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- PDB-3ax0: Crystal structure of Streptomyces tyrosinase in a complex with ca... -

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Basic information

Entry
Database: PDB / ID: 3ax0
TitleCrystal structure of Streptomyces tyrosinase in a complex with caddie Y98F mutant soaked in a Cu(II)-containing solution for 80 hr
Components
  • MelCMelč
  • Tyrosinase
KeywordsOXIDOREDUCTASE/METAL TRANSPORT / TYROSINASE / BINARY COMPLEX / TYPE-3 COPPER / DIOXYGEN / COPPER TRANSFER / 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 and hemocyanins CuB-binding region signature. ...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
COPPER (II) ION / NITRATE ION / MelC / Tyrosinase
Similarity search - Component
Biological speciesStreptomyces castaneoglobisporus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsMatoba, Y. / Sugiyama, M.
Citation
Journal: J.Biol.Chem. / Year: 2011
Title: A molecular mechanism for copper transportation to tyrosinase that is assisted by a metallochaperone, caddie protein
Authors: Matoba, Y. / Bando, N. / Oda, K. / Noda, M. / Higashikawa, F. / Kumagai, T. / Sugiyama, M.
#1: Journal: 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
DepositionMar 26, 2011Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 29, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 31, 2011Group: Database references
Revision 1.3Nov 1, 2023Group: 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 / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_label_alt_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _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_asym_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_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: Tyrosinase
B: MelC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,72711
Polymers46,1632
Non-polymers5649
Water6,089338
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2220 Å2
ΔGint-11 kcal/mol
Surface area13440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.240, 98.200, 55.210
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-503-

CU

21A-707-

HOH

31A-841-

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)
Strain: HUT 6202 / Gene: TYRC / Plasmid: PET-MEL2 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)PLYSS / References: UniProt: Q83WS2, tyrosinase
#2: Protein MelC / Melč / CADDIE PROTEIN ORF378


Mass: 14073.645 Da / Num. of mol.: 1 / Mutation: Y98F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces castaneoglobisporus (bacteria)
Strain: HUT 6202 / Gene: ORF378 / Plasmid: PET-MEL2 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)PLYSS / References: UniProt: Q83WS1
#3: Chemical
ChemComp-CU / COPPER (II) ION / Copper


Mass: 63.546 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cu
#4: Chemical
ChemComp-NO3 / NITRATE ION / Nitrate


Mass: 62.005 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: NO3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 338 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsFOR ENTITY 1, THERE IS DIFFERENCE BETWEEN THE SEQRES AND THE SEQUENCE DATABASE. THE DEPOSITOR ...FOR ENTITY 1, THERE IS DIFFERENCE BETWEEN THE SEQRES AND THE SEQUENCE DATABASE. THE DEPOSITOR STATES THAT SER A 123 IS CORRECT AND SWISSPROT IS INCORRECT AT THIS POSITION.

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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: 1.92 Å3/Da / Density % sol: 35.79 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: PEG 3350, 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: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 9, 2007
RadiationMonochromator: double-crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.4→100 Å / Num. all: 69218 / Num. obs: 69218 / % possible obs: 98.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.4 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 23.1
Reflection shellResolution: 1.4→1.45 Å / Redundancy: 4 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 2.5 / Num. unique all: 6943 / % possible all: 99.8

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Processing

Software
NameClassification
BSSdata collection
CNSrefinement
SHELXL-97refinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1WX2

1wx2


Resolution: 1.4→30 Å / Num. parameters: 12914 / Num. restraintsaints: 12005 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
Details: ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) BY ?
RfactorNum. reflection% reflectionSelection details
Rfree0.198 3505 5.3 %RANDOM
Rwork0.17 ---
all0.17 69185 --
obs0.17 69185 --
Refine analyzeNum. disordered residues: 20 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 3147.5
Refinement stepCycle: LAST / Resolution: 1.4→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2791 0 24 338 3153
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.011
X-RAY DIFFRACTIONs_angle_d0.027
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0275
X-RAY DIFFRACTIONs_zero_chiral_vol0.058
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.066
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.018
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.039
X-RAY DIFFRACTIONs_approx_iso_adps0

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