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- PDB-4x3b: A micro-patterned silicon chip as sample holder for macromolecula... -

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Basic information

Entry
Database: PDB / ID: 4x3b
TitleA micro-patterned silicon chip as sample holder for macromolecular crystallography experiments with minimal background scattering
ComponentsLysozyme C
KeywordsHYDROLASE / lysozyme microcrystals
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: 2.1 Å
AuthorsRoedig, P. / Vartiainen, I. / Duman, R. / Panneerselvam, S. / Stuebe, N. / Lorbeer, O. / Warmer, M. / Sutton, G. / Stuart, D.I. / Weckert, E. ...Roedig, P. / Vartiainen, I. / Duman, R. / Panneerselvam, S. / Stuebe, N. / Lorbeer, O. / Warmer, M. / Sutton, G. / Stuart, D.I. / Weckert, E. / David, C. / Wagner, A. / Meents, A.
CitationJournal: Sci Rep / Year: 2015
Title: A micro-patterned silicon chip as sample holder for macromolecular crystallography experiments with minimal background scattering.
Authors: Roedig, P. / Vartiainen, I. / Duman, R. / Panneerselvam, S. / Stube, N. / Lorbeer, O. / Warmer, M. / Sutton, G. / Stuart, D.I. / Weckert, E. / David, C. / Wagner, A. / Meents, A.
History
DepositionNov 28, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jun 10, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: 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)14,5678
Polymers14,3311
Non-polymers2367
Water1,892105
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area890 Å2
ΔGint-67 kcal/mol
Surface area6500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.210, 78.210, 37.380
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-336-

HOH

21A-360-

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-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-NA / SODIUM ION


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


Mass: 18.015 Da / Num. of mol.: 105 / 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: 1.99 Å3/Da / Density % sol: 38.32 %
Crystal growTemperature: 293 K / Method: batch mode / pH: 4 / Details: 0.1 M Sodium Acetate pH 4.0, 8% (w/v) NaCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.96862 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 3, 2014
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96862 Å / Relative weight: 1
ReflectionResolution: 2.1→19.55 Å / Num. obs: 6784 / % possible obs: 94.5 % / Observed criterion σ(I): -3 / Redundancy: 7.7 % / Biso Wilson estimate: 26.14 Å2 / Rmerge F obs: 0.98 / Rmerge(I) obs: 0.251 / Rrim(I) all: 0.263 / Χ2: 0.907 / Net I/σ(I): 5.95 / Num. measured all: 52295
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Highest resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
2.1-2.30.6180.4082.755975167014880.46489.1
2.3-2.50.8780.3513.545422118610510.38388.6
2.5-2.80.9110.3214.367196119311510.34796.5
2.8-30.9510.2965.3340525655590.31598.9
3-3.50.9540.2897.78100829169080.30299.1
3.5-40.9750.2989.7862215185170.3199.8
4-60.9780.2210.8394647687610.22999.1
6-100.9890.16111.530782722680.16898.5
10-150.9870.13613.8660758580.142100
15-200.9780.13814.1215917160.14694.1
200.9980.2868.33391370.31253.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 193L

193l


Resolution: 2.1→19.55 Å / FOM work R set: 0.8373 / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 22.3 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2288 678 10 %
Rwork0.186 6099 -
obs0.1904 6777 94.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 76.35 Å2 / Biso mean: 26.48 Å2 / Biso min: 12.11 Å2
Refinement stepCycle: final / Resolution: 2.1→19.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1001 0 7 105 1113
Biso mean--38.82 29.39 -
Num. residues----129
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0171040
X-RAY DIFFRACTIONf_angle_d0.9151410
X-RAY DIFFRACTIONf_chiral_restr0.063145
X-RAY DIFFRACTIONf_plane_restr0.003184
X-RAY DIFFRACTIONf_dihedral_angle_d13.75369
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1002-2.26210.2961240.25051121X-RAY DIFFRACTION89
2.2621-2.48940.25521250.22451117X-RAY DIFFRACTION89
2.4894-2.84860.24791360.21861223X-RAY DIFFRACTION96
2.8486-3.58540.26461410.18011276X-RAY DIFFRACTION99
3.5854-19.550.17931520.15451362X-RAY DIFFRACTION99

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