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- PDB-2g4p: Anomalous substructure of lysozyme at pH 4.5 -

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Basic information

Entry
Database: PDB / ID: 2g4p
TitleAnomalous substructure of lysozyme at pH 4.5
ComponentsLysozyme C
Keywordshydrolase / Allergen / anomalous substructure of lysozyme crystallized at pH 4.5
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 / FOURIER SYNTHESIS / Resolution: 1.84 Å
AuthorsMueller-Dieckmann, C. / Weiss, M.S.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2007
Title: On the routine use of soft X-rays in macromolecular crystallography. Part IV. Efficient determination of anomalous substructures in biomacromolecules using longer X-ray wavelengths.
Authors: Mueller-Dieckmann, C. / Panjikar, S. / Schmidt, A. / Mueller, S. / Kuper, J. / Geerlof, A. / Wilmanns, M. / Singh, R.K. / Tucker, P.A. / Weiss, M.S.
History
DepositionFeb 22, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 20, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance

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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)14,5798
Polymers14,3311
Non-polymers2487
Water2,522140
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)78.660, 78.660, 37.120
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-243-

HOH

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Components

#1: Protein Lysozyme C / 1 / 4-beta-N-acetylmuramidase C / Allergen Gal d 4 / Gal d IV


Mass: 14331.160 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Tissue: egg white / References: UniProt: P00698, lysozyme
#2: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 140 / 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 Å3/Da / Density % sol: 38.59 %

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, Hamburg / Beamline: X12 / Wavelength: 2 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jan 1, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 2 Å / Relative weight: 1
ReflectionResolution: 1.84→30 Å / Num. obs: 10564 / Observed criterion σ(F): 0 / Observed criterion σ(I): 0

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
DENZOdata reduction
CCP4(SCALA)data scaling
FFTphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.84→30 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.922 / SU B: 5.241 / SU ML: 0.086 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.137 / ESU R Free: 0.132 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21397 217 2.1 %RANDOM
Rwork0.16585 ---
obs0.16683 10347 99.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 21.904 Å2
Baniso -1Baniso -2Baniso -3
1-0.33 Å20 Å20 Å2
2--0.33 Å20 Å2
3----0.67 Å2
Refinement stepCycle: LAST / Resolution: 1.84→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms998 0 7 140 1145
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.0211024
X-RAY DIFFRACTIONr_bond_other_d0.0020.02888
X-RAY DIFFRACTIONr_angle_refined_deg1.8491.91387
X-RAY DIFFRACTIONr_angle_other_deg1.05332054
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4355128
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.2912350
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.43915167
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.5491511
X-RAY DIFFRACTIONr_chiral_restr0.1220.2144
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021168
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02229
X-RAY DIFFRACTIONr_nbd_refined0.2190.2233
X-RAY DIFFRACTIONr_nbd_other0.1990.2887
X-RAY DIFFRACTIONr_nbtor_refined0.1640.2502
X-RAY DIFFRACTIONr_nbtor_other0.0870.2503
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1950.295
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0650.23
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2790.243
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.220.211
X-RAY DIFFRACTIONr_mcbond_it1.3441.5810
X-RAY DIFFRACTIONr_mcbond_other0.281.5270
X-RAY DIFFRACTIONr_mcangle_it1.9392.51006
X-RAY DIFFRACTIONr_scbond_it4.4135481
X-RAY DIFFRACTIONr_scangle_it6.42410381
LS refinement shellResolution: 1.84→1.888 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.325 16 -
Rwork0.242 745 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: -0.749 Å / Origin y: 20.3737 Å / Origin z: 18.9854 Å
111213212223313233
T-0.0616 Å2-0.0157 Å20.0051 Å2--0.0544 Å2-0.0101 Å2---0.0539 Å2
L1.6498 °2-0.9594 °2-0.0715 °2-2.3138 °2-0.3326 °2--1.209 °2
S-0.0525 Å °-0.0216 Å °-0.0673 Å °0.0885 Å °0.0257 Å °0.1372 Å °0.0147 Å °-0.075 Å °0.0268 Å °

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