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- PDB-3p66: Time-dependent and Protein-directed In Situ Growth of Gold Nanopa... -

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Basic information

Entry
Database: PDB / ID: 3p66
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 / old Nanoparticles / Porous Materials
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
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: 1.36 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 11, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 9, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)15,9079
Polymers14,3311
Non-polymers1,5768
Water3,801211
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Lysozyme C
hetero molecules

A: Lysozyme C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,81418
Polymers28,6622
Non-polymers3,15116
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z+1/21
Buried area3080 Å2
ΔGint-72 kcal/mol
Surface area11950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.543, 78.543, 37.154
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-2021-

HOH

21A-2135-

HOH

31A-2198-

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-AU3 / GOLD 3+ ION


Mass: 196.967 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Au
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 211 / Source method: isolated from a natural source / Formula: H2O
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: 2 Å3/Da / Density % sol: 38.47 %
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 24, 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: 1.31→50 Å / Num. obs: 28492 / % possible obs: 97.3 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 27.5 % / Rmerge(I) obs: 0.162 / Rsym value: 0.162 / Net I/σ(I): 62.2

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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: 1.36→10 Å / Num. parameters: 4877 / Num. restraintsaints: 4133 / 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
Rfree0.2433 1381 -RANDOM
Rwork0.2159 ---
obs0.2192 26325 94.2 %-
all-26753 --
Refine analyzeNum. disordered residues: 0 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 1218
Refinement stepCycle: LAST / Resolution: 1.36→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1000 0 8 211 1219
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.009
X-RAY DIFFRACTIONs_angle_d0.025
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0268
X-RAY DIFFRACTIONs_zero_chiral_vol0.057
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.054
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.009
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.054
X-RAY DIFFRACTIONs_approx_iso_adps0

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