5)

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 10, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.05→39.5 Å / Num. obs: 8025 / % possible obs: 100 % / Redundancy: 29.1 % / CC1/2: 0.9 / Net I/σ(I): 5.54
Reflection shellResolution: 2.05→2.09 Å / Redundancy: 19.6 % / Mean I/σ(I) obs: 1.19 / Num. unique obs: 390 / CC1/2: 0.48 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHASERphasing
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.22data extraction
cctbx.xfeldata reduction
cctbx.primedata scaling
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4WM6

4wm6


Resolution: 2.05→39.5 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 18.85
RfactorNum. reflection% reflection
Rfree0.2332 803 10.01 %
Rwork0.2053 --
obs0.2081 8021 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 76.1 Å2 / Biso mean: 17.2652 Å2 / Biso min: 3.02 Å2
Refinement stepCycle: final / Resolution: 2.05→39.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1001 0 1 104 1106
Biso mean--12.78 23.09 -
Num. residues----129
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031069
X-RAY DIFFRACTIONf_angle_d0.7031457
X-RAY DIFFRACTIONf_chiral_restr0.157151
X-RAY DIFFRACTIONf_plane_restr0.003192
X-RAY DIFFRACTIONf_dihedral_angle_d24.703655
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
2.05-2.17850.29321300.25591165
2.1785-2.34660.26081300.2331163
2.3466-2.58280.24131320.20871197
2.5828-2.95640.23511340.20271197
2.9564-3.72430.21491320.18491197
3.7243-39.50.20541450.18771299
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)
10.04240.0148-0.0020.00930.0038-0.0020.07070.17230.025-0.0294-0.0067-0.0338-0.07940.05960.00770.15760.03190.04810.20130.02090.15426.6945-16.4417-9.5325
20.09020.02540.01940.12060.14930.19620.0247-0.05780.0004-0.0021-0.0714-0.0128-0.0388-0.0079-0.08340.04490.0008-0.01330.08250.03190.0796.734-24.4873-2.1307
30.06050.0454-0.08070.09450.01870.32160.07540.00810.02320.02110.08950.03510.13370.04490.10290.05880.03890.0215-0.06790.2020.0022-10.6099-18.1112-0.406
40.002-0.0036-0.00170.0159-0.00950.021-0.00020.0058-0.0371-0.00530.00710.04530.01040.01860.02-0.05780.23150.0095-0.15410.03110.092-5.7403-17.84031.5432
50.1429-0.0651-0.04990.06640.05150.0397-0.1018-0.0805-0.07120.0716-0.0159-0.02990.09560.0517-0.07430.10570.07410.00260.16340.03270.0488-8.83-15.948310.5163
60.0623-0.0433-0.00680.03060.00440.0037-0.0231-0.13980.00070.15690.02510.01690.0058-0.13380.02080.22790.0641-0.02460.3325-0.04530.1066-4.5188-14.102214.1853
70.01140.0052-0.01550.0164-0.02070.02960.032-0.03380.0596-0.0616-0.0615-0.0552-0.01380.009-0.0080.12410.04440.02840.12150.03640.1621-1.4719-9.75410.6957
80.027-0.01130.00550.037-0.00540.00810.04080.00140.16310.0726-0.0196-0.0759-0.04710.06640.00390.0873-0.00310.02120.1219-0.0340.1615.2007-17.67215.6124
90.00850.01860.00320.0460.02830.01650.09230.03080.00930.0940.0493-0.06830.0533-0.19930.04950.0762-0.0069-0.00290.1570.01850.0949-0.1558-29.99123.3154
100.04690.00610.00980.0201-0.01110.01160.04540.05-0.05850.00450.0232-0.04530.0204-0.00550.04190.14580.10010.1174-0.0714-0.05750.11615.3966-32.2587-8.1554
110.0742-0.02220.02510.0086-0.00730.0104-0.02530.04790.06270.0154-0.0386-0.1172-0.03440.0997-0.02820.39350.02270.16440.43290.00510.310712.756-23.0363-15.0491
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 14 )A1 - 14
2X-RAY DIFFRACTION2chain 'A' and (resid 15 through 36 )A15 - 36
3X-RAY DIFFRACTION3chain 'A' and (resid 37 through 50 )A37 - 50
4X-RAY DIFFRACTION4chain 'A' and (resid 51 through 58 )A51 - 58
5X-RAY DIFFRACTION5chain 'A' and (resid 59 through 68 )A59 - 68
6X-RAY DIFFRACTION6chain 'A' and (resid 69 through 78 )A69 - 78
7X-RAY DIFFRACTION7chain 'A' and (resid 79 through 88 )A79 - 88
8X-RAY DIFFRACTION8chain 'A' and (resid 89 through 99 )A89 - 99
9X-RAY DIFFRACTION9chain 'A' and (resid 100 through 114 )A100 - 114
10X-RAY DIFFRACTION10chain 'A' and (resid 115 through 123 )A115 - 123
11X-RAY DIFFRACTION11chain 'A' and (resid 124 through 129 )A124 - 129

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