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- PDB-1do5: HUMAN COPPER CHAPERONE FOR SUPEROXIDE DISMUTASE DOMAIN II -

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Basic information

Entry
Database: PDB / ID: 1do5
TitleHUMAN COPPER CHAPERONE FOR SUPEROXIDE DISMUTASE DOMAIN II
ComponentsHUMAN COPPER CHAPERONE FOR SUPEROXIDE DISMUTASE DOMAIN II
KeywordsCHAPERONE / BETA-BARREL
Function / homology
Function and homology information


protein maturation by copper ion transfer / positive regulation of oxidoreductase activity / superoxide metabolic process / Detoxification of Reactive Oxygen Species / removal of superoxide radicals / protein-disulfide reductase activity / cellular response to oxidative stress / copper ion binding / cadherin binding / nucleus ...protein maturation by copper ion transfer / positive regulation of oxidoreductase activity / superoxide metabolic process / Detoxification of Reactive Oxygen Species / removal of superoxide radicals / protein-disulfide reductase activity / cellular response to oxidative stress / copper ion binding / cadherin binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Heavy-metal-associated domain / Heavy metal-associated domain superfamily / Heavy metal-associated domain, HMA / Heavy-metal-associated domain profile. / Superoxide dismutase, copper/zinc binding domain / Copper/Zinc superoxide dismutase signature 2. / Superoxide dismutase, copper/zinc, binding site / Superoxide dismutase (Cu/Zn) / superoxide dismutase copper chaperone / Superoxide dismutase, copper/zinc binding domain / Copper/zinc superoxide dismutase (SODC) ...Heavy-metal-associated domain / Heavy metal-associated domain superfamily / Heavy metal-associated domain, HMA / Heavy-metal-associated domain profile. / Superoxide dismutase, copper/zinc binding domain / Copper/Zinc superoxide dismutase signature 2. / Superoxide dismutase, copper/zinc, binding site / Superoxide dismutase (Cu/Zn) / superoxide dismutase copper chaperone / Superoxide dismutase, copper/zinc binding domain / Copper/zinc superoxide dismutase (SODC) / Superoxide dismutase-like, copper/zinc binding domain superfamily / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Copper chaperone for superoxide dismutase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.75 Å
AuthorsLamb, A.L. / Wernimont, A.K. / Pufahl, R.A. / O'Halloran, T.V. / Rosenzweig, A.C.
CitationJournal: Biochemistry / Year: 2000
Title: Crystal structure of the second domain of the human copper chaperone for superoxide dismutase.
Authors: Lamb, A.L. / Wernimont, A.K. / Pufahl, R.A. / O'Halloran, T.V. / Rosenzweig, A.C.
History
DepositionDec 18, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 18, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HUMAN COPPER CHAPERONE FOR SUPEROXIDE DISMUTASE DOMAIN II
B: HUMAN COPPER CHAPERONE FOR SUPEROXIDE DISMUTASE DOMAIN II
C: HUMAN COPPER CHAPERONE FOR SUPEROXIDE DISMUTASE DOMAIN II
D: HUMAN COPPER CHAPERONE FOR SUPEROXIDE DISMUTASE DOMAIN II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,4308
Polymers65,1684
Non-polymers2624
Water46826
1
A: HUMAN COPPER CHAPERONE FOR SUPEROXIDE DISMUTASE DOMAIN II
B: HUMAN COPPER CHAPERONE FOR SUPEROXIDE DISMUTASE DOMAIN II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,7154
Polymers32,5842
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1480 Å2
ΔGint-6 kcal/mol
Surface area13410 Å2
MethodPISA
2
C: HUMAN COPPER CHAPERONE FOR SUPEROXIDE DISMUTASE DOMAIN II
D: HUMAN COPPER CHAPERONE FOR SUPEROXIDE DISMUTASE DOMAIN II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,7154
Polymers32,5842
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1470 Å2
ΔGint-7 kcal/mol
Surface area13260 Å2
MethodPISA
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5070 Å2
ΔGint-21 kcal/mol
Surface area24550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.186, 66.716, 88.033
Angle α, β, γ (deg.)90.00, 96.63, 90.00
Int Tables number5
Space group name H-MC121
DetailsThe biological assembly is a dimer constructed from chain A with chain B or chain C with chain D

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Components

#1: Protein
HUMAN COPPER CHAPERONE FOR SUPEROXIDE DISMUTASE DOMAIN II


Mass: 16292.058 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PET24D / Production host: Escherichia coli (E. coli) / References: UniProt: O14618
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 26 / 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: 2.62 Å3/Da / Density % sol: 53.08 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 6.5
Details: MES buffer and PEG20000, pH 6.5, VAPOR DIFFUSION, temperature 298K
Crystal grow
*PLUS
Temperature: 25 ℃ / Method: vapor diffusion, hanging drop
Details: drop consists of equal amounts of protein and reservoir solutions
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
17 mg/mlprotein1drop
2100 mMMES1reservoir
312 %PEG200001reservoir

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Data collection

DiffractionMean temperature: 113 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 5ID-B / Wavelength: 1
DetectorType: MARRESEARCH / Detector: CCD / Date: Aug 8, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.75→20 Å / Num. all: 57239 / Num. obs: 17097 / % possible obs: 96.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 2 % / Biso Wilson estimate: 39.7 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 6.7
Reflection shellResolution: 2.75→2.83 Å / Redundancy: 2 % / Rmerge(I) obs: 0.312 / % possible all: 96.5
Reflection shell
*PLUS
% possible obs: 96.5 % / Mean I/σ(I) obs: 2.5

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS0.9refinement
RefinementResolution: 2.75→19.21 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 197368.16 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.283 1600 10 %RANDOM
Rwork0.228 ---
all0.228 14376 --
obs0.228 15976 90.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 38.12 Å2 / ksol: 0.429 e/Å3
Displacement parametersBiso mean: 32.1 Å2
Baniso -1Baniso -2Baniso -3
1-11.66 Å20 Å2-0.41 Å2
2---3.12 Å20 Å2
3----8.55 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.45 Å0.34 Å
Luzzati d res low-5 Å
Luzzati sigma a0.52 Å0.41 Å
Refinement stepCycle: LAST / Resolution: 2.75→19.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4467 0 0 26 4493
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d25.7
X-RAY DIFFRACTIONc_improper_angle_d0.77
X-RAY DIFFRACTIONc_mcbond_it1.431.5
X-RAY DIFFRACTIONc_mcangle_it2.522
X-RAY DIFFRACTIONc_scbond_it1.882
X-RAY DIFFRACTIONc_scangle_it2.942.5
LS refinement shellResolution: 2.75→2.92 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.379 275 11.4 %
Rwork0.315 2139 -
obs--82.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PAPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
Software
*PLUS
Name: CNS / Version: 0.9 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg25.7
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.77

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