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- PDB-3p4z: Time-dependent and Protein-directed In Situ Growth of Gold Nanopa... -

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Basic information

Entry
Database: PDB / ID: 3p4z
TitleTime-dependent and Protein-directed In Situ Growth of Gold Nanoparticles in a Single Crystal of Lysozyme
ComponentsLysozyme C
KeywordsHYDROLASE / Binding Sites / Bio-Nano Hybrids / Gold Nanoparticles / Porous Materials
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
: / GOLD 3+ ION / Lysozyme C
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO / Resolution: 1.6 Å
AuthorsWei, H. / Wang, Z. / Zhang, J. / House, S. / Gao, Y.-G. / Yang, L. / Robinson, H. / Tan, L.H. / Xing, H. / Hou, C. ...Wei, H. / Wang, Z. / Zhang, J. / House, S. / Gao, Y.-G. / Yang, L. / Robinson, H. / Tan, L.H. / Xing, H. / Hou, C. / Robertson, I.M. / Zuo, J.-M. / Lu, Y.
CitationJournal: Nat Nanotechnol / Year: 2011
Title: Time-dependent, protein-directed growth of gold nanoparticles within a single crystal of lysozyme.
Authors: Wei, H. / Wang, Z. / Zhang, J. / House, S. / Gao, Y.G. / Yang, L. / Robinson, H. / Tan, L.H. / Xing, H. / Hou, C. / Robertson, I.M. / Zuo, J.M. / Lu, Y.
History
DepositionOct 7, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 9, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: 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)14,7965
Polymers14,3311
Non-polymers4654
Water4,270237
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)78.584, 78.584, 37.121
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-2031-

HOH

21A-2104-

HOH

31A-2142-

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-AU / GOLD ION


Mass: 196.967 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Au
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-AU3 / GOLD 3+ ION


Mass: 196.967 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Au
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 237 / 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: 38.48 %
Crystal growTemperature: 298 K / Method: evaporation / pH: 4.5
Details: 6.5% NaCl (w/v) in 0.1 M sodium acetate, pH 4.5, EVAPORATION, temperature 298K

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Data collection

DiffractionMean temperature: 123.2 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 1.0988 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Nov 11, 2009
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0988 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 15391 / % possible obs: 97.5 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 25.7 % / Rmerge(I) obs: 0.157 / Rsym value: 0.157 / Net I/σ(I): 29.1

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPin the CCP4 Packagephasing
SHELXL-97refinement
HKL-2000data reduction
X-PLORrefinement
RefinementMethod to determine structure: AB INITIO / Resolution: 1.6→10 Å / Num. parameters: 4979 / Num. restraintsaints: 4146 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: ANISOTROPIC SCALING APPLIED BY THE METHOD OF PARKIN, MOEZZI & HOPE, J.APPL.CRYST.28(1995)53-56
RfactorNum. reflection% reflectionSelection details
Rfree0.2358 716 -RANDOM
Rwork0.1933 ---
obs0.1933 13695 88.7 %-
all-14084 --
Refine analyzeNum. disordered residues: 0 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 1240.5
Refinement stepCycle: LAST / Resolution: 1.6→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1000 0 4 237 1241
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.007
X-RAY DIFFRACTIONs_angle_d0.022
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0243
X-RAY DIFFRACTIONs_zero_chiral_vol0.036
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.041
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.008
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.065
X-RAY DIFFRACTIONs_approx_iso_adps0

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