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- PDB-1ws7: Crystal Structure of Mavicyanin from Cucurbita pepo medullosa (Zu... -

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Basic information

Entry
Database: PDB / ID: 1ws7
TitleCrystal Structure of Mavicyanin from Cucurbita pepo medullosa (Zucchini)
ComponentsMavicyanin
KeywordsELECTRON TRANSPORT / Reduced form / Mavicyanin / 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 (I) ION / Mavicyanin
Similarity search - Component
Biological speciesCucurbita pepo (plant)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsXie, Y. / Inoue, T. / Miyamoto, Y. / Matsumura, H. / Kataoka, 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: Version format compliance
Revision 1.3Jul 11, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.4Apr 3, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _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: Mavicyanin
B: Mavicyanin
C: Mavicyanin
D: Mavicyanin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,8198
Polymers47,5654
Non-polymers2544
Water8,503472
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)62.660, 62.660, 244.860
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-CU1 / COPPER (I) ION / Copper


Mass: 63.546 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cu
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 472 / 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: 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

DiffractionMean temperature: 100 K
Diffraction sourceSource: SEALED TUBE / Type: RIGAKU R-AXIS IV / Wavelength: 1.5414 Å
RadiationMonochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5414 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. all: 232315 / Num. obs: 40261 / % possible obs: 95.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 95.5 % / Biso Wilson estimate: 12.8 Å2 / Rmerge(I) obs: 0.061 / Rsym value: 0.061 / Net I/σ(I): 11.4
Reflection shellResolution: 1.9→50 Å / Redundancy: 83.8 % / Rmerge(I) obs: 0.123 / Mean I/σ(I) obs: 11.4 / Num. unique all: 2367 / Rsym value: 0.123 / % possible all: 83.8

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Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: structure of oxidized mavicyanin

Resolution: 1.9→32.62 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 298035.75 / 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
Rfree0.23 2014 5 %RANDOM
Rwork0.188 ---
all0.191 232315 --
obs0.188 23717 94.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 50.9848 Å2 / ksol: 0.405692 e/Å3
Displacement parametersBiso mean: 21.1 Å2
Baniso -1Baniso -2Baniso -3
1-0.66 Å21.47 Å20 Å2
2--0.66 Å20 Å2
3----1.31 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.24 Å0.19 Å
Luzzati d res low-5 Å
Luzzati sigma a0.1 Å0.05 Å
Refinement stepCycle: LAST / Resolution: 1.9→32.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3246 0 4 472 3722
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d26
X-RAY DIFFRACTIONc_improper_angle_d0.74
LS refinement shellResolution: 1.9→2.02 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.221 277 4.7 %
Rwork0.192 5628 -
obs-2367 83.4 %
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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