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- PDB-1wxc: Crystal Structure of the copper-free Streptomyces castaneoglobisp... -

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Basic information

Entry
Database: PDB / ID: 1wxc
TitleCrystal Structure of the copper-free Streptomyces castaneoglobisporus tyrosinase complexed with a caddie protein
Components
  • MelC
  • tyrosinase
KeywordsOXIDOREDUCTASE/METAL TRANSPORT / tyrosinase / binary complex / type-3 copper / OXIDOREDUCTASE-METAL TRANSPORT COMPLEX
Function / homology
Function and homology information


melanin biosynthetic process / oxidoreductase activity / copper ion binding / metal ion binding
Similarity search - Function
Tyrosinase co-factor MelC1 / Tyrosinase co-factor MelC1 / protein ne1242 fold / protein ne1242 domain like / Copper chaperone GriE/MELC1 superfamily / di-copper center containing domain from catechol oxidase / Di-copper center containing domain from catechol oxidase / Tyrosinase CuA-binding region signature. / : / Common central domain of tyrosinase ...Tyrosinase co-factor MelC1 / Tyrosinase co-factor MelC1 / protein ne1242 fold / protein ne1242 domain like / Copper chaperone GriE/MELC1 superfamily / di-copper center containing domain from catechol oxidase / Di-copper center containing domain from catechol oxidase / 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 / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
NITRATE ION / MelC / Tyrosinase
Similarity search - Component
Biological speciesStreptomyces castaneoglobisporus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 1.2 Å
AuthorsMatoba, Y. / Kumagai, T. / Yamamoto, A. / Yoshitsu, H. / Sugiyama, M.
CitationJournal: J.Biol.Chem. / Year: 2006
Title: Crystallographic Evidence That the Dinuclear Copper Center of Tyrosinase Is Flexible during Catalysis
Authors: Matoba, Y. / Kumagai, T. / Yamamoto, A. / Yoshitsu, H. / Sugiyama, M.
History
DepositionJan 20, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 31, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Assembly

Deposited unit
A: tyrosinase
B: MelC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,5416
Polymers46,2932
Non-polymers2484
Water7,080393
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2650 Å2
ΔGint-3 kcal/mol
Surface area13270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.664, 96.734, 54.574
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-619-

HOH

21A-622-

HOH

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Components

#1: Protein tyrosinase


Mass: 32089.564 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces castaneoglobisporus (bacteria)
Gene: tyrc / Plasmid: pET-mel2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: Q83WS2, tyrosinase
#2: Protein MelC / caddie protein ORF378


Mass: 14203.812 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces castaneoglobisporus (bacteria)
Gene: orf378 / Plasmid: pET-mel2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: Q83WS1
#3: Chemical
ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: NO3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 393 / 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: 1.89 Å3/Da / Density % sol: 34.9 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: peg3350, sodium nitrate, hepes, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.6199 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 16, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.6199 Å / Relative weight: 1
ReflectionResolution: 1.2→100 Å / Num. all: 104674 / Num. obs: 102888 / % possible obs: 97.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Redundancy: 8.1 % / Rmerge(I) obs: 0.085 / Rsym value: 0.08 / Net I/σ(I): 16.4
Reflection shellResolution: 1.2→1.26 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.366 / Mean I/σ(I) obs: 4.6 / Num. unique all: 15330 / Rsym value: 0.329 / % possible all: 99

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Processing

Software
NameVersionClassification
SHELXmodel building
SHELXL-97refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
SHARPphasing
RefinementMethod to determine structure: MIRAS / Resolution: 1.2→30 Å / Num. parameters: 12894 / Num. restraintsaints: 11800 / Cross valid method: FREE R / σ(F): 1 / σ(I): 1 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2083 5063 5.3 %RANDOM
Rwork0.1799 ---
all0.1812 102888 --
obs0.1799 100937 94.3 %-
Refine analyzeNum. disordered residues: 15 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 3150
Refinement stepCycle: LAST / Resolution: 1.2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2808 0 16 393 3217
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.013
X-RAY DIFFRACTIONs_angle_d0.028
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0275
X-RAY DIFFRACTIONs_zero_chiral_vol0.072
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.079
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.028
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.032
X-RAY DIFFRACTIONs_approx_iso_adps0
LS refinement shellResolution: 1.2→1.28 Å
RfactorNum. reflection% reflection
Rfree0.285 845 -
Rwork0.249 --
obs-17238 92.25 %

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