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- PDB-1ws8: Crystal Structure of Mavicyanin from Cucurbita pepo medullosa (Zu... -

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Basic information

Entry
Database: PDB / ID: 1ws8
TitleCrystal Structure of Mavicyanin from Cucurbita pepo medullosa (Zucchini)
Componentsmavicyanin
KeywordsELECTRON TRANSPORT / mavicyanin / oxidized form / phytocyanin / cupredoxin
Function / homology
Function and homology information


electron transfer activity / metal ion binding
Similarity search - Function
Mavicyanin / Phytocyanin domain / Phytocyanin / Plastocyanin-like domain / Phytocyanin domain profile. / Blue (type 1) copper protein, binding site / Type-1 copper (blue) proteins signature. / Cupredoxins - blue copper proteins / Cupredoxin / Immunoglobulin-like ...Mavicyanin / Phytocyanin domain / Phytocyanin / Plastocyanin-like domain / Phytocyanin domain profile. / Blue (type 1) copper protein, binding site / Type-1 copper (blue) proteins signature. / Cupredoxins - blue copper proteins / Cupredoxin / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
COPPER (II) ION / Mavicyanin
Similarity search - Component
Biological speciesCucurbita pepo (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.6 Å
AuthorsXie, Y. / Inoue, T. / Miyamoto, Y. / Matsumura, H. / Kunishige, K. / Yamaguchi, K. / Nojini, M. / Suzuki, S. / Kai, Y.
CitationJournal: J.Biochem.(Tokyo) / Year: 2005
Title: Structural reorganization of the copper binding site involving Thr15 of mavicyanin from Cucurbita pepo medullosa (zucchini) upon reduction.
Authors: Xie, Y. / Inoue, T. / Miyamoto, Y. / Matsumura, H. / Kataoka, K. / Yamaguchi, K. / Nojini, M. / Suzuki, S. / Kai, Y.
History
DepositionNov 2, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 23, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: mavicyanin
B: mavicyanin
C: mavicyanin
D: mavicyanin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,00310
Polymers47,5654
Non-polymers4386
Water4,810267
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.920, 63.920, 245.350
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: Protein
mavicyanin


Mass: 11891.242 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cucurbita pepo (plant) / Production host: Escherichia coli (E. coli) / References: UniProt: P80728
#2: Chemical
ChemComp-CU / COPPER (II) ION / Copper


Mass: 63.546 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cu
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 267 / 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: 2

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Sample preparation

CrystalDensity Matthews: 3 Å3/Da / Density % sol: 59 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: ammonium sulfate, sodium cacodylate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONPhoton Factory BL-18B11
SYNCHROTRONSPring-8 BL40B221.3050, 1.3790, 1.3803, 1.393
Detector
TypeIDDetectorDateDetails
WEISSENBERG1DIFFRACTOMETEROct 10, 2002mirrors
ADSC QUANTUM 42CCDMay 17, 2003mirrors
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1MIRRORSSINGLE WAVELENGTHMx-ray1
2MIRRORSMADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
111
21.3051
31.3791
41.38031
51.3931
ReflectionResolution: 1.6→50 Å / Num. all: 314972 / Num. obs: 71278 / % possible obs: 86 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 93.2 % / Biso Wilson estimate: 19.3 Å2 / Rmerge(I) obs: 0.038 / Rsym value: 0.038 / Net I/σ(I): 13
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 81.3 % / Rmerge(I) obs: 0.175 / Mean I/σ(I) obs: 13 / Num. unique all: 3776 / Rsym value: 0.175 / % possible all: 81.3

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Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MAD / Resolution: 1.6→36.72 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 616918.6 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
Details: RESOLUTION-DEPENDENT WEIGHTING SCHEME OTHER REFINEMENT REMARKS: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.211 3613 5.1 %RANDOM
Rwork0.193 ---
obs0.193 37768 95.7 %-
all-314972 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 40.5222 Å2 / ksol: 0.34844 e/Å3
Displacement parametersBiso mean: 25 Å2
Baniso -1Baniso -2Baniso -3
1-1.82 Å20.88 Å20 Å2
2--1.82 Å20 Å2
3----3.64 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.21 Å0.19 Å
Luzzati d res low-5 Å
Luzzati sigma a0.16 Å0.17 Å
Refinement stepCycle: LAST / Resolution: 1.6→36.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3219 0 16 267 3502
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d25.9
X-RAY DIFFRACTIONc_improper_angle_d0.74
LS refinement shellResolution: 1.6→1.7 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.265 518 4.8 %
Rwork0.257 10290 -
obs-37763 87.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
X-RAY DIFFRACTION4GLL.PARAMPACK_016.TOP

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