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- PDB-1wx5: Crystal Structure of the copper-free Streptomyces castaneoglobisp... -

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Basic information

Entry
Database: PDB / ID: 1wx5
TitleCrystal Structure of the copper-free Streptomyces castaneoglobisporus tyrosinase complexed with a caddie protein in the monoclinic crystal
Components
  • MelCMelč
  • tyrosinase
KeywordsOXIDOREDUCTASE/METAL TRANSPORT / tyrosinase / binary complex / flexibility / 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
Biological speciesStreptomyces castaneoglobisporus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.02 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 19, 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 1.3Oct 25, 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_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_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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.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_conn.ptnr2_label_seq_id / _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
C: tyrosinase
D: MelC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,7279
Polymers92,5874
Non-polymers1405
Water8,971498
1
A: tyrosinase
B: MelC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,3875
Polymers46,2932
Non-polymers943
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2330 Å2
ΔGint-47 kcal/mol
Surface area13270 Å2
MethodPISA
2
C: tyrosinase
D: MelC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,3394
Polymers46,2932
Non-polymers462
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2260 Å2
ΔGint-36 kcal/mol
Surface area13400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.850, 93.200, 65.590
Angle α, β, γ (deg.)90.00, 93.80, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein tyrosinase /


Mass: 32089.564 Da / Num. of mol.: 2
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 / Melč / caddie protein ORF378


Mass: 14203.812 Da / Num. of mol.: 2
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-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 498 / 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: 1.94 Å3/Da / Density % sol: 36.7 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: PEG4000, ammonium chloride, hepes, pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS VII / Detector: IMAGE PLATE / Date: Sep 5, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.02→40.68 Å / Num. all: 46350 / Num. obs: 46161 / % possible obs: 99.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Redundancy: 5.01 % / Biso Wilson estimate: 3.5 Å2 / Rmerge(I) obs: 0.125 / Rsym value: 0.125 / Net I/σ(I): 7.3
Reflection shellResolution: 2.02→2.09 Å / Redundancy: 4.34 % / Rmerge(I) obs: 0.278 / Mean I/σ(I) obs: 3.4 / Num. unique all: 4564 / Rsym value: 0.278 / % possible all: 98.9

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Processing

Software
NameVersionClassification
X-PLOR3.851refinement
CrystalClear(MSC/RIGAKU)data reduction
CrystalClear(MSC/RIGAKU)data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1WXC

1wxc


Resolution: 2.02→30 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.291 2290 5 %RANDOM
Rwork0.201 ---
all0.206 46161 --
obs0.201 45956 99.2 %-
Displacement parametersBiso mean: 21.1 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.35 Å0.23 Å
Luzzati d res low-5 Å
Luzzati sigma a0.49 Å0.3 Å
Refinement stepCycle: LAST / Resolution: 2.02→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5524 0 5 498 6027
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.006
X-RAY DIFFRACTIONx_angle_deg1.2
X-RAY DIFFRACTIONx_dihedral_angle_d25.6
X-RAY DIFFRACTIONx_improper_angle_d0.6
X-RAY DIFFRACTIONx_mcbond_it2.941.5
X-RAY DIFFRACTIONx_mcangle_it3.952
X-RAY DIFFRACTIONx_scbond_it4.322
X-RAY DIFFRACTIONx_scangle_it5.312.5
LS refinement shellResolution: 2.02→2.15 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.374 356 4.7 %
Rwork0.28 7189 -
obs-7574 98.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMTOPHCSDX.PRO
X-RAY DIFFRACTION2TOPH19.SOL

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