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- PDB-3l6w: Structure of the collar functional unit (KLH1-H) of keyhole limpe... -

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Basic information

Entry
Database: PDB / ID: 3l6w
TitleStructure of the collar functional unit (KLH1-H) of keyhole limpet hemocyanin
ComponentsHemocyanin 1
KeywordsOXYGEN BINDING / HEMOCYANIN / CUPREDOXIN DOMAIN / COPPER-BINDING PROTEIN / METAL-BINDING
Function / homology
Function and homology information


oxygen carrier activity / oxidoreductase activity / extracellular region / metal ion binding
Similarity search - Function
Haemocyanin beta-sandwich domain / Haemocyanin C-terminal domain superfamily / Haemocyanin beta-sandwich / Tyrosinase CuA-binding region signature. / : / Common central domain of tyrosinase / Tyrosinase and hemocyanins CuB-binding region signature. / Tyrosinase copper-binding domain / Di-copper centre-containing domain superfamily
Similarity search - Domain/homology
Hemocyanin 1 / Hemocyanin 1
Similarity search - Component
Biological speciesMegathura crenulata (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4 Å
AuthorsJaenicke, E. / Buechler, K. / Markl, J. / Decker, H. / Barends, T.R.M.
CitationJournal: Biochem.J. / Year: 2009
Title: The Cupredoxin-like Domains in Hemocyanins.
Authors: Jaenicke, E. / Buchler, K. / Markl, J. / Decker, H. / Barends, T.R.M.
History
DepositionDec 27, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 2, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Nov 1, 2023Group: 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: Hemocyanin 1
B: Hemocyanin 1


Theoretical massNumber of molelcules
Total (without water)113,2482
Polymers113,2482
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)251.020, 251.020, 251.020
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number199
Space group name H-MI213

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Components

#1: Protein Hemocyanin 1 / Coordinate model: Cα atoms only


Mass: 56623.797 Da / Num. of mol.: 2 / Fragment: collar subunit / Source method: isolated from a natural source / Source: (natural) Megathura crenulata (invertebrata) / References: UniProt: Q53IP9, UniProt: Q10583*PLUS

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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: 5.82 Å3/Da / Density % sol: 78.86 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4
Details: 9% PEG 1000, 50mM phosphate/citrate buffer, pH 4.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.97941
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 22, 2006
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97941 Å / Relative weight: 1
ReflectionResolution: 4→30 Å / Num. obs: 22294 / % possible obs: 96.8 % / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.18 / Net I/σ(I): 10.6
Reflection shellResolution: 4→4.2 Å / Rmerge(I) obs: 0.847 / Mean I/σ(I) obs: 3.46 / % possible all: 96.4

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Processing

Software
NameClassification
MAR345data collection
PHASERphasing
RESOLVEmodel building
DMmodel building
XDSdata reduction
XSCALEdata scaling
RESOLVEphasing
DMphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1JS8

1js8


Highest resolution: 4 Å
Details: THE COORDINATES CONTAIN ONLY A CA TRACE. NO REFINEMENT WAS CARRIED OUT
Refinement stepCycle: LAST / Highest resolution: 4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms954 0 0 0 954

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