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- PDB-9mp9: Mix & Quench Time Resolved Lysozyme - NAG1 Complex (1000 ms) -

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Basic information

Entry
Database: PDB / ID: 9mp9
TitleMix & Quench Time Resolved Lysozyme - NAG1 Complex (1000 ms)
ComponentsLysozyme C
KeywordsHYDROLASE / Time resolved / inhibitor / complex
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
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
2-acetamido-2-deoxy-alpha-D-glucopyranose / Lysozyme C
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsMcLeod, M.J. / Indergaard, J.A. / Thorne, R.E.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)DBI-2210041 United States
CitationJournal: Iucrj / Year: 2025
Title: Instrumentation and methods for efficient time-resolved X-ray crystallography of biomolecular systems with sub-10 ms time resolution.
Authors: Indergaard, J.A. / Mahmood, K. / Gabriel, L. / Zhong, G. / Lastovka, A. / McLeod, M.J. / Thorne, R.E.
History
DepositionDec 30, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 7, 2025Provider: repository / Type: Initial release
Revision 1.1May 14, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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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)16,6447
Polymers16,2581
Non-polymers3866
Water1,910106
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)77.889, 77.889, 37.769
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-366-

HOH

21A-387-

HOH

31A-401-

HOH

41A-406-

HOH

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Components

#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 genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Gene: LYZ / Production host: Gallus gallus (chicken) / References: UniProt: P00698, lysozyme
#2: Sugar ChemComp-NDG / 2-acetamido-2-deoxy-alpha-D-glucopyranose / N-acetyl-alpha-D-glucosamine / 2-acetamido-2-deoxy-alpha-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / 2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE


Type: D-saccharide, alpha linking / Mass: 221.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-a-D-glucopyranosamineCOMMON NAMEGMML 1.0
a-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-NA / SODIUM ION


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


Mass: 18.015 Da / Num. of mol.: 106 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 1.76 Å3/Da / Density % sol: 30.18 %
Crystal growTemperature: 293 K / Method: small tubes / pH: 4.6
Details: 0.1 M sodium acetate pH 4.6, 20 % (w/v) sodium chloride, 5 % PEG 4000. NAG1 soaked at 226 mM in 0.1 M sodium acetate pH 4.6 and 17.5 % (w/v) sodium chloride, 5 % (w/v) PEG 4000, and 10 % (w/v) PEG 400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 0.9793 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 7, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.9→77.89 Å / Num. obs: 9203 / % possible obs: 95.84 % / Redundancy: 6.74 % / CC1/2: 0.992 / Rmerge(I) obs: 0.184 / Rpim(I) all: 0.072 / Rrim(I) all: 0.198 / Net I/σ(I): 7.2
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 6.91 % / Rmerge(I) obs: 1.136 / Mean I/σ(I) obs: 0.9 / Num. unique obs: 456 / CC1/2: 0.663 / Rpim(I) all: 0.445 / Rrim(I) all: 1.225 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.21rc1_5170: ???)refinement
DIALSdata reduction
DIALSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→38.94 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.04 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.22 526 5.74 %
Rwork0.1783 --
obs0.1806 9163 95.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.9→38.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1000 0 20 106 1126
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006
X-RAY DIFFRACTIONf_angle_d0.734
X-RAY DIFFRACTIONf_dihedral_angle_d19.884392
X-RAY DIFFRACTIONf_chiral_restr0.049150
X-RAY DIFFRACTIONf_plane_restr0.008184
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-2.090.32241220.22872141X-RAY DIFFRACTION97
2.09-2.390.28941370.19812136X-RAY DIFFRACTION97
2.39-3.020.22781360.19682150X-RAY DIFFRACTION96
3.02-38.940.17281310.15162210X-RAY DIFFRACTION93
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)
12.2966-1.3146-0.22462.66490.09421.34660.28570.37430.592-0.3361-0.3607-0.6931-0.14390.04610.08430.18580.0250.06470.27730.11250.30856.9936-16.1084-9.3061
20.65960.3596-0.66543.79410.92531.1793-0.27580.17490.03370.440.1691-0.68840.06830.41830.09950.181-0.0227-0.05460.27320.11350.290211.9302-23.42261.7927
31.3391-0.7322-0.42931.82780.41110.6810.15220.2452-0.0981-0.0578-0.21630.1848-0.1161-0.13270.03620.16050.01180.03010.1870.00780.174-0.0466-21.4606-5.9913
42.57850.7234-0.8481.5472-0.02452.8588-0.03170.0392-0.070.25850.10790.47830.4439-0.64340.03340.2305-0.02830.08340.2593-0.00420.2206-13.9663-19.45854.3289
51.9611-0.53380.18751.83420.79552.0749-0.1702-0.15790.00230.1494-0.04240.05370.1386-0.07590.21930.21660.02380.01090.2017-0.00060.1904-6.7482-16.39886.8889
68.16332.0203-3.17485.2745-1.5831.6682-0.0961-1.0687-0.10320.6359-0.292-0.5745-0.06210.36250.28930.35970.02140.00390.2966-0.02380.1841-4.6967-13.830114.0514
71.8387-0.83470.16872.62210.06151.5751-0.0210.08460.35240.1605-0.0922-0.3855-0.2220.23310.08290.2132-0.0059-0.01960.2274-0.01530.22582.5932-13.72513.6543
82.6171-1.68983.48133.7776-0.79345.7169-0.1461-0.3703-0.11030.2840.09280.2361-0.1163-0.68320.04760.1708-0.00440.01330.18110.01610.1689-0.206-29.33783.2076
93.17061.7792-1.64112.4803-1.42411.69890.04850.3561-0.2211-0.6059-0.1707-0.65960.10390.7460.13410.2572-0.00840.09350.33680.00880.27988.6703-28.2931-10.6265
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 19 through 32 )
2X-RAY DIFFRACTION2chain 'A' and (resid 33 through 42 )
3X-RAY DIFFRACTION3chain 'A' and (resid 43 through 60 )
4X-RAY DIFFRACTION4chain 'A' and (resid 61 through 68 )
5X-RAY DIFFRACTION5chain 'A' and (resid 69 through 86 )
6X-RAY DIFFRACTION6chain 'A' and (resid 87 through 96 )
7X-RAY DIFFRACTION7chain 'A' and (resid 97 through 118 )
8X-RAY DIFFRACTION8chain 'A' and (resid 119 through 132 )
9X-RAY DIFFRACTION9chain 'A' and (resid 133 through 147 )

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